Contacts of the helix formed by residues 94 - 128 (chain K) in PDB entry 5AYZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 94 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K SER* 4.0 19.3 - - - +
38K GLY 4.0 9.9 - - - +
39K ALA 4.0 2.4 - - - -
40K GLY 3.1 13.3 + - - +
42K SER* 3.1 26.7 - - - +
92K GLY 3.4 0.4 + - - -
93K PRO* 1.3 71.0 - - - +
95K HIS* 1.3 63.6 + - - +
97K LEU* 3.2 5.1 + - - +
98K LEU* 2.9 27.8 + - - +
285K LEU* 4.7 4.3 - - + -
177L ALA* 4.2 12.3 - - + -
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Residues in contact with HIS 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G LEU* 3.7 37.1 - - + +
12G PRO* 6.4 1.6 - - + -
31K ASN* 5.0 4.7 + - - +
34K ALA* 3.8 19.1 - - + -
37K SER* 3.4 11.4 - - - +
38K GLY 3.2 20.3 + - - +
39K ALA* 3.5 26.2 - - + -
93K PRO* 3.6 17.3 - - + +
94K ALA* 1.3 77.6 - - - +
96K CYS* 1.3 77.6 + - - +
98K LEU* 3.1 5.2 + - - +
99K LEU* 2.8 35.8 + - + +
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Residues in contact with CYS 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G PRO* 5.3 9.0 - - - -
64K PHE* 4.3 1.6 - - - -
67K LEU* 3.3 48.8 - - + +
68K ASN* 5.5 1.6 - - - -
69K CYS* 3.6 9.6 - - - -
93K PRO* 2.9 20.6 + - + +
95K HIS* 1.3 107.2 - - - +
97K LEU* 1.3 62.2 + - - +
99K LEU* 3.4 6.0 + - - +
100K GLY* 3.3 17.5 + - - -
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Residues in contact with LEU 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42K SER* 3.7 32.8 - - - +
44K ALA* 4.2 5.6 - - + +
64K PHE* 3.8 10.2 - - + -
69K CYS* 3.6 18.6 - - - -
90K VAL* 3.4 41.5 - - + +
91K ARG 3.7 8.7 - - - -
92K GLY 3.8 2.7 - - - +
93K PRO 3.0 15.0 + - - +
94K ALA* 3.2 5.8 + - - +
96K CYS* 1.3 76.0 - - - +
98K LEU* 1.3 70.8 + - + +
100K GLY 3.5 0.2 + - - -
101K GLU* 3.2 24.3 + - - +
283K LEU* 4.7 3.6 - - + +
285K LEU* 3.7 26.0 - - + -
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Residues in contact with LEU 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K SER* 4.0 16.8 - - - +
94K ALA 2.9 19.0 + - - +
95K HIS* 3.8 5.2 - - - +
97K LEU* 1.3 81.5 - - + +
99K LEU* 1.3 62.0 + - - +
101K GLU* 3.6 32.1 + - - +
102K ARG 4.8 1.2 + - - -
283K LEU* 6.4 0.4 - - + -
285K LEU* 4.4 14.6 - - + -
138L ARG* 5.7 2.4 + - - -
164L LEU* 5.3 3.6 - - - +
173L ASN* 3.6 24.9 - - + +
174L HIS* 3.6 55.5 - - + +
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Residues in contact with LEU 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G PRO* 4.5 13.0 - - + -
12G PRO* 4.4 15.0 - - + -
23K LEU* 4.3 12.1 - - + +
26K ASP* 4.5 12.1 - - + +
27K CYS* 3.9 17.9 - - + -
31K ASN* 3.7 26.9 - - - +
67K LEU* 4.3 22.2 - - + -
95K HIS* 2.8 19.8 + - + +
96K CYS* 3.9 7.0 - - - +
97K LEU 3.3 0.2 - - - -
98K LEU* 1.3 79.4 - - - +
100K GLY* 1.3 60.3 + - - +
102K ARG 4.8 1.9 + - - -
103K VAL* 5.1 1.9 - - - +
138L ARG* 5.5 0.3 + - - -
164L LEU* 3.7 25.9 - - + +
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Residues in contact with GLY 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K LEU* 4.3 7.6 - - - -
63K ILE* 4.1 4.1 - - - +
64K PHE* 4.0 10.3 - - - -
67K LEU* 3.6 21.4 - - - +
96K CYS 3.3 10.9 + - - -
97K LEU 4.0 1.6 - - - -
99K LEU* 1.3 76.6 - - - +
101K GLU* 1.3 65.6 + - - +
102K ARG 3.4 0.8 + - - -
103K VAL* 3.5 2.3 + - - -
104K ALA* 2.9 26.9 + - - +
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Residues in contact with GLU 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64K PHE* 4.3 8.3 - - - -
97K LEU 3.2 15.4 + - - +
98K LEU* 3.6 23.3 - - + +
99K LEU 3.4 2.0 - - - -
100K GLY* 1.3 77.5 - - - +
102K ARG* 1.3 72.3 + - - +
104K ALA* 3.8 0.9 - - - +
105K LEU* 2.9 48.4 + - + +
283K LEU* 3.9 21.8 + - + +
171L LYS* 5.6 9.7 + - - +
172L ASP* 5.4 1.0 - - - +
173L ASN* 3.1 29.4 + - - +
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Residues in contact with ARG 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26K ASP* 3.9 5.4 - - - +
98K LEU 4.8 2.0 + - - -
99K LEU 4.8 1.4 + - - +
100K GLY 3.4 0.4 - - - -
101K GLU* 1.3 86.9 + - - +
103K VAL* 1.3 54.3 + - + +
105K LEU* 3.3 38.6 + - - +
106K ASN* 2.7 67.7 + - - +
281K PHE 5.3 4.4 + - - -
138L ARG* 3.1 68.7 + - + +
139L LYS* 3.9 31.8 - - - +
145L ARG* 5.3 0.2 - - - +
171L LYS* 5.8 2.0 - - - +
274L GLN* 4.7 3.2 + - - +
401L NCN 5.5 2.5 - - - -
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Residues in contact with VAL 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K TRP* 3.7 40.6 - - + +
23K LEU* 4.7 14.4 - - + +
25K GLU* 6.2 0.2 - - - +
26K ASP* 3.8 33.9 - - + +
63K ILE* 3.7 19.7 - - + -
99K LEU 5.1 2.9 + - - +
100K GLY 3.5 6.1 + - - +
101K GLU 3.4 0.4 - - - -
102K ARG* 1.3 75.8 - - + +
104K ALA* 1.3 61.4 + - - +
106K ASN* 3.8 9.9 - - - +
107K THR* 2.7 33.4 + - - +
142L PRO* 4.5 6.5 - - + -
145L ARG* 6.1 0.9 - - - +
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Residues in contact with ALA 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60K PHE* 3.7 21.3 - - + +
63K ILE* 3.7 18.1 - - + +
64K PHE* 3.6 28.3 - - + -
100K GLY 2.9 19.4 + - - +
101K GLU 3.8 2.5 - - - +
103K VAL* 1.3 77.7 - - - +
105K LEU* 1.3 59.1 + - + +
107K THR* 3.4 3.0 + - - -
108K LEU* 3.0 29.6 + - - +
283K LEU* 5.9 0.2 - - + -
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Residues in contact with LEU 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46K LEU* 3.7 29.8 - - + -
60K PHE* 4.7 5.8 - - + -
101K GLU* 2.9 43.4 + - + +
102K ARG* 3.5 31.9 - - - +
104K ALA* 1.3 74.1 - - + +
106K ASN* 1.3 60.0 + - - +
108K LEU* 4.0 3.3 - - + +
109K ALA* 2.8 35.2 + - - +
281K PHE* 3.7 24.1 - - + +
282K SER* 4.0 10.8 - - - -
283K LEU* 4.0 17.3 - - + +
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Residues in contact with ASN 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102K ARG* 2.7 52.6 + - - +
103K VAL* 3.8 8.6 - - - +
105K LEU* 1.3 73.1 - - - +
107K THR* 1.3 62.2 + - - +
109K ALA* 3.9 3.0 - - - +
110K ARG* 3.3 38.6 + - - +
138L ARG 2.9 23.4 + - - -
139L LYS* 3.4 12.6 - - - +
140L THR* 3.1 27.9 + - - +
142L PRO* 4.1 8.8 - - + +
145L ARG* 4.6 3.4 - - - +
274L GLN* 4.1 0.7 - - - +
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Residues in contact with THR 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K TRP* 3.6 20.5 - - + -
56K GLY 5.5 1.1 - - - +
59K PHE* 3.8 28.9 - - + -
60K PHE* 5.5 0.9 - - - +
63K ILE* 4.0 5.1 - - - +
103K VAL 2.7 23.1 + - - -
104K ALA 3.8 3.6 - - - -
106K ASN* 1.3 77.5 - - - +
108K LEU* 1.3 59.3 + - - +
110K ARG* 3.5 1.2 + - - +
111K CYS* 3.0 29.1 + - + +
144K PHE* 4.0 19.7 - - + -
147K VAL* 4.1 9.9 - - + +
142L PRO* 3.4 14.4 - - - +
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Residues in contact with LEU 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46K LEU* 3.9 28.9 - - + -
54K LEU* 4.2 10.3 - - + -
55K ALA 3.3 21.1 - - - +
56K GLY 3.5 26.0 - - - +
57K GLN 3.9 2.9 - - - +
60K PHE* 4.0 17.3 - - + -
73K TRP* 4.5 4.9 - - + -
104K ALA 3.0 17.7 + - - +
105K LEU* 4.0 3.6 - - + +
107K THR* 1.3 74.5 - - - +
109K ALA* 1.3 60.8 + - - +
111K CYS* 4.5 0.4 - - - -
112K SER* 2.9 36.1 + - - +
281K PHE* 3.9 32.5 - - + -
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Residues in contact with ALA 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102K ARG* 6.0 0.9 - - - +
105K LEU 2.8 19.6 + - - +
106K ASN 3.9 3.6 - - - +
108K LEU* 1.3 77.9 - - - +
110K ARG* 1.3 51.9 + - - +
112K SER* 4.0 0.2 - - - -
113K GLY* 2.7 30.0 + - - -
278K ALA* 3.5 14.6 - - + -
279K LEU 3.2 35.6 + - - +
281K PHE* 4.0 11.1 - - + +
274L GLN* 3.9 11.9 - - - +
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Residues in contact with ARG 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106K ASN* 3.3 26.3 + - - +
107K THR 4.1 0.2 - - - +
109K ALA* 1.3 75.6 - - - +
111K CYS* 1.3 67.4 + - - +
113K GLY* 3.4 0.9 + - - +
114K ILE* 3.0 33.7 + - + +
144K PHE* 3.9 19.1 - - + -
148K GLU* 5.7 1.6 - - - +
276K ALA 5.7 0.2 - - - +
278K ALA* 4.4 10.3 - - + +
139L LYS 3.2 17.6 + - - -
140L THR* 3.8 10.3 + - - +
141L THR* 3.1 48.6 + - + +
142L PRO* 4.5 0.4 - - - -
148L GLU* 4.4 0.4 + - - -
273L THR 3.0 27.7 + - - -
274L GLN* 2.9 35.9 + - - +
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Residues in contact with CYS 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55K ALA* 3.3 38.0 - - - +
56K GLY* 3.6 13.2 - - - -
59K PHE* 4.7 0.7 - - - -
107K THR* 3.0 19.9 + - + +
110K ARG* 1.3 77.2 - - - +
112K SER* 1.3 57.1 - - - +
114K ILE* 3.3 6.1 + - - +
115K ALA* 3.0 22.7 + - - +
147K VAL* 3.6 38.6 - - + +
150K TYR* 3.9 12.6 - - - -
151K GLY* 4.0 4.9 - - - -
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Residues in contact with SER 112 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53K VAL 3.3 15.6 + - - +
54K LEU* 3.7 4.0 - - - +
55K ALA* 2.9 32.5 + - - -
108K LEU 2.9 18.3 + - - -
109K ALA 4.0 0.2 - - - -
111K CYS* 1.3 74.6 - - - +
113K GLY* 1.3 56.2 + - - +
115K ALA 3.1 1.4 + - - -
116K SER* 2.7 39.8 + - - -
279K LEU* 3.7 17.7 - - - -
281K PHE* 3.8 11.0 - - - -
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Residues in contact with GLY 113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109K ALA 2.7 20.9 + - - -
110K ARG 3.4 1.5 + - - -
112K SER* 1.3 71.7 - - - +
114K ILE* 1.3 55.6 + - - +
116K SER* 3.5 2.4 + - - -
117K ALA* 3.1 22.2 + - - +
276K ALA* 3.6 15.7 - - - +
277K PRO* 3.3 23.8 - - - +
278K ALA* 4.3 0.9 - - - -
279K LEU* 3.8 12.8 - - - +
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Residues in contact with ILE 114 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110K ARG* 3.0 23.6 + - + +
111K CYS* 3.6 4.7 - - - +
113K GLY* 1.3 75.2 - - - +
115K ALA* 1.3 60.6 + - - +
117K ALA* 3.1 3.6 + - - +
118K ALA* 2.9 27.5 + - - +
148K GLU* 3.5 50.9 - - + +
151K GLY* 3.9 0.9 - - - -
152K LEU* 3.7 34.7 - - + +
272K LEU 3.5 22.4 - - - +
273K THR* 4.0 13.7 - - + +
276K ALA* 4.1 7.9 - - + +
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Residues in contact with ALA 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53K VAL* 4.0 10.1 - - + +
55K ALA* 3.5 29.4 - - + -
111K CYS 3.0 7.4 + - - +
112K SER 3.1 2.4 + - - +
114K ILE* 1.3 77.6 - - - +
116K SER* 1.3 57.9 + - - +
118K ALA* 4.3 0.9 - - - -
119K ALA* 3.0 25.5 + - - +
151K GLY 3.1 23.1 - - - +
154K VAL* 4.2 3.6 - - + -
155K GLY* 3.4 21.9 - - - +
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Residues in contact with SER 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51K PRO 4.9 0.4 - - - -
52K GLY* 3.1 13.6 - - - -
53K VAL* 2.6 35.7 + - - +
112K SER 2.7 22.0 + - - -
113K GLY 3.7 5.2 - - - -
115K ALA* 1.3 72.4 - - - +
117K ALA* 1.3 63.8 + - - +
119K ALA* 3.4 1.6 + - - +
120K ALA* 3.1 23.9 + - - +
279K LEU* 3.7 13.4 - - - +
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Residues in contact with ALA 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113K GLY 3.1 18.0 + - - +
114K ILE 3.1 4.0 + - - +
116K SER* 1.3 73.8 - - - +
118K ALA* 1.3 65.5 + - - +
120K ALA* 3.4 8.0 + - - +
121K ALA* 3.1 18.0 + - - +
253K LEU* 3.7 5.7 - - + +
271K MET* 4.2 12.8 - - + -
272K LEU* 3.5 23.8 - - + +
276K ALA* 3.7 20.4 - - + -
277K PRO* 6.0 0.9 - - + -
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Residues in contact with ALA 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K ILE 2.9 16.1 + - - +
115K ALA* 3.8 4.7 - - - +
117K ALA* 1.3 77.4 - - - +
119K ALA* 1.3 57.3 + - - +
121K ALA* 3.1 3.9 + - - +
122K VAL* 2.9 32.2 + - - +
152K LEU* 3.9 18.2 - - + +
155K GLY* 3.5 13.9 - - - +
157K ALA* 3.8 24.0 - - + +
272K LEU* 3.9 11.6 - - - +
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Residues in contact with ALA 119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53K VAL* 3.7 22.4 - - + -
80K LYS* 4.2 12.8 - - - +
115K ALA 3.0 18.1 + - - +
116K SER 3.9 2.5 - - - +
117K ALA 3.3 0.2 - - - -
118K ALA* 1.3 76.4 - - - +
120K ALA* 1.3 58.2 + - - +
122K VAL* 3.4 4.2 + - - +
123K GLU* 2.8 30.5 + - - +
155K GLY* 3.2 16.8 + - - +
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Residues in contact with ALA 120 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116K SER 3.1 14.0 + - - +
117K ALA* 3.6 9.6 - - - +
119K ALA* 1.3 76.1 - - - +
121K ALA* 1.3 57.1 + - - +
123K GLU* 3.1 8.7 + - - +
124K ALA* 2.8 29.6 + - - +
253K LEU* 4.2 21.5 - - + -
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Residues in contact with ALA 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117K ALA 3.1 10.5 + - - +
118K ALA 3.1 8.0 + - - +
120K ALA* 1.3 76.1 - - - +
122K VAL* 1.3 58.1 + - - +
124K ALA 3.3 1.0 + - - -
125K ALA* 2.8 27.9 + - - +
134K VAL* 3.9 22.0 - - + -
253K LEU* 3.7 19.9 - - + +
256K LEU* 3.3 25.0 - - + +
269K MET* 4.1 6.1 - - - -
272K LEU* 4.3 3.6 - - + -
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Residues in contact with VAL 122 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118K ALA 2.9 21.4 + - - +
119K ALA* 3.9 5.8 - - - +
121K ALA* 1.3 75.7 - - - +
123K GLU* 1.3 57.5 + - - +
125K ALA* 4.1 5.9 - - + +
126K ARG* 3.0 31.7 + - + +
134K VAL* 4.3 18.8 - - + +
155K GLY 4.0 2.7 - - - +
156K GLY* 3.5 35.4 - - - +
157K ALA* 4.2 2.0 - - - +
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Residues in contact with GLU 123 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80K LYS* 5.7 2.4 + - - -
119K ALA 2.8 16.0 + - - +
120K ALA* 3.1 12.1 + - - +
122K VAL* 1.3 73.4 - - - +
124K ALA* 1.3 60.5 + - - +
126K ARG* 3.2 35.8 + - - +
127K GLY* 2.9 26.2 + - - -
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Residues in contact with ALA 124 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120K ALA 2.8 18.0 + - - +
121K ALA* 3.8 4.0 - - - +
123K GLU* 1.3 73.3 - - - +
125K ALA* 1.3 62.2 + - - +
127K GLY* 3.1 11.8 + - - -
128K ALA* 3.2 13.7 + - - +
253K LEU* 4.5 11.4 - - + +
256K LEU* 3.9 16.6 - - + -
257K PRO* 4.3 18.7 - - + +
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Residues in contact with ALA 125 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121K ALA 2.8 21.0 + - - +
122K VAL* 4.1 3.8 - - + +
124K ALA* 1.3 72.9 - - - +
126K ARG* 1.3 62.4 + - - +
128K ALA* 3.3 5.4 + - - -
130K TRP* 3.1 55.2 + - + +
134K VAL* 4.1 13.5 - - + -
256K LEU* 4.2 5.3 - - + +
260K CYS* 4.2 15.9 - - - -
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Residues in contact with ARG 126 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122K VAL* 3.0 22.8 + - + +
123K GLU* 3.2 36.7 + - - +
125K ALA* 1.3 77.4 - - - +
127K GLY* 1.3 71.3 + - - +
128K ALA 3.1 0.2 - - - -
129K GLY* 3.0 20.0 + - - -
130K TRP 4.5 5.8 - - - -
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Residues in contact with GLY 127 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123K GLU 2.9 13.9 + - - -
124K ALA* 3.1 7.3 + - - -
126K ARG* 1.3 89.2 - - - +
128K ALA* 1.3 57.0 + - - +
129K GLY 3.4 0.2 - - - -
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Residues in contact with ALA 128 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124K ALA 3.2 12.5 + - - +
125K ALA 3.3 4.5 + - - +
126K ARG 3.1 1.2 - - - -
127K GLY* 1.3 76.6 - - - +
129K GLY* 1.3 60.1 + - - +
130K TRP* 3.2 5.9 + - - +
257K PRO* 4.1 28.5 - - + +
260K CYS* 4.4 14.1 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il