Contacts of the helix formed by residues 76 - 106 (chain A) in PDB entry 2SPC
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 76 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASN 3.0 11.2 + - - -
73A HIS* 4.0 7.4 - - - -
75A ALA* 1.3 75.1 - - - +
77A ASN* 1.3 58.3 + - - +
79A VAL* 3.4 3.4 + - - +
80A ASP* 2.9 33.0 + - - +
69B ILE* 4.0 27.6 + - - +
72B ASN* 2.9 36.0 + - - +
73B HIS* 4.4 9.7 - - - -
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Residues in contact with ASN 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A HIS* 3.0 33.4 + - - +
74A TYR* 3.6 12.6 - - + +
76A SER* 1.3 80.1 - - - +
78A LEU* 1.3 57.4 + - - +
80A ASP* 4.0 4.3 - - - +
81A GLU* 3.0 32.6 + - - +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TYR* 3.1 34.0 + - + +
75A ALA* 3.4 9.4 - - - +
77A ASN* 1.3 76.5 - - - +
79A VAL* 1.3 66.4 + - - +
81A GLU* 3.4 3.8 + - + +
82A LYS* 2.9 27.4 + - + +
0B GLN 5.8 2.2 - - - +
4B LEU* 3.9 28.7 - - + -
8B MET* 4.2 23.3 - - + -
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA 3.0 12.7 + - - +
76A SER* 3.7 5.6 - - - +
77A ASN 3.3 0.2 - - - -
78A LEU* 1.3 77.8 - - - +
80A ASP* 1.3 56.7 + - - +
82A LYS* 3.4 0.5 + - - +
83A ARG* 3.0 14.6 + - - +
0B GLN* 4.7 1.3 - - - +
4B LEU* 3.3 32.1 - - + -
7B TYR* 3.0 37.8 + - + -
8B MET* 5.1 0.7 - - - -
65B ALA* 3.6 39.7 - - + +
68B LEU* 3.6 23.1 - - + -
69B ILE* 4.1 9.6 - - + -
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Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A SER 2.9 18.1 + - - +
77A ASN* 4.0 4.5 - - - +
79A VAL* 1.3 76.2 - - - +
81A GLU* 1.3 57.8 + - - +
83A ARG* 2.7 36.6 + - - +
84A LYS* 3.0 51.3 + - - +
65B ALA* 5.8 0.2 - - - +
69B ILE* 3.7 22.6 - - + +
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Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASN 3.0 20.7 + - - +
78A LEU* 4.0 4.5 - - + +
80A ASP* 1.3 76.3 - - - +
82A LYS* 1.3 64.1 + - - +
84A LYS* 3.3 36.5 + - - +
85A GLN* 3.1 42.5 + - - +
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Residues in contact with LYS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 2.9 18.7 + - + +
79A VAL 3.6 4.0 - - - +
81A GLU* 1.3 74.2 - - - +
83A ARG* 1.3 64.2 + - - +
85A GLN* 3.1 17.4 + - - +
86A VAL* 3.0 23.8 + - + +
89A ARG* 4.0 5.7 - - - +
7B TYR* 4.2 1.3 - - - +
8B MET* 3.9 36.2 - - + +
11B CYS* 3.7 33.7 - - + -
12B GLU* 4.3 12.9 + - - +
15B GLU* 2.8 39.7 + - - +
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Residues in contact with ARG 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL 3.0 8.5 + - - +
80A ASP* 2.7 40.7 + - - +
81A GLU 3.2 0.2 - - - -
82A LYS* 1.3 76.2 - - - +
84A LYS* 1.3 86.5 + - - +
86A VAL* 3.3 8.1 + - + +
87A LEU* 2.9 58.5 + - + +
7B TYR* 3.3 18.8 + - - +
11B CYS* 5.5 0.7 - - - -
61B LEU* 5.5 2.0 - - + -
62B GLN* 3.7 33.3 + - + +
65B ALA* 4.3 15.1 - - + +
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Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASP* 3.0 36.8 + - - +
81A GLU* 3.5 35.3 + - - +
82A LYS 3.3 0.2 - - - -
83A ARG* 1.3 105.6 - - - +
85A GLN* 1.3 57.1 + - + +
87A LEU* 3.5 5.4 + - - +
88A GLU* 3.0 29.6 + - - +
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Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLU* 3.1 29.7 + - - +
82A LYS* 3.4 20.4 + - + +
84A LYS* 1.3 73.0 - - + +
86A VAL* 1.3 65.2 + - - +
88A GLU* 3.5 5.7 + - - +
89A ARG* 3.1 58.0 + - - +
15B GLU* 4.8 0.2 - - - +
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS* 3.0 18.4 + - - +
83A ARG* 3.5 10.3 - - + +
85A GLN* 1.3 73.8 - - - +
87A LEU* 1.4 60.5 + - + +
89A ARG* 3.2 8.2 + - - +
90A TRP* 2.9 27.2 + - - +
11B CYS* 3.8 33.2 - - + +
14B ALA* 5.5 0.2 - - + -
15B GLU* 3.9 23.6 - - + +
18B MET* 4.0 9.8 - - + +
58B ILE* 4.0 28.0 - - + -
61B LEU* 4.3 12.1 - - + -
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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
----------------------------------------------------------
83A ARG* 2.9 56.3 + - + +
84A LYS* 3.8 4.9 - - - +
86A VAL* 1.4 78.0 - - + +
88A GLU* 1.3 59.5 + - - +
90A TRP* 3.2 12.7 + - + +
91A ARG* 3.0 25.5 + - - +
58B ILE* 3.2 36.6 - - + +
62B GLN* 3.8 17.0 - - + +
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Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LYS 3.0 18.6 + - - +
85A GLN* 3.9 6.5 - - - +
86A VAL 3.2 0.2 - - - -
87A LEU* 1.3 73.8 - - - +
89A ARG* 1.3 62.9 + - + +
90A TRP 3.1 1.6 - - - -
91A ARG* 2.5 67.0 + - - +
92A HIS* 3.3 13.9 + - - +
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Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS* 4.0 5.7 - - - +
85A GLN* 3.1 48.7 + - - +
86A VAL* 3.2 7.4 + - - +
88A GLU* 1.3 78.8 - - + +
90A TRP* 1.3 58.2 + - - +
92A HIS* 3.4 5.7 + - - +
93A LEU* 3.1 24.3 + - - +
15B GLU* 2.3 42.5 + - - +
18B MET* 4.4 13.6 - - + +
19B SER* 6.2 0.2 - - - -
22B GLU* 4.4 2.4 - - - +
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Residues in contact with TRP 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL 2.9 12.6 + - - +
87A LEU* 3.4 12.6 - - + +
88A GLU 3.1 0.2 - - - -
89A ARG* 1.3 76.2 - - - +
91A ARG* 1.3 61.0 + - - +
92A HIS 3.1 0.7 - - - -
93A LEU* 3.4 24.5 - - + -
94A LYS* 2.8 55.1 + - + +
97A LEU* 4.0 9.4 - - + -
18B MET* 3.8 13.4 - - - -
51B ILE* 3.7 11.0 - - + -
54B HIS* 3.3 44.0 - - + -
55B GLU* 2.8 46.1 + - + +
58B ILE* 4.1 28.5 - - + -
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Residues in contact with ARG 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU 3.0 13.6 + - - +
88A GLU* 2.5 52.4 + - - +
89A ARG 3.2 0.4 - - - -
90A TRP* 1.3 81.9 - - - +
92A HIS* 1.3 56.6 + - - +
94A LYS* 4.1 5.1 - - - +
95A GLU* 3.3 36.7 + - + +
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Residues in contact with HIS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 3.3 14.6 + - - +
89A ARG* 3.4 5.1 + - - +
90A TRP 3.1 0.4 - - - -
91A ARG* 1.3 79.2 - - - +
93A LEU* 1.3 67.2 + - - +
95A GLU* 3.3 12.9 + - + +
96A GLY* 3.3 8.1 + - - -
22B GLU* 2.7 36.3 + - - +
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ARG 3.1 12.4 + - - +
90A TRP* 3.3 21.7 + - + +
92A HIS* 1.3 73.8 - - - +
94A LYS* 1.3 54.6 + - - +
96A GLY* 2.6 27.4 + - - -
97A LEU* 3.1 20.2 + - + +
18B MET* 3.7 22.9 - - + +
21B ARG* 3.7 15.9 - - + -
22B GLU* 2.8 49.2 + - + +
25B LEU* 5.0 1.1 - - + +
54B HIS* 3.0 41.5 - - + +
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Residues in contact with LYS 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TRP* 2.8 41.9 + - + +
91A ARG* 4.1 6.1 - - - +
93A LEU* 1.3 76.0 - - - +
95A GLU* 1.3 63.6 + - + +
97A LEU* 3.4 4.2 + - - -
98A ILE* 3.3 44.8 + - + +
51B ILE* 3.8 14.4 - - + -
55B GLU* 2.8 35.3 + - - +
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ARG* 3.3 30.3 + - + +
92A HIS* 3.6 9.2 - - + +
93A LEU 2.9 1.0 + - - -
94A LYS* 1.3 79.6 - - + +
96A GLY* 1.3 65.7 + - - +
98A ILE* 4.2 4.7 - - - +
99A GLU* 3.2 25.1 + - - +
----------------------------------------------------------
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Residues in contact with GLY 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A HIS* 3.3 5.5 + - - -
93A LEU 2.6 14.2 + - - -
95A GLU* 1.3 71.9 - - - +
97A LEU* 1.3 66.4 + - - +
99A GLU* 3.1 5.3 + - - -
100A LYS* 2.8 26.6 + - - +
22B GLU* 6.5 1.1 - - - -
25B LEU* 3.4 15.0 - - - -
----------------------------------------------------------
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TRP* 4.0 13.2 - - + -
93A LEU* 3.1 15.3 + - + +
94A LYS 3.4 2.2 + - - +
96A GLY* 1.3 76.2 - - - +
98A ILE* 1.3 56.7 + - - +
101A ARG* 2.9 22.9 + - - +
21B ARG* 4.0 24.7 - - + -
24B PHE* 4.7 2.0 - - + -
25B LEU* 3.3 32.7 - - + +
47B PHE* 3.2 25.7 - - + -
50B ALA* 4.6 2.9 - - + -
51B ILE* 3.3 41.5 - - + +
54B HIS* 3.9 23.6 - - - +
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Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LYS* 3.3 42.4 + - + +
95A GLU* 4.2 4.0 - - - +
97A LEU* 1.3 73.3 - - - +
99A GLU* 1.3 63.9 + - - +
101A ARG* 3.0 40.5 + - - +
102A SER* 3.0 26.0 + - - +
51B ILE* 3.5 15.7 - - + -
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Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLU* 3.2 18.0 + - - +
96A GLY* 3.1 5.2 + - - +
98A ILE* 1.3 81.0 - - + +
100A LYS* 1.3 54.5 + - + +
102A SER* 2.7 40.2 + - - -
103A ARG* 2.8 41.2 + - + +
----------------------------------------------------------
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLY* 2.8 20.5 + - - +
99A GLU* 1.3 74.1 - - + +
101A ARG* 1.3 56.5 + - - +
103A ARG* 3.3 44.7 + - - +
104A LEU* 3.2 35.7 + - - +
25B LEU* 3.6 17.4 - - + +
28B ASP* 2.3 50.9 + - - +
29B ASP* 3.9 15.3 - - + +
30B ASP 5.8 0.2 - - - -
43B LYS* 4.6 2.8 - - - +
47B PHE* 3.5 18.2 - - + -
----------------------------------------------------------
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Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU 2.9 14.8 + - - +
98A ILE* 3.0 58.3 + - - +
99A GLU 3.0 0.4 - - - -
100A LYS* 1.3 77.3 - - - +
102A SER* 1.3 61.4 + - - +
104A LEU* 3.6 17.6 - - - +
105A GLY 5.4 0.2 - - - +
44B HIS* 3.3 35.6 + - + +
47B PHE* 3.8 31.6 - - + -
48B ASP* 2.9 29.0 + - - +
51B ILE* 5.3 3.9 - - - +
----------------------------------------------------------
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Residues in contact with SER 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE* 3.0 9.1 + - - +
99A GLU* 2.7 30.5 + - - -
101A ARG* 1.3 77.1 + - - +
103A ARG* 1.3 54.4 + - - -
104A LEU 2.9 10.9 + - - -
105A GLY 3.0 24.3 + - - +
106A ASP* 3.9 8.2 + - - +
----------------------------------------------------------
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Residues in contact with ARG 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLU* 2.8 40.9 + - - +
100A LYS* 3.3 41.7 + - - +
102A SER* 1.3 70.9 - - - +
104A LEU* 1.3 53.7 + - - +
105A GLY* 2.6 20.5 + - - -
106A ASP* 4.1 9.7 - - - +
28B ASP 4.9 0.2 + - - -
29B ASP* 2.9 29.5 + - - -
30B ASP 5.0 3.6 + - - -
----------------------------------------------------------
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS* 3.2 27.3 + - - +
101A ARG 3.6 15.5 - - - +
102A SER 2.9 1.4 + - - +
103A ARG* 1.3 76.3 - - - +
105A GLY* 1.4 55.1 + - - +
34B GLY 4.8 4.5 - - - +
40B LEU* 3.9 37.7 - - + +
43B LYS* 3.3 42.4 - - + -
44B HIS* 3.7 38.1 - - + +
47B PHE* 4.2 7.4 - - + -
----------------------------------------------------------
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Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A SER 3.0 10.2 - - - +
103A ARG 2.6 10.0 + - - -
104A LEU* 1.4 74.3 - - - +
106A ASP* 1.3 64.2 + - - +
40B LEU* 6.3 0.7 - - - -
----------------------------------------------------------
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Residues in contact with ASP 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A SER* 3.9 12.6 - - - +
103A ARG* 4.1 10.0 - - - +
105A GLY* 1.3 79.8 - - - +
----------------------------------------------------------
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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