Contacts of the helix formed by residues 87 - 120 (chain B) in PDB entry 1T7S
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 87 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ASP* 3.9 13.5 - - - +
75B LYS* 4.1 0.5 - - - -
76B ILE* 3.1 45.0 + - + +
86B VAL* 1.3 74.2 - - - +
88B ASP* 1.3 58.5 + - - +
89B ALA* 3.2 7.2 + - - +
90B GLY 2.7 32.1 + - - -
91B PHE* 2.6 33.9 + - - +
159B ILE* 4.6 1.6 - - - -
160B ILE* 3.8 20.3 - - + +
161B THR* 5.9 0.7 - - - -
162B GLU* 5.6 3.4 - - + +
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Residues in contact with ASP 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ASP* 1.3 73.8 - - - +
89B ALA* 1.3 64.6 + - - +
91B PHE* 3.1 9.9 + - - +
92B LYS* 3.0 33.8 + - - +
159B ILE* 4.6 13.3 - - - +
160B ILE 4.7 6.1 - - - +
161B THR* 6.0 0.3 - - - -
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ASP 4.9 1.8 - - - +
75B LYS* 4.3 15.9 - - + -
87B ASP* 3.2 14.0 + - - +
88B ASP* 1.3 78.7 - - - +
90B GLY* 1.3 60.3 + - - +
92B LYS* 3.5 11.0 + - - +
93B MSE 3.3 38.0 + - + +
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Residues in contact with GLY 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE 3.7 0.4 - - - -
77B ILE* 3.6 19.3 - - - +
86B VAL* 2.9 24.0 - - - +
87B ASP* 2.7 18.0 + - - -
89B ALA* 1.3 70.7 - - - +
91B PHE* 1.3 65.6 + - - +
92B LYS 3.2 0.4 - - - -
93B MSE 3.5 10.8 + - - +
94B LEU* 3.2 20.4 + - - +
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Residues in contact with PHE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B VAL* 3.1 14.1 - - + +
87B ASP 2.6 20.1 + - - +
88B ASP* 3.4 10.5 - - - +
90B GLY* 1.3 74.5 - - - +
92B LYS* 1.3 71.9 + - + +
94B LEU* 3.4 5.5 + - - +
95B MSE 3.0 61.2 + - + +
157B MSE 4.3 18.6 - - + -
159B ILE* 3.9 31.6 - - + -
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Residues in contact with LYS 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ASP* 3.0 21.7 + - - +
89B ALA* 3.6 12.3 - - - +
91B PHE* 1.3 86.3 - - + +
93B MSE 1.3 66.8 + - - +
95B MSE 3.0 17.1 + - - +
96B GLN* 3.0 19.1 + - + +
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Residues in contact with MSE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LYS* 3.7 36.8 - - + +
77B ILE* 3.6 22.7 - - + -
89B ALA* 3.3 28.8 + - + +
90B GLY* 3.6 12.8 - - - +
91B PHE 3.4 0.2 - - - -
92B LYS* 1.3 77.3 - - - +
94B LEU* 1.3 59.9 + - + +
96B GLN* 3.0 16.5 + - - +
97B TYR* 2.8 27.6 + - - +
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 4.6 12.8 - - + -
79B MSE 3.3 35.4 - - + -
84B ALA* 5.0 2.5 - - + -
86B VAL* 4.6 11.2 - - + -
90B GLY 3.2 12.0 + - - +
91B PHE 3.6 8.1 - - - +
92B LYS 3.2 0.2 - - - -
93B MSE 1.3 82.1 - - + +
95B MSE 1.3 53.2 + - - +
97B TYR* 3.5 16.3 - - + -
98B GLU* 2.6 44.9 + - + +
153B THR* 5.4 1.6 - - + -
157B MSE 3.2 44.0 - - + -
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Residues in contact with MSE 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B PHE* 3.0 56.3 + - + +
92B LYS* 3.0 10.5 + - - +
94B LEU* 1.3 75.3 - - - +
96B GLN* 1.3 61.8 + - + +
98B GLU* 3.9 3.7 - - - +
99B LYS* 3.0 23.0 + - - +
154B LEU* 4.5 22.2 - - + -
157B MSE 5.0 6.7 - - - +
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Residues in contact with GLN 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LYS* 3.0 17.0 + - + +
93B MSE 3.0 14.8 + - - +
95B MSE 1.3 74.9 - - + +
97B TYR* 1.3 66.0 + - - +
99B LYS* 3.0 31.8 + - + +
100B HIS* 3.1 7.3 + - - +
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Residues in contact with TYR 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B MSE 2.8 12.7 + - - +
94B LEU* 3.5 21.1 - - + +
96B GLN* 1.3 77.7 - - - +
98B GLU* 1.3 80.1 + - + +
100B HIS* 3.1 34.3 + + + +
101B ASN* 3.3 31.2 + - - +
149B ARG* 4.1 18.0 + - - -
150B HIS* 4.8 2.7 - + - -
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU* 2.6 27.3 + - + +
95B MSE 4.0 5.2 - - - +
97B TYR* 1.3 87.4 - - + +
99B LYS* 1.3 65.4 + - - +
101B ASN* 3.2 4.9 + - - +
102B LEU* 3.0 21.7 + - - +
150B HIS* 3.2 41.9 - - - +
153B THR* 4.2 13.6 - - - +
154B LEU* 3.3 45.0 - - + +
157B MSE 5.0 6.7 - - + -
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Residues in contact with LYS 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B MSE 3.0 15.3 + - - +
96B GLN* 3.0 22.4 + - + +
98B GLU* 1.3 76.1 - - - +
100B HIS* 1.3 69.3 + - + +
102B LEU* 3.0 13.3 + - - +
103B SER* 3.0 25.1 + - - -
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Residues in contact with HIS 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLN 3.1 5.2 + - - +
97B TYR* 3.1 24.1 + + + +
99B LYS* 1.3 87.0 + - - +
101B ASN* 1.3 65.1 + - - +
103B SER* 2.7 28.7 + - - -
104B ASN* 2.9 41.1 + - - +
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Residues in contact with ASN 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TYR* 3.3 36.3 + - - +
98B GLU* 3.2 9.0 + - - +
100B HIS* 1.3 83.5 - - - +
102B LEU* 1.3 57.9 + - - +
104B ASN* 3.1 12.8 + - - +
105B LEU* 2.8 39.8 + - + +
146B GLU* 5.6 2.6 + - - -
149B ARG* 5.3 1.2 - - - +
150B HIS* 2.7 48.8 + - + -
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLU 3.0 11.5 + - - +
99B LYS* 3.0 15.8 + - - +
101B ASN* 1.3 75.8 - - - +
103B SER* 1.3 57.2 + - - +
105B LEU* 3.5 16.7 + - + +
106B GLN* 3.0 28.3 + - + +
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Residues in contact with SER 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LYS* 3.0 16.1 + - - -
100B HIS* 2.7 20.0 + - - -
102B LEU* 1.3 77.9 - - - +
104B ASN* 1.3 61.4 + - - -
106B GLN* 3.2 7.7 + - - +
107B LYS* 2.9 27.0 + - - +
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Residues in contact with ASN 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B HIS* 2.9 44.1 + - - +
101B ASN* 3.1 14.5 + - - +
103B SER* 1.3 77.9 + - - +
105B LEU* 1.3 60.9 + - + +
107B LYS* 3.3 12.5 + - - +
108B ALA* 2.8 30.9 + - - +
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ASN* 2.8 31.5 + - + +
102B LEU* 3.7 20.9 - - + +
104B ASN* 1.3 72.2 - - + +
106B GLN* 1.3 56.3 + - - +
108B ALA* 3.2 2.0 + - + -
109B TYR* 2.7 34.0 + - - +
143B PHE* 3.1 41.3 - - + -
146B GLU* 4.4 22.0 - - + -
147B ALA* 4.2 23.3 - - + +
150B HIS* 5.5 9.4 - - + +
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Residues in contact with GLN 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 3.0 15.4 + - + +
103B SER* 3.4 11.7 - - - +
105B LEU* 1.3 74.8 - - - +
107B LYS* 1.3 58.5 + - - +
109B TYR* 3.5 16.0 - - - +
110B ASP* 2.6 70.0 + - - +
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Residues in contact with LYS 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B SER* 2.9 14.7 + - - +
104B ASN* 3.4 14.8 - - - +
105B LEU 3.2 0.2 - - - -
106B GLN* 1.3 73.7 - - - +
108B ALA* 1.3 67.3 + - - +
110B ASP* 3.1 10.8 + - + +
111B LEU* 2.9 49.4 + - + +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ASN 2.8 20.4 + - - +
105B LEU* 3.4 5.8 - - + +
107B LYS* 1.3 73.6 - - - +
109B TYR* 1.3 63.9 + - - +
111B LEU* 3.5 8.6 + - - +
112B ASN* 3.0 33.7 + - - +
143B PHE* 3.6 19.7 - - + -
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Residues in contact with TYR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU 2.7 20.3 + - - +
106B GLN* 3.5 14.8 - - - +
108B ALA* 1.3 72.0 - - - +
110B ASP* 1.3 78.7 + - - +
112B ASN* 2.9 10.2 + - + +
113B LEU* 2.8 64.9 + - + +
143B PHE* 3.8 21.7 - + + -
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Residues in contact with ASP 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLN* 2.6 56.3 + - - +
107B LYS* 3.3 8.1 - - + +
109B TYR* 1.3 80.6 - - - +
111B LEU* 1.3 66.1 + - + +
113B LEU* 3.2 5.5 + - - +
114B ARG* 3.1 30.8 + - + +
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LYS* 2.9 48.8 + - + +
108B ALA* 3.9 7.4 - - - +
110B ASP* 1.3 76.4 - - + +
112B ASN* 1.3 66.6 + - - +
114B ARG* 3.4 7.1 + - + +
115B ASP* 3.0 31.7 + - - +
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Residues in contact with ASN 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA* 3.0 24.3 + - - +
109B TYR* 2.9 9.2 + - + +
111B LEU* 1.3 80.0 - - - +
113B LEU* 1.3 58.6 + - - +
115B ASP* 3.4 7.0 + - - +
116B VAL* 2.9 35.1 + - + +
136B LEU* 4.6 8.3 - - + +
139B LYS* 3.7 49.7 + - - +
140B VAL* 4.2 17.4 - - + +
143B PHE* 5.0 7.9 - - - +
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR* 2.8 54.4 + - + +
110B ASP* 3.6 10.5 - - - +
112B ASN* 1.3 70.4 - - - +
114B ARG* 1.3 83.5 + - + +
116B VAL* 3.4 7.7 + - + +
117B ALA* 2.9 24.6 + - + +
----------------------------------------------------------
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Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ASN* 3.2 21.1 - - - +
148A GLU* 2.5 36.1 + - - +
110B ASP* 3.1 19.7 + - + +
111B LEU* 3.8 7.6 - - + +
113B LEU* 1.3 90.9 - - + +
115B ASP* 1.3 55.6 + - - +
117B ALA* 3.1 11.3 + - - +
118B ASP* 2.8 35.7 + - - +
----------------------------------------------------------
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Residues in contact with ASP 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU* 3.0 23.1 + - - +
112B ASN* 3.5 6.8 - - - +
114B ARG* 1.3 76.9 - - - +
116B VAL* 1.3 60.0 + - - +
118B ASP* 3.2 6.6 + - - +
119B LEU* 2.8 31.2 + - - +
132B MSE 4.0 23.4 - - + +
136B LEU* 3.8 21.2 - - + +
139B LYS* 5.9 0.9 + - - -
----------------------------------------------------------
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASN 2.9 23.8 + - - +
113B LEU* 3.9 9.2 - - + +
115B ASP* 1.3 75.5 - - - +
117B ALA* 1.3 59.3 + - - +
119B LEU* 3.3 7.4 + - + +
120B GLU* 2.9 54.6 + - + +
136B LEU* 4.5 20.9 - - + -
140B VAL* 5.3 11.0 - - + -
----------------------------------------------------------
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 2.9 16.9 + - + +
114B ARG* 3.2 16.4 - - - +
116B VAL* 1.3 80.7 - - - +
118B ASP* 1.3 60.2 + - - +
120B GLU* 3.7 13.6 + - - +
121B ARG* 3.2 20.3 + - - +
----------------------------------------------------------
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Residues in contact with ASP 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG 2.8 18.1 + - - +
115B ASP* 3.8 7.6 - - - +
117B ALA* 1.3 72.0 - - - +
119B LEU* 1.3 65.9 + - - +
121B ARG* 3.0 51.7 + - - +
122B GLY 4.2 0.9 + - - -
123B PHE* 5.3 2.1 + - - +
132B MSE 5.6 5.5 - - - +
----------------------------------------------------------
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ASP 2.8 18.0 + - - +
116B VAL* 3.6 8.3 - - + +
118B ASP* 1.3 79.0 + - - +
120B GLU* 1.3 67.1 + - + +
122B GLY* 2.9 16.8 + - - -
123B PHE 5.0 0.2 + - - -
124B LEU* 5.0 6.6 - - + +
129B GLN* 3.7 43.3 - - + +
132B MSE 3.6 40.2 - - + -
133B GLY* 4.5 9.4 - - - +
136B LEU* 4.8 7.0 - - + -
----------------------------------------------------------
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B VAL* 2.9 38.5 + - + +
117B ALA* 3.8 12.0 - - - +
119B LEU* 1.3 79.7 - - + +
121B ARG* 1.3 61.6 + - - +
122B GLY* 3.1 2.4 + - - -
----------------------------------------------------------
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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