Contacts of the helix formed by residues 82 - 110 (chain A) in PDB entry 3KM6
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TYR 4.2 2.4 - - - +
80A GLY 3.4 0.6 - - - -
81A LYS* 1.3 107.3 - - + +
83A GLN* 1.3 55.1 + - - +
84A GLN* 3.7 9.8 - - - +
85A GLU* 3.6 18.5 - - + +
86A ALA* 2.8 33.3 + - - +
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Residues in contact with GLN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ASP* 1.3 73.6 + - - +
84A GLN* 1.3 58.6 + - - +
86A ALA* 3.3 10.3 - - - +
87A ALA* 3.1 26.0 + - - +
71B HIS* 4.7 5.1 + - - -
74B ARG* 3.2 49.2 + - + +
75B THR* 3.9 25.0 - - + +
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Residues in contact with GLN 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ASP* 3.3 11.1 - - + +
83A GLN* 1.3 76.4 - - - +
85A GLU* 1.3 65.8 + - + +
87A ALA* 3.3 9.1 + - - +
88A LEU* 3.2 31.2 + - + +
59B ASP* 4.5 11.7 + - - +
60B LEU* 3.7 43.1 - - + +
71B HIS* 5.5 2.2 - - - -
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Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLY* 3.5 8.4 - - - -
81A LYS* 2.9 59.2 + - + +
82A ASP* 3.4 14.4 + - + +
84A GLN* 1.3 76.6 - - + +
86A ALA* 1.3 60.3 + - - +
88A LEU* 3.0 11.2 + - + +
89A VAL* 2.8 35.2 + - - +
144A VAL* 3.7 12.0 - - + +
145A GLY* 3.4 30.1 + - - -
146A ASP 4.8 1.2 + - - -
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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
----------------------------------------------------------
79A TYR* 3.6 29.9 + - + +
82A ASP 2.8 17.6 + - - +
83A GLN* 3.3 10.8 - - - +
85A GLU* 1.3 72.9 - - - +
87A ALA* 1.3 57.6 + - - +
89A VAL* 3.2 4.0 + - - +
90A ASP* 3.0 31.0 + - - -
74B ARG* 3.6 30.1 - - - +
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLN 3.1 13.3 + - - +
84A GLN* 3.5 10.5 - - - +
85A GLU 3.2 0.4 - - - -
86A ALA* 1.3 75.2 - - - +
88A LEU* 1.3 59.7 + - - +
90A ASP* 3.4 4.3 + - - -
91A MET* 3.0 23.9 + - - +
60B LEU* 4.6 2.0 - - + -
62B LEU* 4.1 21.8 - - + -
67B THR* 3.4 13.0 - - + +
71B HIS* 3.8 26.5 - - + +
74B ARG* 3.8 7.8 - - - +
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLN* 3.2 22.3 + - + +
85A GLU* 3.0 13.7 + - + +
87A ALA* 1.3 72.2 - - - +
89A VAL* 1.3 66.5 + - - +
91A MET* 3.3 28.6 + - + +
92A VAL* 3.1 28.8 + - + +
144A VAL* 3.7 24.5 - - + -
60B LEU* 4.2 22.0 - - + -
61B THR 4.9 2.5 - - - +
62B LEU* 4.3 6.7 - - + -
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TYR* 4.1 4.3 - - + -
80A GLY* 4.1 16.6 - - - +
85A GLU 2.8 18.5 + - - +
86A ALA 3.2 7.6 + - - +
88A LEU* 1.3 77.9 - - - +
90A ASP* 1.3 61.3 + - - +
92A VAL* 3.4 0.5 + - - +
93A ASN* 3.0 21.3 + - - +
144A VAL* 3.9 20.0 - - + -
149A SER* 3.7 32.8 - - - +
150A PHE* 3.4 36.6 - - + -
151A ALA* 3.7 11.2 - - + +
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Residues in contact with ASP 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG* 2.8 26.5 + - - +
79A TYR* 2.5 25.6 + - - -
86A ALA 3.0 10.8 + - - -
87A ALA* 3.6 7.8 - - - +
89A VAL* 1.3 76.8 - - - +
91A MET* 1.3 57.4 + - - +
93A ASN* 3.1 2.5 + - - +
94A ASP* 2.8 30.8 + - - +
150A PHE* 3.7 1.6 - - - -
67B THR* 3.1 22.6 + - + +
70B ARG* 3.5 14.0 - - - +
74B ARG* 2.7 32.9 + - - -
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Residues in contact with MET 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA 3.0 17.2 + - - +
88A LEU* 3.6 30.7 - - + +
90A ASP* 1.3 76.3 - - - +
92A VAL* 1.3 56.8 + - + +
94A ASP* 3.6 2.1 + - - +
95A GLY 3.1 12.1 + - - -
132A LEU* 4.5 15.5 - - + -
48B LEU* 3.7 31.9 - - + -
49B TYR* 2.8 25.8 + - + -
61B THR 4.5 3.8 - - - +
62B LEU* 4.2 9.9 - - - -
63B TYR* 3.5 41.1 - - + +
64B GLN* 4.2 0.4 - - + +
67B THR* 3.1 15.1 + - + -
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 3.1 15.6 + - + +
89A VAL 3.7 6.7 - - - +
91A MET* 1.3 76.1 - - + +
93A ASN* 1.3 60.5 + - - +
95A GLY* 3.1 3.6 + - - -
96A VAL* 2.9 37.8 + - + +
129A PHE* 3.9 9.2 - - + -
132A LEU* 3.8 24.2 - - + -
143A ILE* 3.7 26.2 - - + +
144A VAL* 3.8 18.2 - - + -
151A ALA* 3.9 18.6 - - + +
155A LEU* 4.8 1.8 - - + -
49B TYR* 3.4 7.5 + - - -
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Residues in contact with ASN 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN* 3.0 31.7 - - - +
69A LEU* 4.1 1.3 - - - +
70A ARG* 4.1 13.4 - - - +
89A VAL 3.0 16.6 + - - +
90A ASP 3.1 3.6 + - - +
92A VAL* 1.3 77.6 - - - +
94A ASP* 1.3 57.6 + - - +
96A VAL* 3.2 6.5 + - - +
97A GLU* 2.9 26.2 + - - +
150A PHE* 3.6 33.7 - - + -
151A ALA* 3.9 6.6 - - + +
154A ASN* 2.9 30.7 + - - +
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Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG* 3.3 21.3 + - - -
90A ASP 2.8 19.3 + - - +
91A MET 4.0 0.2 - - - +
93A ASN* 1.3 71.6 + - - +
95A GLY* 1.3 57.1 + - - +
97A GLU* 3.4 8.7 + - - +
98A ASP* 3.1 32.4 + - - +
64B GLN* 3.5 28.1 - - + +
66B ASN* 3.7 13.2 - - - +
67B THR* 2.8 34.5 + - - -
70B ARG* 4.5 3.3 + - - -
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Residues in contact with GLY 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A MET 3.1 7.7 + - - -
92A VAL 3.1 8.6 + - - -
94A ASP* 1.3 74.3 - - - +
96A VAL* 1.3 62.9 + - - +
98A ASP* 3.3 5.1 + - - +
99A LEU* 3.3 19.2 + - - +
129A PHE* 3.6 12.0 - - - -
49B TYR* 3.5 28.9 - - - -
64B GLN* 3.6 9.3 - - - +
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL* 2.9 23.1 + - + +
93A ASN* 3.5 9.0 - - - +
95A GLY* 1.3 75.1 - - - +
97A GLU* 1.3 57.3 + - - +
99A LEU 3.3 1.7 + - - -
100A ARG* 2.9 29.0 + - - +
129A PHE* 3.8 20.2 - - + -
151A ALA 4.8 1.1 - - - +
154A ASN* 3.4 44.0 - - + +
155A LEU* 3.8 28.5 - - + +
158A LEU* 3.8 19.3 - - + +
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Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 2.7 43.7 + - - -
66A ASN* 2.9 28.7 + - - +
93A ASN* 2.9 17.2 + - - +
94A ASP* 3.6 10.3 - - - +
96A VAL* 1.3 76.0 - - - +
98A ASP* 1.3 61.9 + - - +
100A ARG* 4.1 8.6 + - - -
101A CYS* 2.9 34.2 + - + +
154A ASN* 5.2 1.8 + - - +
221A GSH 5.2 2.4 + - - +
97B GLU* 6.5 1.1 - - + -
98B ASP* 5.5 2.6 - - - +
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Residues in contact with ASP 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ASP 3.1 15.5 + - - +
95A GLY* 3.6 9.4 - - - +
96A VAL 3.3 0.2 - - - -
97A GLU* 1.3 79.3 - - - +
99A LEU* 1.3 62.6 - - - +
101A CYS* 3.5 6.3 + - - +
102A LYS* 3.2 41.0 + - - +
125A GLN* 6.3 0.4 - - - +
49B TYR* 5.8 0.9 - - - +
51B GLN* 4.5 4.7 - - - +
64B GLN* 3.0 13.0 + - - +
97B GLU* 5.6 1.6 - - - +
221B GSH 2.7 35.6 + - - +
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLY 3.3 10.2 + - - +
96A VAL 3.9 5.2 - - - +
98A ASP* 1.3 75.8 - - - +
100A ARG* 1.3 60.9 + - - +
102A LYS* 3.1 12.8 + - + +
103A TYR* 2.9 27.2 + - - +
118A TYR* 3.3 29.8 - - + +
122A LEU* 4.2 4.3 - - + -
125A GLN* 4.0 51.1 - - + +
126A LEU* 4.1 19.5 - - + -
129A PHE* 4.7 3.1 - - + -
158A LEU* 3.8 22.4 - - + -
162A HIS* 4.1 12.3 - - + +
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Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLY 4.0 14.7 + - - -
13A ARG* 3.7 36.5 - - - +
16A ALA* 4.8 2.5 - - - +
96A VAL* 2.9 18.1 + - - +
97A GLU* 3.7 10.3 + - - +
98A ASP 3.3 0.2 - - - -
99A LEU* 1.3 75.9 - - - +
101A CYS* 1.3 57.7 + - - +
103A TYR* 3.2 8.1 + - + +
104A ILE* 2.9 49.1 + - + +
154A ASN* 2.9 45.2 + - - +
157A ASP* 3.0 30.9 + - - +
158A LEU* 3.6 18.6 - - + +
161A ILE* 3.8 17.2 - - - +
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Residues in contact with CYS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 4.5 8.4 - - - +
97A GLU* 2.9 27.9 + - + +
98A ASP* 3.7 7.4 - - - +
100A ARG* 1.3 77.3 - - - +
102A LYS* 1.3 57.1 + - - +
104A ILE* 3.5 4.5 + - - +
105A SER* 3.1 28.7 + - - -
101B CYS* 4.5 21.5 - - - -
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Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASP* 3.2 31.0 + - - +
99A LEU* 3.1 14.8 + - + +
101A CYS* 1.3 74.0 - - + +
103A TYR* 1.3 66.0 + - - +
105A SER* 3.4 6.9 + - - -
106A LEU* 3.1 18.4 + - - +
118A TYR* 3.7 23.0 - - + -
125A GLN* 4.2 29.4 - - + +
51B GLN* 5.4 7.1 + - - +
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Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU 2.9 10.1 + - - +
100A ARG* 3.4 11.0 - - + +
102A LYS* 1.3 76.9 - - - +
104A ILE* 1.3 69.2 + - + +
106A LEU* 3.3 5.6 + - + +
107A ILE* 2.9 58.5 + - + +
118A TYR* 3.3 18.7 + - - +
161A ILE* 3.8 39.4 + - + +
162A HIS* 3.7 24.7 - + + -
165A LEU* 4.2 22.2 - - + -
203A ILE* 3.6 13.3 - - + +
204A ASN* 2.9 33.3 + - - -
209A GLN* 4.3 8.0 + - - +
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Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 3.6 41.1 - - + +
100A ARG* 2.9 29.7 + - + +
101A CYS* 3.9 4.9 - - - +
103A TYR* 1.3 84.7 - - + +
105A SER* 1.3 60.2 + - - +
107A ILE* 3.2 4.2 + - - -
108A VAL* 2.8 42.0 + - + +
204A ASN* 5.5 1.6 - - - +
222A EAA 3.7 37.0 - - + +
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Residues in contact with SER 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A CYS* 3.1 19.7 + - - -
102A LYS* 3.6 8.7 - - - -
103A TYR 3.3 0.2 - - - -
104A ILE* 1.3 76.2 - - - +
106A LEU* 1.3 57.6 + - - +
108A VAL* 5.1 0.2 - - - -
109A THR* 2.7 53.6 + - - +
110A ASN* 5.4 0.2 - - - -
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LYS 3.1 13.7 + - - +
103A TYR 3.3 10.1 - - - +
104A ILE 3.3 0.2 - - - -
105A SER* 1.3 74.2 - - - +
107A ILE* 1.3 66.3 + - + +
110A ASN* 3.1 22.7 + - + +
111A TYR* 2.9 37.3 + - + +
114A GLY* 3.5 36.1 - - - +
115A LYS* 3.5 9.2 - - + +
118A TYR* 3.8 31.4 - - + -
165A LEU* 3.9 31.6 - - + -
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Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 2.9 57.4 + - + +
104A ILE* 3.7 6.3 - - - +
106A LEU* 1.3 75.5 - - + +
108A VAL* 1.3 68.1 + - + +
111A TYR* 3.8 32.4 + - + +
165A LEU* 4.4 4.0 - - + -
204A ASN* 3.7 29.6 - - + +
206A ASN* 2.8 40.0 + - - +
208A LYS* 3.8 14.4 + - + +
209A GLN* 4.1 10.8 - - - +
222A EAA 6.2 0.2 - - + -
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Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ILE* 2.8 40.5 + - + +
105A SER* 5.1 0.2 - - - -
107A ILE* 1.3 86.3 - - + +
109A THR* 1.3 69.5 + - + +
206A ASN* 4.0 10.9 + - - +
208A LYS* 5.6 2.1 + - - -
222A EAA 4.2 21.5 - - + +
----------------------------------------------------------
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Residues in contact with THR 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A SER* 2.7 42.1 + - - +
108A VAL* 1.3 89.2 - - + +
110A ASN* 1.3 67.3 + - - +
----------------------------------------------------------
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Residues in contact with ASN 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A SER 4.7 1.3 - - - +
106A LEU* 3.1 12.6 + - + +
108A VAL 3.9 0.2 - - - -
109A THR* 1.3 89.7 + - - +
111A TYR* 1.3 57.8 + - - +
112A GLU* 3.4 3.1 - - - -
113A ALA* 3.7 17.7 - - - +
114A GLY* 2.7 49.8 + - - +
----------------------------------------------------------
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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