Contacts of the helix formed by residues 78 - 100 (chain B) in PDB entry 2POD
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 GLY 78 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLY* 3.6 13.1 - - - -
78A GLY* 5.1 5.2 - - - -
80A GLU* 3.4 15.7 - - - -
73B GLY 4.9 2.6 + - - -
76B SER 3.2 8.5 + - - -
77B ALA* 1.3 77.8 - - - +
79B ALA* 1.3 65.6 + - - -
80B GLU* 3.3 7.4 - - - -
81B MSE 2.9 13.5 + - - +
82B ARG* 3.0 16.0 + - - +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A SER* 4.7 2.0 - - - -
79A ALA* 3.8 19.3 - - + -
80A GLU* 3.0 11.3 + - - +
40B SER* 3.5 44.6 - - - +
41B ALA* 3.8 8.3 - - - +
44B TYR* 4.0 2.9 - - + -
78B GLY* 1.3 69.4 - - - +
80B GLU* 1.3 59.9 + - - +
82B ARG* 3.4 12.2 + - - +
83B GLY* 2.9 28.6 + - - -
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Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLY* 5.4 0.5 - - - -
40A SER* 4.1 3.0 + - - -
78A GLY* 3.4 10.1 - - - -
79A ALA* 3.1 24.3 + - - +
82A ARG* 2.7 38.7 + - - -
44B TYR* 3.3 39.3 - - + +
72B LEU 4.3 18.1 - - - +
73B GLY* 4.6 6.2 - - - +
78B GLY* 4.2 1.2 - - - -
79B ALA* 1.3 75.9 + - - +
81B MSE 1.3 56.1 + - + +
84B ASN* 2.9 39.3 + - - +
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Residues in contact with MSE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B SER* 5.3 6.1 - - - +
73B GLY 3.7 13.6 + - - +
74B PHE* 3.6 30.5 - - + +
76B SER 3.3 24.0 - - - +
77B ALA* 3.8 0.7 - - - -
78B GLY 2.9 12.7 + - - +
80B GLU* 1.3 79.8 - - + +
82B ARG* 1.3 52.2 + - - +
84B ASN* 3.6 14.0 + - - +
85B SER* 2.5 37.5 + - - -
273B ALA* 3.8 3.8 - - + -
274B THR* 3.9 18.8 - - + -
296B TRP 3.2 24.9 - - - +
298B GLY* 3.7 26.9 - - - -
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Residues in contact with ARG 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 4.1 13.4 - - - +
80A GLU* 2.7 29.7 + - - -
34B THR* 3.4 19.7 + - + +
35B PHE 3.4 20.0 - - - -
36B TYR* 3.0 20.1 + - - +
37B GLY* 3.1 29.3 + - - -
40B SER* 3.2 9.9 + - - -
41B ALA* 4.3 4.7 - - + +
77B ALA 3.1 30.2 + - - +
78B GLY 3.0 9.4 + - - +
79B ALA* 3.7 10.4 - - - +
81B MSE 1.3 73.9 - - - +
83B GLY* 1.3 60.2 + - - +
85B SER* 3.4 1.0 + - - -
86B ALA* 3.0 29.3 + - - +
295B SER 3.4 16.4 - - - +
296B TRP* 3.6 16.6 - - + +
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Residues in contact with GLY 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B THR* 5.1 0.2 - - - -
41B ALA* 4.2 7.9 - - - +
44B TYR* 4.0 5.6 - - - -
45B ILE* 4.0 22.6 - - - +
79B ALA 2.9 17.0 + - - -
80B GLU 3.8 1.1 - - - -
82B ARG* 1.3 74.3 - - - +
84B ASN* 1.3 59.3 + - - +
86B ALA* 3.4 4.6 + - - +
87B LEU* 3.0 37.1 + - - +
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Residues in contact with ASN 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TYR* 2.5 24.4 + - - -
49B ALA* 4.5 0.3 - - - +
65B ALA* 5.6 0.8 + - - -
68B LEU* 2.9 51.2 + - + +
69B SER* 4.3 4.0 - - - +
70B GLY 5.0 0.6 - - - +
80B GLU* 2.9 25.2 + - - +
81B MSE 3.7 17.9 - - - +
83B GLY* 1.3 75.5 - - - +
85B SER* 1.3 56.7 + - - +
87B LEU* 3.4 7.6 + - - +
88B ASP* 2.8 29.6 + - - +
298B GLY* 5.3 3.8 - - - +
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B MSE 2.5 23.0 + - - -
82B ARG 3.7 0.2 - - - -
83B GLY 3.3 0.4 - - - -
84B ASN* 1.3 73.6 - - - +
86B ALA* 1.3 59.5 + - - +
88B ASP* 3.2 3.3 + - - +
89B ILE* 3.0 34.6 + - - +
294B ILE 3.3 21.8 - - - -
295B SER 3.4 21.1 + - - -
297B CYS 4.0 0.3 + - - -
298B GLY* 3.0 21.9 + - - -
299B GLY* 3.4 11.9 - - - +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 3.7 23.6 - - + -
32B GLY* 3.3 12.4 - - - -
33B GLU 3.5 35.3 + - - +
34B THR* 4.0 6.5 - - + +
45B ILE* 5.0 0.4 - - + -
82B ARG 3.0 17.0 + - - +
83B GLY* 3.7 4.5 - - - +
85B SER* 1.3 72.4 - - - +
87B LEU* 1.3 65.4 + - - +
88B ASP 3.3 0.2 + - - -
89B ILE* 3.3 2.8 + - - -
90B ALA* 3.3 18.4 + - - +
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 4.3 11.7 - - + -
20B VAL* 3.7 27.4 - - + -
22B VAL* 4.2 12.1 - - + +
45B ILE* 3.9 16.2 - - + -
49B ALA* 3.7 29.8 - - + -
53B LEU* 3.6 26.2 - - + -
68B LEU* 4.0 16.2 - - + -
83B GLY 3.0 22.0 + - - +
84B ASN* 3.4 7.2 - - - +
86B ALA* 1.3 75.5 - - - +
88B ASP* 1.3 60.6 + - - +
90B ALA* 3.6 6.1 + - - +
91B LEU* 3.2 28.0 + - + +
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Residues in contact with ASP 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 3.7 9.7 - - - +
65B ALA* 4.4 8.8 - - + +
68B LEU* 6.0 0.2 - - - +
84B ASN 2.8 18.9 + - - +
85B SER 3.4 6.3 - - - +
86B ALA 3.2 0.4 - - - -
87B LEU* 1.3 74.1 - - - +
89B ILE* 1.3 65.2 + - - +
91B LEU* 3.1 19.7 + - - +
92B TRP* 3.1 29.7 + - - -
298B GLY 4.2 3.1 - - - +
299B GLY* 3.8 8.5 - - - -
300B LEU 2.7 26.9 + - - -
301B SER* 2.9 34.7 + - - -
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Residues in contact with ILE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU 3.5 15.5 - - - +
32B GLY* 4.1 1.6 - - - -
33B GLU* 3.7 23.6 - - + +
85B SER 3.0 20.5 + - - +
86B ALA 3.8 5.2 - - - +
88B ASP* 1.3 75.4 - - - +
90B ALA* 1.3 57.3 + - - +
92B TRP* 3.1 9.4 + - - +
93B ASP* 2.9 25.1 + - - +
103B ILE* 4.7 0.7 - - - +
294B ILE* 3.8 39.3 - - + +
300B LEU* 4.6 15.7 - - + +
326B VAL* 4.1 9.6 - - + -
327B VAL* 4.5 7.6 - - + -
330B ALA* 4.2 6.7 - - + -
378B LEU* 3.9 21.5 - - + -
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 4.4 2.9 - - + +
22B VAL* 3.8 18.6 - - + -
30B GLY* 3.5 13.2 - - - +
31B LEU 3.5 14.4 + - - +
32B GLY 3.5 19.1 - - - +
86B ALA 3.3 6.4 + - - +
87B LEU* 3.7 10.1 - - - +
88B ASP 3.3 0.2 - - - -
89B ILE* 1.3 79.4 - - - +
91B LEU* 1.3 56.4 + - - +
93B ASP* 3.3 3.3 + - - +
94B ILE* 3.0 33.4 + - - +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ILE* 4.1 14.1 - - + -
22B VAL* 4.5 6.7 - - + -
53B LEU* 4.8 11.2 - - + -
58B PRO* 3.8 42.4 - - + +
61B ILE* 3.5 28.7 - - + +
64B HIS* 4.1 29.6 - - + -
65B ALA 5.8 0.2 - - - +
68B LEU* 6.2 1.3 - - + -
87B LEU* 3.2 16.6 + - + +
88B ASP* 3.1 16.1 + - - +
90B ALA* 1.3 75.6 - - - +
92B TRP* 1.3 56.1 + - - +
94B ILE* 3.5 11.7 + - + +
95B PHE* 3.1 22.5 + - - +
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Residues in contact with TRP 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ILE* 3.4 26.2 - - + +
88B ASP* 3.1 41.8 + - - -
89B ILE 3.1 7.9 + - - +
91B LEU* 1.3 73.0 - - - +
93B ASP* 1.3 63.7 + - - +
95B PHE* 3.6 39.1 - + - +
96B GLY* 3.1 18.4 + - - -
103B ILE* 3.6 21.4 - - + +
106B LEU* 3.9 34.4 - - + +
107B LEU* 4.3 9.2 - - + -
300B LEU* 3.6 31.6 - - + +
301B SER 3.5 8.3 - - - +
304B ARG* 3.4 47.1 - - - -
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Residues in contact with ASP 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLY* 3.5 5.0 - - - -
31B LEU* 2.8 38.5 + - - +
89B ILE 2.9 11.8 + - - +
90B ALA* 3.3 10.3 + - - +
92B TRP* 1.3 76.0 - - - +
94B ILE* 1.3 61.2 + - - +
96B GLY* 3.3 2.9 + - - -
97B LYS* 3.2 47.7 + - - +
103B ILE* 4.0 2.8 - - - +
376B PRO 4.5 0.2 - - - +
377B GLY* 3.5 5.3 - - - -
378B LEU* 3.0 35.2 + - + +
379B GLY 4.7 0.5 + - - -
380B LEU 4.5 2.8 - - - +
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Residues in contact with ILE 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LEU* 3.8 28.5 - - + -
22B VAL* 3.8 37.9 - - + +
24B THR* 4.4 7.2 - - + -
28B ILE* 3.6 21.1 - - + +
29B THR 4.2 0.4 - - - -
30B GLY 3.7 15.5 - - - +
58B PRO* 3.8 26.7 - - + -
59B LEU* 4.3 3.6 - - + -
90B ALA 3.0 18.4 + - - +
91B LEU* 3.6 11.4 - - + +
92B TRP 3.4 0.2 - - - -
93B ASP* 1.3 72.8 - - - +
95B PHE* 1.3 66.4 + - - +
97B LYS 3.1 2.8 + - - -
98B ALA* 2.9 22.3 + - - +
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Residues in contact with PHE 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU* 4.1 37.9 - - + +
61B ILE* 3.7 14.1 - - + -
91B LEU 3.1 15.2 + - - +
92B TRP* 3.6 38.4 - + - +
94B ILE* 1.3 77.3 - - - +
96B GLY* 1.3 61.7 + - - +
98B ALA* 3.5 0.9 + - - +
99B THR* 3.1 45.2 + - + +
106B LEU* 3.7 25.4 - - + -
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Residues in contact with GLY 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TRP 3.1 11.3 + - - -
93B ASP 3.7 1.8 - - - -
94B ILE 3.2 0.4 - - - -
95B PHE* 1.3 77.1 - - - +
97B LYS* 1.3 56.1 + - - +
99B THR* 4.1 0.7 - - - -
100B GLY* 2.9 8.1 + - - -
101B GLN 2.7 45.9 + - - -
106B LEU* 3.5 10.9 - - - +
376B PRO* 3.4 1.0 - - - +
377B GLY* 3.5 15.0 - - - -
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Residues in contact with LYS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 3.5 28.7 - - + -
29B THR* 2.9 25.2 + - - +
93B ASP* 3.2 33.6 + - - +
94B ILE 3.1 2.6 + - - -
96B GLY* 1.3 76.1 - - - +
98B ALA* 1.3 60.7 + - - +
99B THR 3.5 0.3 + - - -
100B GLY* 3.7 6.6 + - - -
376B PRO* 3.9 25.9 - - + +
379B GLY 6.1 0.4 - - - +
380B LEU 4.8 3.1 + - - -
381B GLU* 4.1 28.2 + - - +
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LEU* 4.2 23.1 - - + -
28B ILE* 4.5 5.1 - - + +
59B LEU* 4.4 12.1 - - + -
94B ILE 2.9 17.1 + - - +
95B PHE 3.5 4.2 + - - +
97B LYS* 1.3 76.3 - - - +
99B THR* 1.3 62.9 + - + +
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Residues in contact with THR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 5.7 3.4 - - + -
95B PHE* 3.1 42.3 + - + +
96B GLY 3.5 0.2 + - - -
98B ALA* 1.3 81.4 - - + +
100B GLY* 1.3 62.5 + - - +
101B GLN* 3.4 35.2 + - - +
106B LEU* 3.7 6.8 - - + +
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Residues in contact with GLY 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLY 2.9 7.8 + - - -
97B LYS 3.7 6.2 + - - -
98B ALA 3.6 1.4 - - - -
99B THR* 1.3 78.8 - - - +
101B GLN* 1.3 66.4 + - - +
102B PRO* 4.4 2.8 - - - +
376B PRO* 3.9 21.8 - - - +
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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