Contacts of the helix formed by residues 82 - 116 (chain A) in PDB entry 3F8F
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 THR 82 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLY* 2.5 28.0 + - - +
62A ILE 3.1 6.9 + - - -
63A ILE* 3.5 29.6 - - - +
64A SER* 3.8 4.9 - - - +
80A ARG* 3.7 23.3 - - - +
81A LEU* 1.3 75.9 - - - +
83A GLU* 1.3 60.5 + - - +
84A ILE* 3.5 4.2 + - - -
85A GLY 3.0 13.5 + - - -
86A HIS* 3.0 28.7 + - - -
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 4.5 12.7 + - - +
82A THR* 1.3 74.9 - - - +
84A ILE* 1.3 59.4 + - + +
86A HIS* 3.3 9.8 + - + +
87A GLU* 3.0 28.1 + - - +
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ASP 5.3 3.8 - - - +
61A GLY* 3.9 17.0 - - - +
62A ILE* 5.2 3.4 - - + -
82A THR* 3.3 8.1 + - - +
83A GLU* 1.3 74.7 - - + +
85A GLY* 1.3 60.4 + - - +
87A GLU* 3.7 6.8 - - + +
88A ASN* 2.9 44.8 + - - +
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Residues in contact with GLY 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 3.5 32.1 - - - +
81A LEU* 3.9 11.0 - - - -
82A THR* 3.0 15.7 + - - -
84A ILE* 1.3 76.3 - - - +
86A HIS* 1.3 62.0 + - - +
88A ASN* 3.3 6.2 + - - +
89A MET* 3.0 26.5 + - - +
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Residues in contact with HIS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU 5.7 0.4 - - - -
22A LYS* 4.4 25.6 + - + +
81A LEU* 3.5 43.8 + - + +
82A THR 3.0 22.0 + - - -
83A GLU* 3.3 11.8 + - + +
85A GLY* 1.3 74.1 - - - +
87A GLU* 1.3 62.2 + - - +
89A MET* 3.3 7.0 + - - +
90A ARG* 3.1 20.8 + - - +
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU 3.0 17.6 + - - +
84A ILE* 3.7 9.0 - - + +
86A HIS* 1.3 72.5 - - - +
88A ASN* 1.3 67.9 + - - +
90A ARG* 2.5 48.0 + - - +
91A LEU* 2.9 56.0 + - + +
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Residues in contact with ASN 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 4.1 23.8 - - + +
84A ILE* 2.9 36.0 + - - +
85A GLY* 3.3 8.9 + - - +
87A GLU* 1.3 73.9 - - - +
89A MET* 1.3 58.8 + - + +
91A LEU* 3.2 14.4 + - - +
92A ALA* 2.8 32.1 + - - +
5B PRO* 5.4 8.3 - - - +
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Residues in contact with MET 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 6.2 0.4 - - + -
18A LEU* 3.8 36.6 - - + +
19A ASN* 3.8 23.3 - - - +
22A LYS* 4.0 24.2 - - + +
62A ILE* 6.4 0.4 - - + -
81A LEU* 3.7 29.4 - - + -
85A GLY 3.0 16.7 + - - +
86A HIS* 3.6 9.2 - - - +
88A ASN* 1.3 75.5 - - + +
90A ARG* 1.3 57.8 + - - +
92A ALA* 3.4 0.6 + - - -
93A PHE* 3.0 28.9 + - - +
127A DM1 3.5 30.6 - - + +
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A HIS 3.1 11.2 + - - +
87A GLU* 2.5 49.2 + - - +
89A MET* 1.3 77.0 - - - +
91A LEU* 1.3 62.5 + - - +
93A PHE* 3.2 9.8 + - + +
94A GLU* 2.8 68.9 + - + +
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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
----------------------------------------------------------
87A GLU* 2.9 50.1 + - + +
88A ASN* 3.7 12.3 - - - +
90A ARG* 1.3 81.1 - - - +
92A ALA* 1.3 56.7 + - - +
94A GLU* 3.9 15.7 - - + +
95A SER* 2.9 30.7 + - - -
98A ARG* 5.1 1.0 + - - -
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASN 2.8 16.8 + - - +
89A MET* 3.7 5.2 - - - +
91A LEU* 1.3 75.0 - - - +
93A PHE* 1.3 64.2 + - - +
95A SER* 4.3 4.5 - - - -
96A TRP* 3.1 32.4 + - - +
127A DM1 3.8 18.8 - - + -
8B MET* 3.7 31.9 - - + -
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Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A MET 3.0 11.1 + - - +
90A ARG* 3.5 11.2 - - + +
92A ALA* 1.3 76.8 - - - +
94A GLU* 1.3 68.3 + - + +
96A TRP* 3.9 2.8 - - - +
97A SER* 3.0 41.7 + - - -
127A DM1 3.3 58.7 + - + +
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG* 2.8 54.2 + - + +
91A LEU* 3.9 14.6 - - + +
93A PHE* 1.3 83.7 - - + +
95A SER* 1.3 65.4 + - - +
97A SER* 3.3 7.3 + - - -
98A ARG* 3.1 34.8 + - - +
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Residues in contact with SER 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU 2.9 20.1 + - - -
92A ALA* 3.8 6.1 - - - -
94A GLU* 1.3 76.0 - - - +
96A TRP* 1.3 57.6 + - - +
98A ARG* 3.2 26.4 + - - +
99A VAL* 3.1 25.3 + - - +
8B MET* 5.8 1.1 - - - -
12B GLN* 2.9 29.8 + - - -
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Residues in contact with TRP 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ALA 3.1 23.9 + - - +
93A PHE 4.1 2.2 - - - +
95A SER* 1.3 74.0 - - - +
97A SER* 1.3 59.6 - - - +
99A VAL* 3.3 25.2 + - + +
100A ASP* 3.0 37.8 + - - +
127A DM1 3.3 89.6 - + + +
8B MET* 3.1 33.4 - - + +
11B ALA* 3.8 10.5 - - + -
12B GLN* 3.3 50.0 - - + +
15B VAL* 3.8 15.9 - - + -
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Residues in contact with SER 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 3.0 32.8 + - - -
94A GLU* 3.5 8.7 - - - -
96A TRP* 1.3 77.5 - - - +
98A ARG* 1.3 61.9 + - - +
100A ASP* 3.5 11.7 + - - +
101A LYS* 3.2 19.8 + - - +
127A DM1 5.7 3.3 - - - +
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Residues in contact with ARG 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU 5.1 1.0 + - - -
94A GLU* 3.1 20.2 + - - +
95A SER* 3.2 33.0 + - - +
97A SER* 1.3 74.4 - - - +
99A VAL* 1.3 64.8 + - - +
101A LYS* 3.2 9.4 + - + +
102A ILE* 3.0 31.7 + - + +
42B GLU* 6.2 0.2 - - - -
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A SER 3.1 13.0 + - - +
96A TRP* 3.3 28.9 + - + +
98A ARG* 1.3 74.1 - - - +
100A ASP* 1.3 60.1 + - - +
102A ILE* 3.1 13.4 + - + +
103A ILE* 2.9 45.1 + - + +
12B GLN* 3.6 44.9 - - + +
15B VAL* 4.5 2.9 - - + -
16B ILE* 4.1 22.2 - - + -
43B MET* 5.4 4.0 - - + -
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Residues in contact with ASP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TRP* 3.0 25.3 + - - +
97A SER* 3.6 11.7 - - - +
99A VAL* 1.3 82.1 - - - +
101A LYS* 1.3 56.4 + - - +
103A ILE* 3.3 14.5 + - - +
104A GLU* 2.8 30.8 + - - +
127A DM1 4.2 26.7 + - - +
15B VAL* 5.9 0.3 - - - +
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Residues in contact with LYS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A SER 3.2 12.2 + - - +
98A ARG* 3.2 13.7 + - + +
100A ASP* 1.3 71.5 - - - +
102A ILE* 1.3 61.6 + - + +
104A GLU* 3.3 31.8 + - - +
105A ASN* 2.8 58.4 + - - +
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ARG* 3.0 24.8 + - + +
99A VAL* 3.1 11.0 + - + +
101A LYS* 1.3 75.7 - - + +
103A ILE* 1.3 57.6 + - - +
105A ASN* 3.3 2.8 + - - +
106A LEU* 3.0 38.7 + - + +
16B ILE* 4.5 9.9 - - + -
35B VAL* 4.4 15.9 - - + +
38B ALA* 4.0 25.4 - - + +
39B SER* 3.7 25.8 - - - -
43B MET* 3.7 29.8 - - + -
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Residues in contact with ILE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL* 2.9 29.5 + - + +
100A ASP* 3.5 15.9 - - - +
101A LYS 3.2 0.2 - - - -
102A ILE* 1.3 74.3 - - - +
104A GLU* 1.3 66.6 + - - +
106A LEU* 3.2 12.2 + - + +
107A GLU* 3.1 36.5 + - - +
15B VAL* 3.5 32.8 - - + +
16B ILE* 4.8 9.6 - - + -
19B ASN* 3.3 36.8 - - + +
23B GLN* 6.0 0.2 - - - +
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Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ASP 2.8 13.9 + - - +
101A LYS* 3.3 40.0 + - + +
103A ILE* 1.3 77.6 - - - +
105A ASN* 1.3 59.1 + - - +
107A GLU* 3.5 12.3 + - - +
108A ALA* 3.0 28.3 + - + +
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Residues in contact with ASN 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LYS* 2.8 53.5 + - - +
102A ILE 3.7 2.2 - - - +
103A ILE 3.2 0.2 - - - -
104A GLU* 1.3 75.6 - - - +
106A LEU* 1.3 60.4 + - - +
108A ALA* 3.8 7.8 - - - +
109A ASN* 2.8 43.5 + - - +
38B ALA* 3.1 32.1 - - + +
40B ASN* 5.1 5.7 + - - -
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ILE* 3.0 30.4 + - + +
103A ILE* 3.5 15.7 - - + +
105A ASN* 1.3 76.2 - - - +
107A GLU* 1.3 60.1 + - - +
109A ASN* 4.0 5.5 - - + +
110A LYS* 3.1 24.1 + - - +
16B ILE* 4.4 11.2 - - + +
19B ASN* 4.7 4.7 - - + +
20B VAL* 3.7 30.3 - - + +
23B GLN* 3.9 17.4 - - + +
34B GLN* 3.7 42.3 + - + +
35B VAL* 4.7 2.0 - - + +
38B ALA* 3.8 17.9 - - + +
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Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ILE* 3.1 33.2 + - - +
104A GLU* 3.7 14.1 - - - +
106A LEU* 1.3 74.9 - - - +
108A ALA* 1.3 58.7 + - - +
110A LYS* 3.3 3.6 + - - +
111A LYS* 2.8 52.6 + - - +
19B ASN* 4.2 6.9 - - - +
22B LYS* 5.1 10.6 + - - +
23B GLN* 3.5 30.0 - - - +
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU* 3.0 20.2 + - + +
105A ASN* 3.8 10.5 - - - +
107A GLU* 1.3 74.7 - - - +
109A ASN* 1.3 57.1 + - - +
111A LYS* 3.3 11.4 + - - +
112A SER* 2.8 37.8 + - - -
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Residues in contact with ASN 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASN* 2.8 34.8 + - - +
106A LEU* 4.0 5.6 - - - +
108A ALA* 1.3 71.5 - - - +
110A LYS* 1.3 60.9 + - - +
112A SER* 3.9 7.4 + - - -
113A GLU* 2.9 47.5 + - + +
34B GLN* 5.6 1.6 + - - +
37B GLU* 4.9 5.7 + - - +
38B ALA* 4.4 20.6 - - - +
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Residues in contact with LYS 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU 3.1 19.9 + - - +
107A GLU 3.5 4.5 - - - +
109A ASN* 1.3 76.9 - - - +
111A LYS* 1.3 66.1 + - + +
113A GLU* 4.0 3.7 - - - +
114A ALA* 3.2 23.8 + - + +
22B LYS 4.9 2.2 - - - -
23B GLN* 3.2 57.0 + - + +
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Residues in contact with LYS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLU* 2.8 45.3 + - - +
108A ALA* 3.6 9.1 - - - +
110A LYS* 1.3 77.7 - - + +
112A SER* 1.3 61.8 + - - +
114A ALA* 3.4 7.6 + - - +
115A ILE* 3.4 28.8 + - + +
23B GLN* 6.2 0.2 - - - +
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Residues in contact with SER 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA 2.8 19.3 + - - -
109A ASN* 3.5 11.3 + - - -
111A LYS* 1.3 69.3 - - - +
113A GLU* 1.3 69.8 + - - +
114A ALA 3.1 2.2 + - - -
115A ILE* 3.4 13.3 + - - +
116A LYS* 3.2 43.3 + - - +
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Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ASN* 2.9 29.6 + - + +
110A LYS* 4.2 4.3 - - - +
112A SER* 1.3 81.3 + - - +
114A ALA* 1.3 59.0 + - - +
116A LYS* 3.8 24.9 - - + +
----------------------------------------------------------
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Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LYS* 3.2 20.1 + - + +
111A LYS* 3.5 8.3 - - - +
112A SER 3.1 0.6 - - - -
113A GLU* 1.3 77.2 - - - +
115A ILE* 1.3 66.6 + - + +
116A LYS 4.1 3.3 - - - -
----------------------------------------------------------
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Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 3.4 17.9 + - + +
112A SER* 3.4 13.6 + - - +
114A ALA* 1.3 81.0 - - + +
116A LYS* 1.3 67.7 + - + +
----------------------------------------------------------
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Residues in contact with LYS 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A SER* 3.2 32.9 + - - +
113A GLU* 3.8 23.1 - - + +
114A ALA 3.4 3.6 - - - -
115A ILE* 1.3 84.9 - - + +
----------------------------------------------------------
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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