Contacts of the helix formed by residues 97 - 123 (chain K) in PDB entry 5XVO
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 THR 97 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95K ALA 3.9 9.9 - - - +
96K TRP* 1.3 73.2 - - - +
98K GLU* 1.3 66.6 + - - +
99K GLU* 3.7 6.7 + - - +
100K ARG* 3.0 27.9 + - - +
101K LYS* 3.0 22.5 + - - +
278K GLN* 3.5 19.1 + - - +
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Residues in contact with GLU 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96K TRP 3.9 1.4 + - - -
97K THR* 1.3 73.3 - - - +
99K GLU* 1.3 62.3 + - - +
101K LYS* 3.4 31.6 + - - +
102K GLY 3.1 16.1 + - - -
142K PHE* 3.6 25.0 - - + -
202K LEU 4.9 1.4 - - - +
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Residues in contact with GLU 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97K THR* 3.1 6.8 + - - +
98K GLU* 1.3 80.4 - - - +
100K ARG* 1.3 58.5 + - - +
102K GLY* 3.0 4.2 + - - -
103K GLN* 2.9 51.7 + - + +
141K LEU* 4.1 13.2 - - + +
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Residues in contact with ARG 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96K TRP 5.5 0.2 - - - -
97K THR* 3.0 26.3 + - - +
99K GLU* 1.3 77.5 - - - +
101K LYS* 1.3 64.0 + - + +
103K GLN* 3.3 23.0 + - - +
104K VAL* 3.0 32.3 + - - +
275K VAL* 3.1 37.8 + - - +
276K LEU* 3.7 28.7 - - + +
278K GLN* 3.4 32.7 + - - +
280K GLU 3.5 6.3 + - - -
281K GLU* 3.0 37.4 + - - +
282K GLY 5.2 0.6 - - - +
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Residues in contact with LYS 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96K TRP* 4.0 34.1 + - + +
97K THR 3.0 16.3 + - - +
98K GLU* 3.4 37.4 + - - +
100K ARG* 1.3 76.8 - - - +
102K GLY* 1.3 52.5 + - - +
104K VAL* 3.9 0.5 - - - +
105K TRP* 2.8 37.8 + - - +
142K PHE* 3.9 2.9 - - + -
201K GLY 4.8 6.3 + - - +
202K LEU* 4.0 46.1 + - + +
276K LEU* 4.0 10.1 - - + -
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Residues in contact with GLY 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98K GLU 3.1 7.5 + - - -
99K GLU 3.0 8.4 + - - -
101K LYS* 1.3 74.5 - - - +
103K GLN* 1.3 65.0 + - - +
106K THR* 2.6 33.1 + - - -
141K LEU* 4.0 10.1 - - - -
142K PHE* 3.2 33.3 - - - -
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Residues in contact with GLN 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K GLU* 2.9 45.4 + - - +
100K ARG* 3.3 33.2 + - - +
102K GLY* 1.3 76.1 - - - +
104K VAL* 1.3 60.2 + - + +
106K THR* 3.9 1.8 - - - -
107K ALA* 2.9 31.6 + - - +
141K LEU* 3.9 17.4 - - + +
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Residues in contact with VAL 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100K ARG* 3.0 23.0 + - - +
101K LYS 3.9 2.2 - - - +
103K GLN* 1.3 80.3 - - + +
105K TRP* 1.3 63.8 + - - +
107K ALA* 3.4 2.4 + - - +
108K ILE* 3.0 46.0 + - + +
202K LEU* 4.0 9.2 - - + -
272K VAL* 4.0 19.1 - - + -
275K VAL* 3.6 30.3 - - + -
276K LEU* 3.9 17.9 - - + -
283K VAL* 4.0 16.6 - - + -
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Residues in contact with TRP 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101K LYS 2.8 23.0 + - - +
102K GLY 4.0 1.6 - - - +
104K VAL* 1.3 73.6 - - - +
106K THR* 1.3 70.3 + - - +
108K ILE* 3.2 8.1 + - + +
109K ILE* 2.9 60.1 + - + +
142K PHE* 3.6 33.2 - + + -
143K ASP* 3.7 21.1 - - + -
148K GLU* 3.9 15.0 - - - -
202K LEU* 4.0 22.8 - - + +
203K LYS* 3.6 38.5 - - + +
216K ASP* 3.6 37.2 + - + +
219K GLU* 5.8 3.3 + - + +
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Residues in contact with THR 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102K GLY 2.6 23.6 + - - -
103K GLN* 3.9 2.9 - - - -
105K TRP* 1.3 83.8 - - + +
107K ALA* 1.3 64.9 + - - +
109K ILE* 3.4 5.9 + - + +
110K ALA* 3.0 23.7 + - - +
139K LEU* 4.6 21.3 - - + -
140K ARG 3.9 23.1 - - - +
141K LEU* 3.6 7.3 - - + -
142K PHE 3.1 21.9 + - - +
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Residues in contact with ALA 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103K GLN 2.9 19.0 + - - +
104K VAL* 3.4 6.7 - - - +
106K THR* 1.3 75.5 - - - +
108K ILE* 1.3 62.3 + - - +
110K ALA* 3.3 8.6 - - - +
111K GLN* 3.2 27.0 + - - +
283K VAL* 4.2 24.0 - - + -
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Residues in contact with ILE 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104K VAL* 3.0 32.1 + - + +
105K TRP* 3.4 10.1 - - + +
106K THR 3.2 0.2 - - - -
107K ALA* 1.3 78.3 - - - +
109K ILE* 1.3 69.6 + - + +
111K GLN* 3.0 21.4 + - - +
112K LYS* 3.1 8.7 + - - +
202K LEU* 4.8 5.8 - - + -
216K ASP* 3.5 22.4 - - + +
217K LEU* 4.2 26.2 - - + +
219K GLU* 4.1 5.2 - - + -
220K PRO* 3.7 22.8 - - + +
268K TYR* 3.9 13.9 - - - +
272K VAL* 4.3 8.1 - - + -
283K VAL* 4.5 10.3 - - + -
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Residues in contact with ILE 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105K TRP* 2.9 68.9 + - + +
106K THR* 3.5 10.8 - - - +
108K ILE* 1.3 78.1 - - + +
110K ALA* 1.3 64.8 + - - +
112K LYS* 3.0 11.6 + - + +
113K ILE* 2.9 28.2 + - + +
139K LEU* 3.5 31.6 - - + -
143K ASP* 4.3 1.3 - - + -
148K GLU* 4.0 32.1 - - + +
219K GLU* 4.8 13.9 - - + -
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Residues in contact with ALA 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106K THR 3.0 13.4 + - - +
107K ALA* 3.3 13.2 - - - +
108K ILE 3.1 0.2 - - - -
109K ILE* 1.3 78.7 - - - +
111K GLN* 1.3 57.9 + - + +
113K ILE* 3.2 2.7 + - - +
114K THR* 2.8 34.1 + - - -
136K ARG* 3.6 20.3 - - + +
139K LEU* 3.9 20.9 - - + -
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Residues in contact with GLN 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107K ALA* 3.2 14.7 + - - +
108K ILE* 3.0 8.8 + - - +
110K ALA* 1.3 77.6 - - + +
112K LYS* 1.3 62.1 + - - +
114K THR* 3.5 7.3 + - - -
115K ASN* 3.0 31.4 + - - -
220K PRO* 4.0 10.6 - - + +
268K TYR* 3.3 17.8 + - - -
283K VAL* 3.3 18.0 - - - +
284K PRO 2.9 22.7 + - - -
285K GLU* 3.6 22.8 - - + +
286K PHE 3.1 28.6 + - - +
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Residues in contact with LYS 112 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108K ILE 3.1 5.6 + - - +
109K ILE* 3.0 14.1 + - + +
111K GLN* 1.3 78.0 - - - +
113K ILE* 1.3 53.3 + - - +
115K ASN* 3.0 5.9 + - - +
116K GLN* 2.8 69.1 + - + +
148K GLU* 3.4 36.4 + - + +
152K ALA* 4.7 8.1 - - - +
219K GLU* 3.4 53.2 + - + +
220K PRO* 3.9 9.1 - - - +
222K ARG* 4.4 11.1 - - + +
223K PRO* 4.3 4.2 - - + +
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Residues in contact with ILE 113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109K ILE* 2.9 21.9 + - + +
110K ALA 3.7 6.3 - - - +
112K LYS* 1.3 78.9 - - + +
114K THR* 1.3 62.6 + - - +
116K GLN* 3.1 19.3 + - - +
117K SER* 2.9 22.6 + - - -
132K LEU* 3.6 35.8 - - + +
133K LEU* 4.9 0.4 - - - +
135K MET 5.2 0.4 - - - -
136K ARG* 4.0 14.4 - - + +
139K LEU* 4.2 24.9 - - + -
147K ARG* 4.6 2.5 - - + +
148K GLU* 4.1 27.1 - - - +
151K ALA* 4.3 15.3 - - + -
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Residues in contact with THR 114 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110K ALA 2.8 22.9 + - - -
111K GLN* 3.5 11.4 - - - -
113K ILE* 1.3 72.9 - - - +
115K ASN* 1.3 60.0 + - - +
117K SER* 2.4 28.9 + - - +
118K LEU* 2.8 29.5 + - + +
133K LEU* 5.1 4.7 - - + +
136K ARG* 3.4 33.2 + - - +
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Residues in contact with ASN 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111K GLN 3.0 21.0 + - - +
112K LYS 3.5 3.4 - - - +
114K THR* 1.3 76.6 - - - +
116K GLN* 1.3 67.7 + - - +
118K LEU* 3.9 9.2 - - - +
119K HIS* 3.0 20.1 + - - +
220K PRO* 3.0 23.8 + - - +
223K PRO* 3.7 17.6 - - + +
286K PHE* 3.1 23.9 + - - +
287K GLY* 3.2 21.0 - - - -
288K ILE* 3.3 31.7 + - + +
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Residues in contact with GLN 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112K LYS* 2.8 53.7 + - + +
113K ILE* 3.4 21.8 - - - +
115K ASN* 1.3 71.1 - - - +
117K SER* 1.3 63.5 + - - +
119K HIS* 3.3 1.8 + - - -
120K LEU* 3.0 17.8 + - - +
132K LEU* 3.7 5.8 - - + -
148K GLU 4.8 0.3 - - - +
151K ALA* 4.3 12.5 - - - +
152K ALA* 4.2 13.7 + - - +
155K TYR* 3.2 63.3 - - + -
156K PHE* 4.9 4.2 - - - -
222K ARG* 6.3 1.0 - - - +
223K PRO* 4.0 8.3 - - + +
226K ASP* 4.9 2.4 + - - -
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Residues in contact with SER 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113K ILE 2.9 10.7 + - - -
114K THR* 2.4 28.6 + - - +
116K GLN* 1.3 77.7 - - - +
118K LEU* 1.3 59.2 + - - +
120K LEU* 2.8 10.5 + - - +
121K ALA* 2.8 26.5 + - - -
129K ALA* 3.4 20.0 - - - +
132K LEU* 3.8 13.9 - - - +
133K LEU* 2.9 36.9 - - - +
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Residues in contact with LEU 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114K THR* 2.8 34.2 + - + +
115K ASN* 3.8 20.9 - - - +
116K GLN 3.4 0.2 - - - -
117K SER* 1.3 75.3 + - - +
119K HIS* 1.3 57.6 + - - +
121K ALA* 3.4 11.2 + - + +
122K GLN* 2.9 27.0 + - - +
287K GLY* 5.2 2.5 - - - -
288K ILE* 4.0 27.8 - - + +
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Residues in contact with HIS 119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115K ASN 3.0 14.7 + - - +
116K GLN 3.4 8.3 - - - +
118K LEU* 1.3 74.9 - - - +
120K LEU* 1.3 64.7 + - - +
122K GLN* 3.2 34.3 - - - +
123K ARG* 3.2 34.7 + - - +
155K TYR* 2.8 29.6 + - - +
159K LEU* 3.7 21.6 - - + +
223K PRO* 4.7 2.4 + - + -
226K ASP* 3.8 7.0 - - - +
227K GLN* 3.5 30.8 - - + -
230K TYR* 4.3 4.4 - - + +
288K ILE* 3.9 11.4 - - + +
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Residues in contact with LEU 120 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116K GLN 3.0 11.9 + - - +
117K SER 2.8 7.4 + - - +
119K HIS* 1.3 72.7 - - - +
121K ALA* 1.3 66.0 + - - +
123K ARG* 2.9 14.0 + - - +
124K ASP 3.4 0.2 + - - -
125K TYR* 3.1 29.0 + - + +
128K LYS* 4.1 17.9 - - + +
129K ALA* 4.2 8.3 - - + +
132K LEU* 3.7 38.8 - - + -
155K TYR* 3.8 16.6 - - + +
158K THR* 3.8 30.5 - - + +
159K LEU* 3.8 26.7 - - + -
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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
----------------------------------------------------------
117K SER 2.8 11.0 + - - +
118K LEU* 3.4 17.3 - - + +
120K LEU* 1.3 75.0 - - - +
122K GLN* 1.3 57.5 + - - +
124K ASP* 2.8 26.0 + - - +
125K TYR 4.5 5.6 - - - +
126K GLY* 4.8 5.1 + - - +
129K ALA* 3.9 15.5 - - + +
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Residues in contact with GLN 122 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118K LEU 2.9 14.8 + - - +
119K HIS* 3.2 34.0 - - + +
121K ALA* 1.3 77.4 - - - +
123K ARG* 1.3 77.9 + - - +
124K ASP* 3.5 8.3 + - - +
227K GLN* 3.3 24.1 + - - +
231K GLU* 5.4 2.6 + - - -
288K ILE* 5.9 0.8 + - - -
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Residues in contact with ARG 123 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119K HIS* 3.2 34.6 + - - +
120K LEU 2.9 8.1 + - - +
122K GLN* 1.3 98.2 + - - +
124K ASP* 1.3 70.0 + - - +
125K TYR* 3.2 29.3 + - + -
159K LEU* 4.2 11.9 - - + -
227K GLN* 3.5 11.3 + - - +
230K TYR* 3.2 38.8 - - + +
231K GLU* 3.1 41.4 + - - +
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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