Contacts of the helix formed by residues 78 - 100 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLY 4.8 3.2 + - - -
76A SER* 3.2 9.3 + - - -
77A ALA* 1.3 79.2 - - - +
79A ALA* 1.3 60.3 + - - -
80A GLU* 3.4 5.8 - - - -
81A MSE 3.0 4.8 + - - +
82A ARG* 2.9 30.3 + - - +
73B GLY* 3.7 11.6 - - - -
78B GLY* 5.1 5.6 - - - -
80B GLU* 3.4 13.9 - - - -
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A SER* 3.6 44.4 - - - +
41A ALA* 3.9 7.4 - - - -
44A TYR* 4.0 2.7 - - - -
78A GLY* 1.3 68.4 - - - -
80A GLU* 1.3 63.2 + - - +
82A ARG* 3.3 16.3 + - - +
83A GLY* 2.9 28.4 + - - -
40B SER* 5.0 0.9 - - - -
79B ALA* 3.8 16.2 - - + -
80B GLU* 3.1 10.7 + - - +
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Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TYR* 3.3 39.3 - - + +
70A GLY* 6.4 0.7 - - - +
72A LEU 4.3 15.9 - - - +
73A GLY* 4.9 6.2 - - - +
78A GLY* 4.1 0.7 - - - -
79A ALA* 1.3 77.7 + - - +
81A MSE 1.3 55.4 + - - +
84A ASN* 3.0 38.5 + - - +
37B GLY* 5.6 0.2 - - - -
40B SER* 4.2 2.2 + - - +
78B GLY* 3.4 10.0 - - - -
79B ALA* 3.0 26.5 + - - +
82B ARG* 2.7 37.6 + - - -
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Residues in contact with MSE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A SER* 5.5 4.3 - - - +
73A GLY 3.7 6.2 + - - +
74A PHE* 3.3 36.1 - - + +
76A SER 3.3 25.8 - - - +
77A ALA* 3.9 0.4 - - - -
78A GLY* 3.0 12.7 + - - +
80A GLU* 1.3 78.3 - - - +
82A ARG* 1.3 53.3 + - - +
84A ASN* 3.5 12.9 + - - +
85A SER* 2.4 36.6 + - - -
273A ALA* 3.9 2.9 - - + -
274A THR* 3.8 26.0 - - + -
296A TRP 3.1 24.9 - - - +
297A CYS 4.0 0.4 - - - +
298A GLY* 3.8 20.4 - - - -
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Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 3.5 26.4 + - + +
35A PHE 3.5 19.7 - - - -
36A TYR* 2.9 19.0 + - - -
37A GLY* 3.1 29.5 + - - -
40A SER* 3.3 8.5 + - - -
41A ALA* 4.2 3.7 - - + +
77A ALA 3.3 23.7 + - - +
78A GLY 2.9 18.5 + - - +
79A ALA* 3.6 13.8 - - - +
81A MSE 1.3 73.6 - - - +
83A GLY* 1.3 65.5 + - - +
85A SER* 3.4 1.4 + - - -
86A ALA* 3.1 18.0 + - - +
295A SER 3.5 7.9 - - - +
296A TRP* 3.7 23.1 - - + -
72B LEU* 3.8 17.6 - - - +
80B GLU* 2.7 29.9 + - - -
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Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 5.1 0.4 - - - -
41A ALA* 4.2 7.5 - - - +
44A TYR* 4.2 2.5 - - - -
45A ILE* 3.8 31.8 - - - +
79A ALA 2.9 16.4 + - - -
80A GLU 3.9 0.9 - - - -
82A ARG* 1.3 74.5 - - - +
84A ASN* 1.3 63.4 + - - +
86A ALA* 3.5 3.9 + - - +
87A LEU* 3.2 27.0 + - - +
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Residues in contact with ASN 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TYR* 2.6 24.8 + - - -
49A ALA* 4.3 1.0 - - - +
65A ALA 5.6 0.2 + - - -
68A LEU* 2.7 53.4 + - + +
69A SER* 4.3 2.8 - - - +
70A GLY 5.0 1.0 - - - +
80A GLU* 3.0 25.2 + - - +
81A MSE 3.7 15.6 - - - +
83A GLY* 1.3 76.1 - - - +
85A SER* 1.3 60.8 + - - +
87A LEU* 3.5 7.3 - - - +
88A ASP* 3.1 23.6 + - - +
298A GLY* 5.0 4.4 - - - +
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A MSE 2.4 26.2 + - - -
82A ARG 3.7 0.7 - - - -
83A GLY 3.2 0.4 - - - -
84A ASN* 1.3 75.1 - - - +
86A ALA* 1.3 64.1 + - - +
88A ASP* 3.3 3.1 + - - +
89A ILE* 3.1 28.8 + - - +
294A ILE 3.4 17.9 - - - -
295A SER* 3.4 25.6 + - - -
296A TRP 3.9 0.7 - - - -
298A GLY* 3.1 19.2 + - - -
299A GLY* 3.5 12.4 - - - +
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 5.2 0.4 - - + -
20A VAL* 3.7 20.6 - - + -
32A GLY* 3.3 12.9 - - - -
33A GLU 3.6 38.3 + - - +
34A THR* 3.9 7.0 - - + +
82A ARG 3.1 15.9 + - - +
83A GLY* 4.0 4.0 - - - +
84A ASN 3.4 0.2 - - - -
85A SER* 1.3 74.3 - - - +
87A LEU* 1.3 63.4 + - - +
89A ILE* 3.3 2.8 + - - -
90A ALA* 3.3 18.0 + - - +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.6 12.1 - - + -
20A VAL* 3.6 28.0 - - + -
22A VAL* 4.5 10.7 - - + +
45A ILE* 3.4 35.7 - - + -
49A ALA* 3.8 17.3 - - + -
50A ALA* 5.9 0.2 - - - -
53A LEU* 4.3 20.4 - - + -
68A LEU* 3.9 19.3 - - + -
83A GLY 3.2 11.9 + - - +
84A ASN* 3.5 5.6 - - - +
86A ALA* 1.3 76.9 - - - +
88A ASP* 1.3 57.2 + - - +
90A ALA* 3.5 7.0 + - - +
91A LEU* 3.1 33.6 + - + +
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Residues in contact with ASP 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE* 4.0 9.6 - - - +
65A ALA* 4.3 10.5 + - + +
84A ASN 3.1 15.7 + - - +
85A SER 3.4 6.3 - - - +
86A ALA 3.2 0.4 - - - -
87A LEU* 1.3 77.5 - - - +
89A ILE* 1.3 64.2 + - - +
91A LEU* 3.2 10.1 + - - +
92A TRP* 3.0 36.7 + - - -
298A GLY 4.2 2.9 - - - +
299A GLY* 3.9 10.5 - - - -
300A LEU 2.9 25.8 + - - -
301A SER* 3.0 30.9 + - - -
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU 3.6 14.8 - - - +
32A GLY* 4.1 1.3 - - - -
33A GLU* 3.5 27.4 - - + +
85A SER 3.1 16.0 + - - +
86A ALA 3.3 5.6 + - - +
88A ASP* 1.3 74.6 - - - +
90A ALA* 1.3 56.4 + - - +
92A TRP* 3.2 6.1 + - - +
93A ASP* 2.9 24.6 + - - +
103A ILE* 4.6 1.2 - - - +
294A ILE* 3.8 34.1 - - + +
295A SER* 4.4 6.3 - - - -
300A LEU* 4.5 19.3 - - + +
326A VAL* 4.1 8.7 - - + -
327A VAL* 4.5 5.2 - - + -
330A ALA* 4.2 7.2 - - + -
378A LEU* 3.9 21.3 - - + -
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.7 2.7 - - + +
22A VAL* 3.8 19.5 - - + -
30A GLY* 3.5 17.3 - - - +
31A LEU 3.5 13.1 + - - +
32A GLY* 3.5 19.3 - - - +
86A ALA 3.3 6.6 + - - +
87A LEU* 3.6 9.2 - - - +
88A ASP 3.3 0.2 - - - -
89A ILE* 1.3 74.8 - - - +
91A LEU* 1.3 61.5 + - - +
93A ASP* 3.1 4.2 + - - +
94A ILE* 2.9 27.3 + - - +
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 4.0 13.9 - - + -
22A VAL* 4.5 7.0 - - + -
53A LEU* 4.4 11.2 - - + -
58A PRO* 3.7 43.9 - - + +
61A ILE* 3.6 20.9 - - + +
64A HIS* 3.9 31.4 - - + -
68A LEU* 6.2 0.7 - - + -
87A LEU* 3.1 19.0 + - + +
88A ASP* 3.2 14.5 + - - +
90A ALA* 1.3 75.0 - - - +
92A TRP* 1.3 58.4 + - - +
94A ILE* 3.5 11.5 + - + +
95A PHE* 3.0 28.1 + - - +
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Residues in contact with TRP 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE* 3.5 25.8 - - + +
88A ASP* 3.0 46.2 + - - -
89A ILE 3.4 7.9 - - - +
91A LEU* 1.3 74.3 - - - +
93A ASP* 1.3 59.7 + - - +
95A PHE* 3.5 34.3 - + - +
96A GLY 3.0 23.6 + - - -
103A ILE* 3.6 20.0 - - + +
106A LEU* 3.8 34.6 - - + +
107A LEU* 4.1 12.6 - - + -
300A LEU* 3.7 28.0 - - + -
301A SER 3.7 7.7 - - - +
304A ARG* 3.5 46.7 - - - -
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Residues in contact with ASP 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLY* 3.4 1.5 - - - -
31A LEU* 2.9 34.6 + - - +
89A ILE 2.9 12.9 + - - +
90A ALA* 3.1 10.1 + - - +
92A TRP* 1.3 73.5 - - - +
94A ILE* 1.3 64.2 + - - +
96A GLY* 3.4 2.1 + - - -
97A LYS* 3.1 52.2 + - - +
103A ILE* 3.9 6.2 - - - +
376A PRO 4.4 0.2 - - - +
377A GLY* 3.6 4.0 - - - -
378A LEU* 3.0 37.5 + - + +
380A LEU 4.8 3.0 - - - +
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Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 3.9 17.5 - - + -
22A VAL* 3.8 41.5 - - + +
24A THR* 4.3 9.9 - - + -
28A ILE* 4.1 16.9 - - + +
29A THR 4.2 2.2 - - - -
30A GLY* 3.6 17.7 - - - +
58A PRO* 3.8 34.3 - - + -
59A LEU* 4.2 3.6 - - + -
90A ALA 2.9 12.2 + - - +
91A LEU* 3.6 12.1 - - + +
93A ASP* 1.3 71.7 - - - +
95A PHE* 1.3 57.2 + - - +
97A LYS* 3.0 3.9 + - - +
98A ALA* 2.8 32.6 + - - +
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Residues in contact with PHE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 4.1 36.8 - - + +
61A ILE* 3.8 16.8 - - + -
91A LEU 3.0 17.7 + - - +
92A TRP* 3.5 38.4 - + - +
93A ASP 3.4 0.2 - - - -
94A ILE* 1.3 75.8 - - - +
96A GLY* 1.3 61.4 + - - +
98A ALA* 3.5 1.0 + - - +
99A THR* 2.8 46.2 + - + +
106A LEU* 3.7 26.5 - - + -
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Residues in contact with GLY 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A TRP 3.0 10.9 + - - -
93A ASP 3.8 1.3 - - - -
94A ILE 3.2 0.2 - - - -
95A PHE* 1.3 77.4 - - - +
97A LYS* 1.3 56.5 + - - +
99A THR* 3.4 1.1 + - - -
100A GLY* 2.9 9.9 + - - -
101A GLN 2.8 45.5 + - - +
106A LEU* 3.4 11.3 - - - +
376A PRO* 3.4 1.6 - - - +
377A GLY* 3.6 13.7 - - - -
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Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 3.8 28.4 - - + +
29A THR* 2.7 34.5 + - - +
31A LEU* 5.3 0.8 - - - +
93A ASP* 3.1 39.9 + - - +
94A ILE 3.0 5.1 + - - +
96A GLY* 1.3 76.3 - - - +
98A ALA* 1.3 61.5 + - - +
99A THR 3.4 0.5 + - - -
100A GLY* 3.7 7.8 + - - -
376A PRO* 4.0 21.8 - - + +
379A GLY 6.3 0.2 - - - +
380A LEU 4.8 5.3 + - - -
381A GLU* 4.1 28.0 + - - +
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Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 4.0 24.5 - - + -
28A ILE* 4.7 8.2 - - + +
59A LEU* 4.3 13.7 - - + -
94A ILE 2.8 15.8 + - - +
95A PHE 3.8 4.5 - - - +
97A LYS* 1.3 78.0 - - - +
99A THR* 1.3 62.1 + - + +
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Residues in contact with THR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 5.5 4.0 - - + -
95A PHE* 2.8 44.2 + - + +
96A GLY* 3.4 4.3 + - - -
98A ALA* 1.3 81.3 - - + +
100A GLY* 1.3 62.2 + - - +
101A GLN* 3.5 32.6 + - - +
106A LEU* 3.7 6.4 - - + +
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Residues in contact with GLY 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLY 2.9 8.1 + - - -
97A LYS 3.7 5.5 + - - -
98A ALA 3.6 1.6 - - - -
99A THR* 1.3 77.5 - - - +
101A GLN* 1.3 67.6 + - - +
102A PRO* 4.2 3.5 - - - +
376A PRO* 3.8 23.2 - - - +
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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