Contacts of the helix formed by residues 82 - 108 (chain R) in PDB entry 5I2D
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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80R ALA 3.9 1.8 + - - +
81R MET* 1.3 75.2 - - - +
83R HIS* 1.3 65.7 + - - +
84R GLU* 3.9 17.4 + - - +
85R ALA* 3.1 23.4 + - - +
86R LEU* 2.9 25.8 + - - +
83S HIS* 5.4 1.6 - - - -
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Residues in contact with HIS 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82R ASP* 1.3 74.4 - - - +
84R GLU* 1.3 60.6 + - - +
86R LEU* 3.3 10.2 + - - +
87R HIS* 2.9 43.1 + + - +
81S MET 4.1 14.8 - - - -
82S ASP* 5.4 2.7 - - - -
83S HIS* 5.3 12.1 + - - +
86S LEU* 3.6 27.9 - - + +
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Residues in contact with GLU 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82R ASP* 3.3 16.5 + - - +
83R HIS* 1.3 80.2 - - - +
85R ALA* 1.3 56.7 - - - +
87R HIS* 3.2 9.1 + - + +
88R ARG* 2.9 51.1 + - + +
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Residues in contact with ALA 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50R TYR* 4.8 1.5 + - - +
81R MET* 3.7 26.0 - - + -
82R ASP* 3.1 24.4 + - - +
84R GLU* 1.3 77.0 - - - +
86R LEU* 1.3 56.7 + - - +
88R ARG* 3.2 25.3 + - - +
89R VAL* 2.9 34.1 + - - +
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Residues in contact with LEU 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56R LEU* 5.6 1.3 - - + -
78R PRO 5.3 0.4 - - - +
81R MET* 4.0 31.0 - - + +
82R ASP 2.9 21.4 + - - +
83R HIS* 3.6 5.6 - - - +
85R ALA* 1.3 76.7 - - - +
87R HIS* 1.3 56.2 + - - +
89R VAL* 3.4 6.0 + - + +
90R ALA* 2.9 29.6 + - - +
83S HIS* 3.6 39.7 - - + +
86S LEU* 4.2 34.2 - - + +
87S HIS* 4.6 17.9 - - + +
90S ALA* 5.2 13.5 - - + -
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Residues in contact with HIS 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R HIS* 2.9 26.6 + + + +
84R GLU* 3.2 14.1 + - + +
86R LEU* 1.3 77.8 - - - +
88R ARG* 1.3 57.3 + - + +
90R ALA* 3.3 6.1 + - - +
91R ARG* 2.9 35.8 + - + +
56S LEU* 5.7 8.3 + - + -
78S PRO* 5.1 12.1 - - + -
79S ARG* 5.9 3.4 - - - -
81S MET* 6.2 0.2 - - + -
86S LEU* 4.4 23.3 - - + +
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Residues in contact with ARG 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22R ARG* 4.3 11.3 - - - +
50R TYR* 3.6 26.0 + - + +
84R GLU* 2.9 50.6 + - + +
85R ALA* 3.6 25.4 - - - +
87R HIS* 1.3 75.4 - - + +
89R VAL* 1.3 58.6 + - - +
91R ARG* 3.8 6.4 - - - +
92R ASN* 2.9 32.4 + - - +
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Residues in contact with VAL 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20R LEU* 4.7 2.0 - - + -
50R TYR* 3.9 35.9 - - + -
56R LEU* 4.0 19.7 - - + -
81R MET* 3.8 28.0 - - + -
85R ALA* 2.9 21.4 + - + +
86R LEU* 3.7 7.6 - - + +
88R ARG* 1.3 76.4 - - - +
90R ALA* 1.3 57.2 + - - +
92R ASN* 3.8 0.9 - - - +
93R LEU* 2.9 50.8 + - + +
90S ALA* 5.0 7.4 - - + -
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Residues in contact with ALA 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R LEU 2.9 18.3 + - - +
87R HIS* 3.6 6.7 - - - +
89R VAL* 1.3 78.1 - - - +
91R ARG* 1.3 62.5 + - - +
93R LEU* 3.3 7.0 + - - +
94R ALA* 2.9 24.3 + - - +
56S LEU* 4.9 22.1 - - + +
86S LEU* 5.0 12.8 - - + +
89S VAL* 4.9 10.1 - - + -
90S ALA* 6.0 5.4 - - + +
93S LEU* 4.2 7.3 - - - +
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Residues in contact with ARG 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87R HIS* 2.9 21.9 + - + +
88R ARG* 3.8 7.2 - - - +
90R ALA* 1.3 75.1 - - - +
92R ASN* 1.3 60.3 + - - +
94R ALA* 3.2 4.5 + - - +
95R ARG* 2.9 40.2 + - - +
56S LEU 4.1 14.1 + - - +
57S GLU* 3.6 43.2 + - + +
59S LYS* 5.8 3.6 - - - +
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Residues in contact with ASN 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48R GLY 3.5 6.4 + - - +
49R ASP* 2.6 32.7 + - - +
50R TYR* 2.7 33.7 + - + +
88R ARG 2.9 18.4 + - - +
89R VAL 3.9 0.2 - - - +
91R ARG* 1.3 75.6 - - + +
93R LEU* 1.3 60.0 + - - +
95R ARG* 3.3 16.0 + - - +
96R GLN* 2.4 56.8 + - - +
99R ARG* 5.0 0.2 - - - +
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Residues in contact with LEU 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43R ARG* 6.0 1.3 - - - +
50R TYR* 4.6 10.1 - - + +
53R GLU* 4.5 19.5 - - + +
56R LEU* 4.4 10.3 - - + -
89R VAL* 2.9 41.4 + - + +
90R ALA* 3.7 4.5 - - - +
92R ASN* 1.3 73.6 - - - +
94R ALA* 1.3 61.4 + - - +
96R GLN* 3.4 17.8 + - - +
97R MET* 2.9 28.8 + - - +
90S ALA* 4.2 22.7 - - - +
93S LEU* 4.3 23.3 - - + +
94S ALA* 4.7 7.4 - - + +
97S MET* 4.2 17.3 - - + +
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Residues in contact with ALA 94 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90R ALA 2.9 13.8 + - - +
91R ARG* 3.4 8.3 - - - +
93R LEU* 1.3 73.9 - - - +
95R ARG* 1.3 59.9 + - - +
97R MET* 3.2 8.8 + - - +
98R ARG* 2.9 28.1 + - - +
53S GLU* 3.8 30.6 - - + +
56S LEU* 4.7 4.0 - - + -
57S GLU* 3.6 24.1 - - + +
93S LEU* 4.7 5.5 - - + +
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Residues in contact with ARG 95 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49R ASP* 5.2 0.8 + - - -
91R ARG* 2.9 34.6 + - - +
92R ASN* 3.5 20.2 - - - +
94R ALA* 1.3 77.2 - - - +
96R GLN* 1.3 58.0 - - - +
98R ARG* 3.2 12.0 + - - +
99R ARG* 2.9 47.5 + - - +
195R ALA* 2.4 45.3 + - - +
57S GLU* 3.9 25.5 + - + +
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Residues in contact with GLN 96 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43R ARG* 3.3 29.6 + - - +
44R HIS 4.8 2.5 - - - +
45R VAL* 4.3 5.7 - - - +
49R ASP* 3.5 15.7 - - - +
50R TYR* 2.7 30.0 + - - +
92R ASN* 2.4 43.5 + - - +
93R LEU* 3.9 10.4 - - - +
95R ARG* 1.3 73.2 - - - +
97R MET* 1.3 60.0 + - - +
99R ARG* 3.9 25.9 - - - +
100R VAL* 2.9 32.4 + - - +
97S MET* 4.2 12.1 - - + +
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Residues in contact with MET 97 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93R LEU 2.9 13.7 + - - +
94R ALA* 3.3 12.8 - - - +
96R GLN* 1.3 75.8 - - - +
98R ARG* 1.3 64.9 + - - +
100R VAL* 3.1 7.1 - - - +
101R GLN* 3.0 34.9 + - - +
43S ARG* 4.1 25.4 - - - +
53S GLU* 3.6 30.1 - - + +
93S LEU* 4.2 17.5 - - + +
96S GLN* 4.2 10.1 - - + -
97S MET* 3.7 42.6 - - + +
100S VAL* 4.4 12.3 - - + -
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Residues in contact with ARG 98 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94R ALA 2.9 12.5 + - - +
95R ARG* 3.2 13.7 + - - +
97R MET* 1.3 78.4 - - - +
99R ARG* 1.3 58.4 - - - +
101R GLN* 3.3 10.0 + - - +
102R ALA* 2.9 25.2 + - - +
193R GLU* 4.1 23.7 + - + -
195R ALA* 5.3 7.0 + - - -
53S GLU* 5.5 1.5 + - + -
54S GLU* 5.4 7.0 - - + -
57S GLU* 2.5 41.2 + - - +
58S GLY* 4.6 6.9 - - - -
60S ALA 5.2 6.0 + - - -
62S ARG* 4.0 44.0 - - + +
63S TYR* 3.3 13.8 + - + +
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Residues in contact with ARG 99 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44R HIS* 3.1 24.4 + - - +
46R LEU* 3.3 27.5 - - - +
49R ASP* 2.6 40.2 + - - -
95R ARG* 2.9 29.8 + - - +
96R GLN* 3.9 20.0 - - - +
98R ARG* 1.3 78.9 - - + +
100R VAL* 1.3 59.5 + - - +
102R ALA* 3.4 7.4 + - - +
103R TYR* 2.9 28.2 + - - +
122R PHE* 6.1 1.0 - - - -
192R LEU* 5.0 1.7 - - - +
193R GLU* 4.2 19.4 + - + +
194R ALA 4.9 0.8 - - - -
195R ALA* 3.7 37.7 + - - +
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Residues in contact with VAL 100 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R LEU 3.9 1.6 - - - +
43R ARG* 3.8 30.1 - - + -
96R GLN 2.9 19.7 + - - +
97R MET* 3.1 25.8 - - - +
99R ARG* 1.3 75.2 - - - +
101R GLN* 1.3 60.0 + - + +
103R TYR* 3.4 6.1 + - + +
104R GLU* 2.9 27.9 + - - +
97S MET* 4.5 5.4 - - - -
100S VAL* 4.3 21.5 - - + -
101S GLN* 4.8 5.6 - - + -
104S GLU* 3.2 30.5 - - - +
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Residues in contact with GLN 101 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97R MET* 3.0 35.4 + - - +
98R ARG* 3.7 4.9 - - - +
100R VAL* 1.3 77.9 - - + +
102R ALA* 1.3 59.0 + - - +
104R GLU* 3.1 23.0 - - - +
105R ALA* 2.9 26.2 + - - +
30S VAL* 3.2 16.2 - - - +
42S LEU* 3.8 14.0 - - + +
43S ARG* 2.9 30.2 + - - +
53S GLU* 3.6 18.4 + - - -
54S GLU* 6.0 0.2 - - - -
63S TYR* 3.6 33.8 + - + -
100S VAL* 4.9 3.4 - - + -
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Residues in contact with ALA 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98R ARG 2.9 13.9 + - - +
99R ARG 3.6 5.4 - - - +
100R VAL 3.3 0.2 - - - -
101R GLN* 1.3 76.1 - - - +
103R TYR* 1.3 58.0 + - - +
105R ALA* 3.3 8.3 + - - +
106R HIS* 2.9 26.5 + - - +
192R LEU* 3.8 9.1 - - + +
193R GLU* 3.5 31.6 - - + -
62S ARG* 5.2 3.4 - - - +
63S TYR* 3.2 17.1 + - - +
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Residues in contact with TYR 103 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R THR* 3.0 21.6 + - - -
42R LEU 3.3 23.3 - - - -
43R ARG* 4.7 3.6 - - - -
44R HIS* 4.0 23.8 - + - +
99R ARG 2.9 17.7 + - - +
100R VAL* 3.5 8.3 - - + +
102R ALA* 1.3 74.5 - - - +
104R GLU* 1.3 63.4 + - - +
106R HIS* 3.1 31.0 + + - +
107R LEU* 2.9 40.8 + - + +
119R TYR* 5.5 0.9 - + - -
147R ASP 4.0 0.9 + - - -
148R ALA* 3.3 32.0 + - - +
192R LEU* 3.9 21.7 - - + +
104S GLU* 3.1 23.3 - - - -
108S GLN* 5.6 0.2 + - - -
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Residues in contact with GLU 104 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100R VAL 2.9 17.1 + - - +
101R GLN* 3.1 20.8 - - - +
103R TYR* 1.3 76.5 - - - +
105R ALA* 1.3 63.3 + - - +
107R LEU* 3.3 15.4 + - - +
108R GLN* 3.4 25.6 + - - +
42S LEU* 2.8 40.1 - - + +
100S VAL* 3.3 19.7 - - + +
103S TYR* 3.1 23.6 - - - -
104S GLU* 3.5 27.8 - - + +
107S LEU* 4.0 5.8 - - + +
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Residues in contact with ALA 105 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101R GLN 2.9 12.5 + - - +
102R ALA* 3.5 11.7 - - - +
103R TYR 3.3 0.2 - - - -
104R GLU* 1.3 76.4 - - - +
106R HIS* 1.3 59.7 + - - +
108R GLN* 3.2 4.3 + - - +
109R THR* 2.6 34.4 + - - +
32S GLU* 4.6 18.2 - - + +
34S LEU* 4.7 10.0 - - + +
40S ILE* 4.3 12.3 - - + +
42S LEU* 4.2 9.8 - - + +
63S TYR* 5.7 0.7 - - - +
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Residues in contact with HIS 106 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102R ALA 2.9 14.5 + - - +
103R TYR* 3.1 35.0 + + - +
105R ALA* 1.3 75.7 - - - +
107R LEU* 1.3 78.2 + - + +
108R GLN 3.1 1.2 + - - -
109R THR* 3.2 9.2 + - - +
115R ARG* 3.4 37.6 - - + -
118R ARG* 3.0 60.5 + - + +
119R TYR* 4.5 8.6 - - + +
148R ALA 3.3 22.4 + - - -
149R THR* 4.5 0.4 - - - -
192R LEU* 4.0 19.4 - - + +
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Residues in contact with LEU 107 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103R TYR* 2.9 53.9 + - + +
104R GLU* 3.3 10.9 + - - +
106R HIS* 1.3 95.6 - - + +
108R GLN* 1.3 64.1 + - + +
115R ARG* 3.4 22.8 + - - +
147R ASP 5.7 0.2 - - - +
148R ALA 3.8 6.7 - - - +
149R THR* 4.0 2.2 - - - -
150R ALA* 4.0 30.2 - - + +
104S GLU* 4.1 7.9 - - + +
108S GLN* 3.3 30.1 - - + +
----------------------------------------------------------
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Residues in contact with GLN 108 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104R GLU* 3.4 14.7 + - - +
105R ALA 3.2 6.0 + - - +
106R HIS 3.1 0.6 - - - -
107R LEU* 1.3 84.0 - - + +
109R THR* 1.3 62.3 + - - +
110R GLY 4.0 4.0 + - - -
115R ARG* 6.0 0.4 - - - +
34S LEU* 4.4 9.7 - - + +
38S ARG* 5.7 3.1 + - - -
40S ILE* 3.3 37.1 - - + +
41S THR 5.4 0.6 + - - -
107S LEU* 3.3 31.5 - - + +
147S ASP 5.0 1.0 - - - +
150S ALA* 3.3 40.5 + - + +
----------------------------------------------------------
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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