Contacts of the helix formed by residues 82 - 112 (chain K) in PDB entry 4V1M
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 ASP 82 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K ASN* 4.5 0.4 - - - +
77K THR* 4.1 2.0 - - - -
80K GLY 3.9 2.3 + - - +
81K TYR* 1.3 80.3 - - - +
83K PRO* 1.3 71.8 - - - +
84K LYS* 2.7 46.0 + - - +
85K ASP* 3.2 27.1 + - - +
86K ALA* 3.0 19.8 + - - +
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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
----------------------------------------------------------
29K ASN* 3.4 32.8 - - - +
30K ALA 4.9 0.2 - - - -
31K VAL* 3.8 25.6 - - + -
75K ILE* 3.7 27.2 - - + +
77K THR* 3.6 22.0 - - + +
82K ASP* 1.3 95.0 - - - +
84K LYS* 1.4 55.4 + - + +
86K ALA* 3.2 3.3 + - + +
87K LEU* 2.9 29.8 + - - +
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Residues in contact with LYS 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C LEU* 4.4 13.1 - - + +
265C MET* 5.0 12.0 + - - +
266C ASP* 3.9 22.5 + - - +
21K ILE* 3.9 43.9 - - + +
31K VAL* 5.5 5.6 - - + -
33K ILE* 6.1 1.1 - - + -
82K ASP* 2.7 24.5 + - - +
83K PRO* 1.4 70.9 - - + +
85K ASP* 1.4 51.4 + - - +
87K LEU* 3.3 10.7 + - - +
88K LYS* 2.9 37.6 + - + +
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Residues in contact with ASP 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81K TYR* 4.1 13.3 - - + -
82K ASP* 3.2 29.9 + - - +
84K LYS* 1.4 76.6 - - - +
86K ALA* 1.3 55.6 + - - +
88K LYS* 3.2 14.3 + - - +
89K ASN* 2.8 42.7 + - - +
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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
----------------------------------------------------------
50K LEU* 3.7 4.9 - - + +
53K ASP* 4.2 3.4 - - - +
56K VAL* 3.8 13.7 - - + -
75K ILE* 4.3 4.7 - - + -
77K THR* 3.7 27.6 - - + -
81K TYR* 3.2 23.0 + - + +
82K ASP 3.0 7.1 + - - +
83K PRO* 3.3 9.9 - - + +
85K ASP* 1.3 73.8 - - - +
87K LEU* 1.3 60.7 + - - +
89K ASN* 3.3 3.8 + - - +
90K ALA* 3.0 24.6 + - - +
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Residues in contact with LEU 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C ILE* 4.7 1.6 - - + -
262C LEU* 3.9 33.2 - - + -
19K LEU* 4.7 2.9 - - + -
21K ILE* 5.7 0.2 - - + -
33K ILE* 4.2 26.7 - - + -
35K PHE* 4.3 15.0 - - + -
46K ILE* 3.7 29.4 - - + -
50K LEU* 3.9 8.6 - - - +
73K LEU* 4.2 9.6 - - + -
75K ILE* 3.7 8.1 - - + -
83K PRO 2.9 11.9 + - - +
84K LYS* 3.4 9.4 - - - +
86K ALA* 1.3 74.4 - - - +
88K LYS* 1.4 57.2 - - - +
90K ALA* 3.4 1.2 + - - +
91K CYS* 3.0 42.8 + - - +
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Residues in contact with LYS 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C LEU* 3.4 18.9 + - + +
262C LEU* 3.6 36.8 - - + -
263C THR* 3.2 23.0 + - - -
266C ASP* 3.6 18.6 + - - -
84K LYS* 2.9 16.2 + - + +
85K ASP* 3.2 19.7 + - - +
87K LEU* 1.4 74.8 - - - +
89K ASN* 1.4 56.6 + - - +
91K CYS* 3.4 4.3 - - - +
92K ASN* 3.1 36.5 + - - +
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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
----------------------------------------------------------
53K ASP* 5.0 3.8 - - - +
81K TYR* 3.2 24.4 + - - +
85K ASP* 2.8 29.8 + - - +
86K ALA 3.7 3.8 - - - +
88K LYS* 1.4 74.9 - - - +
90K ALA* 1.3 59.2 + - - +
92K ASN* 3.2 12.6 + - - +
93K SER* 2.8 31.2 + - - -
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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
----------------------------------------------------------
46K ILE* 4.7 5.6 - - + +
49K GLU* 4.0 20.7 - - + +
50K LEU* 3.7 29.6 - - + +
53K ASP* 5.7 2.4 + - + +
86K ALA 3.0 16.1 + - - +
87K LEU* 3.8 2.9 - - - +
89K ASN* 1.3 74.5 - - - +
91K CYS* 1.3 61.3 + - - +
93K SER* 3.6 6.9 - - - -
94K ILE* 3.0 32.4 + - + +
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Residues in contact with CYS 91 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C VAL* 3.2 35.0 - - + +
258C ILE* 3.9 30.7 - - - -
259C LEU* 3.4 24.0 - - + -
262C LEU* 5.1 0.4 - - - -
46K ILE* 4.6 8.7 - - - +
87K LEU* 3.0 33.5 + - - +
88K LYS 3.4 6.5 - - - +
90K ALA* 1.3 76.1 - - - +
92K ASN* 1.4 62.3 + - - +
94K ILE* 3.5 3.8 - - - +
95K ILE* 3.3 14.2 + - - +
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Residues in contact with ASN 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C LEU* 3.6 22.3 - - - +
88K LYS* 3.1 23.2 + - - +
89K ASN* 3.4 14.6 + - - +
91K CYS* 1.4 75.3 - - - +
93K SER* 1.3 65.6 + - - +
95K ILE* 3.0 10.9 + - - +
96K ASN* 3.0 37.5 + - - +
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Residues in contact with SER 93 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49K GLU* 2.7 26.0 + - - -
89K ASN 2.8 19.5 + - - -
90K ALA* 3.6 4.7 - - - -
92K ASN* 1.3 71.2 - - - +
94K ILE* 1.4 51.1 + - - +
96K ASN* 3.2 10.3 + - - +
97K LYS* 2.8 52.9 + - - +
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Residues in contact with ILE 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C MET* 3.7 12.7 - - + +
255C VAL* 3.6 26.9 - - + -
45K LEU* 3.8 42.8 - - + +
46K ILE* 3.9 20.0 - - + +
49K GLU* 3.4 23.8 - - + -
90K ALA 3.0 21.9 + - - +
91K CYS* 3.5 9.4 - - - +
93K SER* 1.4 74.3 + - - +
95K ILE* 1.4 56.2 + - - +
97K LYS* 3.1 6.2 + - - +
98K LEU* 2.9 45.0 + - + +
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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
----------------------------------------------------------
252C GLN* 3.4 42.6 + - + +
255C VAL* 3.7 10.5 - - + -
256C ALA* 3.6 35.7 - - + +
259C LEU* 3.8 14.4 - - + -
91K CYS 3.3 13.6 + - - +
92K ASN* 3.0 12.1 + - - +
94K ILE* 1.4 75.3 - - - +
96K ASN* 1.3 61.7 + - - +
98K LEU* 3.1 3.5 + - - -
99K GLY* 2.8 32.1 + - - -
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Residues in contact with ASN 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92K ASN* 3.0 32.0 + - - +
93K SER* 3.6 9.3 - - - +
95K ILE* 1.3 82.6 - - - +
97K LYS* 1.4 60.3 + - + +
99K GLY* 3.4 2.5 + - - +
100K ALA* 3.2 21.5 + - - +
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Residues in contact with LYS 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C GLY* 6.0 1.6 - - - -
6C PRO* 3.4 29.4 - - + +
26C ASP* 4.0 9.7 + - - -
29C MET* 3.9 23.6 - - + -
49K GLU* 2.7 32.0 + - - +
52K ASN* 3.9 9.9 - - - +
93K SER* 2.8 30.4 + - - +
94K ILE 3.4 7.4 - - - +
96K ASN* 1.4 77.1 - - + +
98K LEU* 1.4 56.6 - - - +
100K ALA* 3.3 3.5 + - - +
101K LEU 3.1 21.1 + - - -
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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
----------------------------------------------------------
29C MET* 3.7 26.2 - - + -
33C LEU* 5.8 3.8 - - + -
248C ILE* 3.2 27.0 - - + +
251C LEU* 3.9 25.6 - - + -
252C GLN* 3.7 42.6 - - + +
94K ILE* 2.9 37.4 + - + +
95K ILE* 3.5 5.4 - - - +
97K LYS* 1.4 71.9 - - - +
99K GLY* 1.3 60.5 + - - +
101K LEU* 3.2 11.7 + - + +
102K LYS* 3.0 25.6 + - - +
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Residues in contact with GLY 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C GLN* 3.5 18.4 - - - +
95K ILE 2.8 12.8 + - - -
96K ASN* 3.4 4.2 + - - -
97K LYS 3.3 0.4 - - - -
98K LEU* 1.3 77.0 - - - +
100K ALA* 1.3 55.2 + - - +
102K LYS* 3.6 5.4 + - - +
103K THR* 2.8 32.5 + - - -
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Residues in contact with ALA 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLU* 4.2 2.5 - - - +
4C GLU* 3.6 27.4 - - + +
5C GLY* 4.1 21.5 - - - +
6C PRO* 4.2 5.4 - - + -
96K ASN 3.2 12.1 + - - +
97K LYS* 3.6 9.0 - - - +
98K LEU 3.3 0.2 - - - -
99K GLY* 1.3 72.2 - - - +
101K LEU* 1.3 55.7 + - - +
103K THR* 3.2 5.6 + - - -
104K ASN* 2.8 42.1 + - - +
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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
----------------------------------------------------------
6C PRO* 3.7 36.9 - - + +
8C VAL* 3.8 20.4 - - + -
22C LEU* 3.9 24.2 - - + -
25C VAL* 5.4 2.9 - - + -
29C MET* 6.1 2.0 - - + -
33C LEU* 4.2 17.0 - - + -
244C VAL* 5.7 1.1 - - + -
248C ILE* 3.8 28.0 - - + -
97K LYS 3.1 13.3 + - - +
98K LEU* 3.2 19.9 + - + +
100K ALA* 1.3 75.2 - - - +
102K LYS* 1.3 55.9 + - - +
104K ASN* 3.9 0.7 - - - -
105K PHE* 2.9 30.6 + - + +
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Residues in contact with LYS 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C VAL* 3.7 23.8 - - + +
248C ILE* 3.8 17.2 - - + +
249C ASP* 3.2 44.8 + - - +
252C GLN* 3.9 12.7 + - - +
98K LEU 3.0 15.7 + - - +
99K GLY* 3.7 6.7 - - - +
101K LEU* 1.3 72.0 - - - +
103K THR* 1.4 57.7 + - - +
105K PHE* 2.9 4.6 + - - +
106K GLU* 2.8 63.5 + - - +
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Residues in contact with THR 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLU* 3.4 17.3 - - - +
4C GLU* 5.4 2.8 + - - +
99K GLY 2.8 20.9 + - - -
100K ALA* 3.6 6.5 - - - -
102K LYS* 1.4 77.4 - - - +
104K ASN* 1.3 51.6 + - - +
106K GLU* 3.3 12.6 + - - +
107K THR* 2.5 38.0 + - - +
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Residues in contact with ASN 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLU* 2.8 46.8 + - - +
4C GLU 4.5 0.8 - - - +
5C GLY 4.8 0.4 - - - +
6C PRO 3.0 26.8 + - - +
7C GLN* 3.8 16.8 - - - +
8C VAL* 4.1 16.0 - - + +
100K ALA* 2.8 24.1 + - - +
101K LEU 3.9 3.6 - - - +
103K THR* 1.3 69.7 - - - +
105K PHE* 1.4 63.2 + - - +
107K THR* 3.6 7.1 + - - -
108K GLU* 3.2 25.6 + - - +
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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
----------------------------------------------------------
8C VAL* 3.6 30.2 - - + +
10C ILE* 4.0 10.5 - - + -
18C VAL* 3.9 26.9 - - + -
20C PHE* 4.4 5.8 - + - -
22C LEU* 6.1 0.2 - - + -
241C ASP* 3.8 31.4 - - + -
244C VAL* 3.8 33.9 - - + -
245C VAL* 4.0 17.5 - - + -
248C ILE* 4.5 8.3 - - + -
101K LEU 2.9 20.1 + - - +
102K LYS 2.9 4.0 + - - +
104K ASN* 1.4 72.0 - - - +
106K GLU* 1.3 58.5 + - - +
108K GLU* 3.2 3.5 + - - +
109K TRP* 2.8 52.8 + + + +
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Residues in contact with GLU 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C GLN* 6.2 0.2 - - - +
245C VAL* 3.4 24.9 - - + +
102K LYS* 2.8 47.8 + - + +
103K THR* 3.5 16.1 + - - +
105K PHE* 1.3 76.6 - - - +
107K THR* 1.4 63.6 + - - +
109K TRP* 3.1 4.3 + - - +
110K ASN* 3.1 35.4 + - - +
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Residues in contact with THR 107 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLU* 4.7 2.6 + - - -
103K THR* 2.5 32.2 + - - +
104K ASN* 3.6 8.0 + - - -
105K PHE 3.3 0.2 - - - -
106K GLU* 1.4 74.4 - - - +
108K GLU* 1.3 62.7 + - - +
110K ASN* 3.5 11.2 + - - +
111K LEU* 3.1 34.0 + - + +
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Residues in contact with GLU 108 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL* 3.6 22.2 - - + +
9C LYS* 3.6 12.4 - - - +
10C ILE* 2.8 46.9 + - + +
104K ASN 3.2 15.6 + - - +
105K PHE* 3.7 3.1 - - - +
107K THR* 1.3 74.5 - - - +
109K TRP* 1.3 63.3 + - - +
111K LEU* 3.4 28.4 + - + +
112K GLN* 3.3 33.0 + - - +
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Residues in contact with TRP 109 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 3.4 14.5 - - + +
13C ALA* 3.8 18.4 - - + -
14C SER 4.1 19.7 - - - -
18C VAL* 3.6 27.6 - - + -
240C VAL* 4.5 2.2 - - + -
241C ASP* 3.5 46.4 + - + -
105K PHE* 2.8 39.7 + + + +
106K GLU* 3.5 5.6 - - - +
108K GLU* 1.3 68.0 - - - +
110K ASN* 1.3 74.1 + - - +
111K LEU 3.1 1.8 - - - -
112K GLN* 2.9 32.2 + - + +
114K LEU 4.1 16.4 - - - -
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Residues in contact with ASN 110 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106K GLU* 3.1 25.8 + - - +
107K THR* 3.6 12.3 - - - +
109K TRP* 1.3 87.0 - - - +
111K LEU* 1.4 63.2 + - + +
112K GLN 3.6 6.1 + - - +
113K THR* 5.5 0.2 + - - -
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Residues in contact with LEU 111 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107K THR* 3.1 27.6 - - + +
108K GLU* 3.5 30.5 - - + +
109K TRP 3.1 0.8 - - - -
110K ASN* 1.4 78.1 - - + +
112K GLN* 1.3 69.1 + - - +
113K THR* 3.9 6.6 + - - -
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Residues in contact with GLN 112 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 3.9 34.3 + - + +
11C ARG 5.2 1.6 - - - +
12C GLU* 5.2 3.8 + - - -
13C ALA* 4.4 21.0 + - + +
108K GLU* 3.3 37.9 + - - +
109K TRP* 2.9 23.0 + - + +
110K ASN 3.7 6.2 - - - +
111K LEU* 1.3 83.9 - - - +
113K THR* 1.4 63.1 + - - +
114K LEU* 3.8 5.5 + - + +
----------------------------------------------------------
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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