Contacts of the helix formed by residues 82 - 111 (chain K) in PDB entry 5IYB
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 SER 82 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C THR* 3.0 12.6 + - - +
274C ILE 3.4 15.9 + - - -
275C ASN* 3.4 31.7 + - - -
29K ASN* 4.3 4.5 - - - -
77K THR* 3.7 0.2 - - - -
81K TYR* 1.3 80.7 - - - +
83K PRO* 1.3 68.2 - - - +
84K GLN* 2.8 28.9 + - - -
85K GLU* 3.2 17.2 + - - +
86K ALA 3.3 8.3 + - - -
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Residues in contact with PRO 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C THR* 6.3 1.3 - - + -
29K ASN* 3.6 20.9 - - - +
30K ALA 4.5 0.4 - - - -
31K CYS* 3.8 25.4 - - + +
33K PHE* 4.2 4.0 - - - -
75K VAL* 3.7 35.6 - - + +
77K THR* 3.3 25.1 - - + +
82K SER* 1.3 87.5 - - - +
84K GLN* 1.3 75.6 + - - +
86K ALA* 4.0 3.4 - - + +
87K PHE* 3.2 23.7 + - - +
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Residues in contact with GLN 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C LEU* 5.1 2.2 - - + +
267C ILE* 5.7 1.3 - - + -
272C LEU 3.5 17.9 + - - +
273C THR* 2.9 16.4 + - - +
274C ILE* 3.5 34.8 - - + +
21K ILE* 3.7 22.5 - - + +
31K CYS* 3.2 27.2 - - - +
33K PHE* 4.1 19.4 - - + -
82K SER* 2.8 13.2 + - - -
83K PRO* 1.3 83.6 - - - +
85K GLU* 1.3 60.6 + - - +
87K PHE* 3.4 3.8 + - - +
88K THR* 2.9 31.8 + - - -
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Residues in contact with GLU 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C ILE* 3.8 15.4 + - + +
275C ASN* 4.7 16.5 + - - +
81K TYR* 3.0 32.9 - - + -
82K SER* 3.2 13.7 + - - +
84K GLN* 1.3 78.4 - - - +
86K ALA* 1.3 52.5 + - - +
88K THR* 3.1 9.1 + - - -
89K ASN* 2.8 54.5 + - - +
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Residues in contact with ALA 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C TYR* 4.9 0.5 + - - -
50K LEU* 3.5 5.7 - - + +
53K ASP* 4.3 3.6 - - - +
56K VAL* 4.2 22.2 - - + -
75K VAL* 5.3 0.7 - - + -
77K THR* 4.3 5.8 - - + -
81K TYR* 3.3 33.6 + - + +
82K SER 3.3 5.1 + - - +
83K PRO* 4.0 7.4 - - + +
84K GLN 3.3 0.6 - - - -
85K GLU* 1.3 76.8 - - - +
87K PHE* 1.3 58.3 + - - +
89K ASN* 4.0 2.1 - - - +
90K ALA* 2.9 33.4 + - - +
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Residues in contact with PHE 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C LEU* 4.7 4.7 - - + -
263C LEU* 3.5 27.6 - - + -
19K ILE* 4.7 6.3 - - + -
33K PHE* 4.2 39.3 - + + -
35K ILE* 4.6 10.8 - - + -
46K ILE* 3.4 29.1 - - + +
50K LEU* 3.9 21.9 - - + +
73K ILE* 3.9 24.7 - - + -
75K VAL* 5.3 1.3 - - + -
83K PRO 3.2 17.2 + - - +
84K GLN 3.5 5.2 - - - +
85K GLU 3.3 0.2 - - - -
86K ALA* 1.3 80.5 - - - +
88K THR* 1.3 60.5 + - - +
90K ALA* 3.6 1.0 + - - +
91K ILE* 3.3 39.8 + - + +
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Residues in contact with THR 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C GLN* 3.6 30.2 - - - +
263C LEU* 3.9 12.1 - - - +
264C SER* 6.1 0.4 - - - +
267C ILE* 5.6 2.8 - - - +
274C ILE* 4.6 8.8 - - - +
84K GLN 2.9 16.6 + - - -
85K GLU* 3.4 10.8 - - - -
87K PHE* 1.3 77.6 - - - +
89K ASN* 1.3 67.4 + - - +
91K ILE 3.4 2.1 + - - -
92K THR* 3.1 30.5 + - - +
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Residues in contact with ASN 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 3.6 39.4 - - + +
3C TYR* 3.6 2.9 - - - +
81K TYR* 3.5 20.2 + - - +
85K GLU* 2.8 36.4 + - - +
86K ALA* 4.0 3.6 - - - +
88K THR* 1.3 77.0 - - - +
90K ALA* 1.3 58.5 + - - +
92K THR* 3.3 5.6 + - - -
93K ASP* 2.9 34.1 + - - +
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Residues in contact with ALA 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C TYR* 3.3 15.8 + - - +
46K ILE* 5.0 5.4 - - + +
49K GLN* 3.6 28.5 + - + +
50K LEU* 3.8 22.0 - - + +
53K ASP* 6.3 0.7 - - + -
86K ALA 2.9 19.0 + - - +
87K PHE 4.0 3.1 - - - +
89K ASN* 1.3 75.9 - - - +
91K ILE* 1.3 62.1 + - - +
94K LEU* 3.1 25.0 + - - +
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Residues in contact with ILE 91 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C LEU* 4.3 20.2 - - + +
259C LEU* 4.1 18.2 - - + -
260C GLN* 3.6 25.4 - - - +
263C LEU* 4.7 0.9 - - + -
46K ILE* 3.6 21.5 - - + -
87K PHE* 3.3 44.6 + - + +
88K THR 3.8 3.8 - - - +
89K ASN 3.3 0.6 - - - -
90K ALA* 1.3 76.0 - - - +
92K THR* 1.3 60.7 + - - +
94K LEU* 3.1 10.4 + - + +
95K ILE* 2.9 43.8 + - + +
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Residues in contact with THR 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C GLN* 3.0 19.1 + - - -
88K THR* 3.1 17.7 + - - +
89K ASN* 4.0 5.8 + - - -
91K ILE* 1.3 79.5 - - - +
93K ASP* 1.3 59.4 + - - +
95K ILE* 3.4 11.8 + - + +
96K SER* 2.8 33.0 + - - +
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Residues in contact with ASP 93 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 3.4 31.6 + - + +
3C TYR* 3.1 28.7 - - + +
4C ALA* 3.0 33.8 + - - +
49K GLN* 4.0 2.4 + - - +
89K ASN 2.9 17.8 + - - +
90K ALA 4.1 2.0 - - - +
92K THR* 1.3 77.1 - - - +
94K LEU* 1.3 57.0 + - - +
96K SER* 3.2 9.4 + - - -
97K GLU* 2.8 28.5 + - - +
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Residues in contact with LEU 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL* 4.4 7.9 - - + -
256C LEU* 3.6 25.1 - - + -
45K ILE* 3.5 41.7 - - + -
46K ILE* 4.9 6.1 - - + +
49K GLN* 3.9 30.4 - - + +
90K ALA 3.1 20.2 + - - +
91K ILE* 3.1 9.5 + - + +
93K ASP* 1.3 74.1 - - - +
95K ILE* 1.3 59.1 + - - +
97K GLU* 3.8 11.4 - - - +
98K LEU* 2.9 43.8 + - + +
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Residues in contact with ILE 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C LYS* 4.0 26.2 - - + +
256C LEU* 3.9 21.1 - - + -
257C SER* 3.8 30.1 - - - +
260C GLN* 5.1 5.4 - - + +
91K ILE* 2.9 34.3 + - + +
92K THR* 3.6 13.9 - - + +
93K ASP 3.3 0.2 - - - -
94K LEU* 1.3 74.2 - - - +
96K SER* 1.3 55.7 + - - +
98K LEU* 3.4 7.3 + - - +
99K SER* 2.7 38.3 + - - +
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Residues in contact with SER 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92K THR* 2.8 20.1 + - - +
93K ASP* 3.4 15.6 - - - -
95K ILE* 1.3 75.6 - - - +
97K GLU* 1.3 60.5 + - - +
99K SER* 3.3 7.9 + - - -
100K LEU* 2.9 28.4 + - - +
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Residues in contact with GLU 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ALA* 4.1 17.3 - - + +
5C ASN* 3.9 21.5 - - - +
7C PRO* 3.4 48.3 - - + +
25C ASN 4.4 0.3 - - - +
26C THR* 4.0 14.3 + - - -
27C ASP 5.2 0.5 + - - -
30C VAL* 4.8 6.1 - - - +
49K GLN* 3.8 19.4 + - - +
52K LYS* 3.9 6.6 + - - -
93K ASP* 2.8 19.7 + - - +
94K LEU* 3.8 14.5 - - + +
96K SER* 1.3 72.8 - - - +
98K LEU* 1.3 62.5 + - + +
100K LEU* 3.4 5.1 + - - -
101K LEU* 3.1 18.7 + - - +
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Residues in contact with LEU 98 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL* 4.3 12.8 - - + -
34C ILE* 4.1 29.2 - - + -
249C LEU* 4.8 17.5 - - + +
252C LEU* 4.1 24.9 - - + -
253C LYS* 5.3 11.0 - - + +
256C LEU* 4.1 22.4 - - + -
45K ILE* 6.4 0.4 - - + -
94K LEU* 2.9 33.2 + - + +
95K ILE* 3.6 6.1 - - - +
97K GLU* 1.3 75.9 - - + +
99K SER* 1.3 52.5 + - - +
101K LEU* 3.0 12.4 + - + +
102K GLU* 2.7 35.0 + - - +
----------------------------------------------------------
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Residues in contact with SER 99 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C LYS* 3.2 24.3 - - - +
95K ILE* 2.7 24.4 + - - +
96K SER* 3.3 8.2 + - - -
98K LEU* 1.3 72.9 - - - +
100K LEU* 1.3 60.0 + - - +
102K GLU* 3.4 12.4 - - - +
103K GLU* 2.8 36.9 + - - +
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Residues in contact with LEU 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ASN 5.2 2.0 - - - +
6C GLN* 4.5 4.5 - - + -
7C PRO* 4.0 17.0 - - + -
96K SER 2.9 16.7 + - - +
97K GLU* 3.6 7.9 - - + +
98K LEU 3.3 0.2 - - - -
99K SER* 1.3 75.2 - - - +
101K LEU* 1.3 60.4 + - - +
103K GLU* 3.4 7.4 + - + -
104K ARG* 2.9 81.5 + - + +
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Residues in contact with LEU 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PRO* 4.0 28.0 - - + +
8C THR 4.4 0.2 - - - +
9C VAL* 4.2 22.9 - - + -
23C ILE* 4.1 31.9 - - + -
26C THR* 5.9 0.9 - - - +
30C VAL* 5.1 3.8 - - + -
34C ILE* 3.7 30.3 - - + -
249C LEU* 4.6 13.5 - - + -
97K GLU 3.1 12.4 + - - +
98K LEU* 3.0 16.0 + - + +
100K LEU* 1.3 75.6 - - - +
102K GLU* 1.3 58.0 + - - +
104K ARG* 4.6 0.9 - - + -
105K PHE* 2.9 33.4 + - + +
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Residues in contact with GLU 102 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C LEU* 3.5 28.6 - - + +
249C LEU* 4.3 23.8 - - + +
250C SER* 3.5 17.3 + - - +
253C LYS* 3.2 29.9 + - - -
98K LEU 2.7 17.3 + - - +
99K SER* 3.4 10.9 - - - +
100K LEU 3.2 0.2 - - - -
101K LEU* 1.3 74.2 - - - +
103K GLU* 1.3 62.4 + - - +
105K PHE* 3.5 3.0 + - - +
106K ARG* 3.2 43.8 + - - +
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Residues in contact with GLU 103 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K SER* 2.8 25.7 + - - +
100K LEU* 3.8 10.1 - - + +
102K GLU* 1.3 74.4 - - + +
104K ARG* 1.3 64.1 + - + +
106K ARG* 2.8 42.3 + - - +
107K VAL* 3.3 31.8 + - - +
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Residues in contact with ARG 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLN* 3.2 45.5 + - - +
7C PRO 3.6 14.7 + - - +
8C THR* 3.7 17.1 - - - +
9C VAL* 3.5 13.6 - - + +
100K LEU* 2.9 47.1 + - + +
101K LEU* 4.0 4.3 - - - +
103K GLU* 1.3 77.4 - - + +
105K PHE* 1.3 56.9 + - - +
107K VAL* 3.6 5.8 + - - +
108K ALA* 3.0 28.9 + - - +
----------------------------------------------------------
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Residues in contact with PHE 105 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 3.6 27.7 - - + +
11C ILE* 3.5 22.4 - - + -
19C VAL* 5.1 4.7 - - + -
21C PHE* 4.7 12.3 - + - -
242C GLU* 4.0 24.2 - - + -
245C VAL* 3.9 31.4 - - + -
246C LEU* 4.5 8.1 - - + -
249C LEU* 4.9 10.8 - - + -
101K LEU* 2.9 21.9 + - + +
102K GLU* 3.6 6.7 - - - +
104K ARG* 1.3 74.9 - - - +
106K ARG* 1.3 68.2 + - + +
108K ALA* 3.1 2.9 + - - +
109K ILE* 2.8 55.7 + - + +
----------------------------------------------------------
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Residues in contact with ARG 106 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C LEU* 3.6 33.3 - - + +
102K GLU* 3.2 38.4 + - - +
103K GLU* 2.8 46.4 + - - +
105K PHE* 1.3 81.2 - - + +
107K VAL* 1.3 62.0 + - - +
109K ILE* 3.2 9.7 + - - +
110K LYS* 2.9 27.9 + - - +
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Residues in contact with VAL 107 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103K GLU* 3.3 22.8 + - - +
104K ARG* 3.9 6.5 - - - +
106K ARG* 1.3 77.5 - - + +
108K ALA* 1.3 66.8 + - - +
110K LYS* 3.3 23.0 + - + +
111K ASP* 3.3 17.5 + - + +
----------------------------------------------------------
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Residues in contact with ALA 108 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 3.9 21.5 - - + +
10C ARG* 5.3 0.4 - - - -
11C ILE* 3.9 24.3 - - + +
104K ARG 3.0 19.3 + - - +
105K PHE 3.4 4.5 - - - +
107K VAL* 1.3 78.4 - - - +
109K ILE* 1.3 62.6 + - - +
110K LYS 3.5 0.2 + - - -
111K ASP* 3.6 18.8 + - - +
113K GLN* 5.8 0.9 - - - +
----------------------------------------------------------
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Residues in contact with ILE 109 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 4.3 22.2 - - + -
14C LEU* 4.6 12.6 - - + -
19C VAL* 5.1 3.6 - - + -
242C GLU* 3.8 29.6 - - + -
105K PHE* 2.8 43.7 + - + +
106K ARG* 3.4 11.9 - - + +
108K ALA* 1.3 75.8 - - - +
110K LYS* 1.3 66.6 + - - +
113K GLN* 4.0 10.5 - - + +
116K ILE* 3.2 38.4 - - + +
----------------------------------------------------------
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Residues in contact with LYS 110 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106K ARG 2.9 13.2 + - - +
107K VAL* 3.3 18.4 + - + +
109K ILE* 1.3 78.5 - - - +
111K ASP* 1.3 60.5 + - + +
112K LYS 3.2 8.8 + - - -
113K GLN 3.5 13.3 + - - +
116K ILE* 4.3 15.6 - - + +
----------------------------------------------------------
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Residues in contact with ASP 111 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107K VAL* 3.3 15.4 + - + +
108K ALA* 3.9 12.5 - - - +
109K ILE 3.4 1.7 - - - -
110K LYS* 1.3 76.6 - - - +
112K LYS* 1.3 72.6 + - - +
113K GLN* 3.5 3.7 - - - +
----------------------------------------------------------
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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