Contacts of the helix formed by residues 104 - 135 (chain B) in PDB entry 1GDT
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 GLY 104 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B SER 4.2 0.9 - - - -
99B THR* 3.2 35.2 - - - -
100B ASP* 3.7 5.3 + - - -
101B GLY 3.7 5.3 + - - -
102B GLU 3.3 1.8 - - - -
103B MET* 1.3 80.7 - - - +
105B LYS* 1.3 64.4 + - - -
107B VAL* 3.0 13.3 + - - +
108B VAL* 3.1 17.1 + - - +
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Residues in contact with LYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASP* 6.0 1.6 - - - -
101B GLY 5.1 0.4 + - - -
102B GLU 4.2 5.0 + - - +
103B MET 2.9 4.2 + - - +
104B GLY* 1.3 70.9 - - - +
106B MET* 1.3 76.6 + - + +
108B VAL* 3.4 6.3 + - - +
109B THR* 3.1 37.4 + - - +
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Residues in contact with MET 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLY 3.7 24.0 - - - +
97A ILE* 4.0 13.7 - - + -
98A SER* 4.1 13.9 - - - +
103A MET* 5.4 12.1 - - + -
106A MET* 6.3 1.3 - - + -
102B GLU 5.0 0.6 + - - +
103B MET* 2.7 17.3 + - - +
105B LYS* 1.3 85.3 - - + +
107B VAL* 1.3 66.4 + - + +
109B THR* 3.1 15.3 + - - -
110B ILE* 2.8 43.4 + - + +
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A MET* 4.4 19.3 - - + -
110A ILE* 4.1 7.9 - - + +
97B ILE* 3.3 28.9 - - + -
98B SER 3.2 30.5 - - - +
99B THR* 4.7 2.2 - - + -
103B MET* 3.2 31.8 + - + -
104B GLY 3.0 5.4 + - - +
106B MET* 1.3 77.5 - - + +
108B VAL* 1.3 59.8 + - - +
110B ILE* 3.2 8.8 + - - +
111B LEU* 2.9 32.9 + - + +
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 6.3 0.4 - - + -
80B ILE* 4.2 16.6 - - + -
81B LYS* 5.3 12.1 - - + -
84B ASP* 4.2 21.8 - - - +
99B THR* 3.6 33.0 - - + +
104B GLY 3.1 12.0 + - - +
105B LYS* 3.8 7.0 - - - +
107B VAL* 1.3 74.6 - - - +
109B THR* 1.3 60.5 + - - +
111B LEU* 3.0 10.5 + - + +
112B SER* 2.9 38.5 + - - +
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Residues in contact with THR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASP 3.8 22.0 - - - +
97A ILE* 4.4 4.9 - - + +
105B LYS* 3.1 31.2 + - - +
106B MET* 3.1 16.1 + - - -
108B VAL* 1.3 78.5 - - - +
110B ILE* 1.3 61.1 + - - +
112B SER* 3.8 6.4 + - - -
113B ALA* 3.2 21.0 + - + +
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE* 4.0 27.6 - - + -
103A MET* 6.2 1.8 - - + -
106A MET* 4.4 16.4 - - + -
107A VAL* 3.8 40.2 - - + +
110A ILE* 3.5 29.6 - - + -
106B MET* 2.8 35.8 + - + +
107B VAL* 3.6 4.3 - - - +
109B THR* 1.3 73.6 - - - +
111B LEU* 1.3 68.6 + - - +
113B ALA* 2.8 14.2 + - - +
114B VAL* 2.9 22.4 + - + +
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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
----------------------------------------------------------
110A ILE* 3.5 37.5 - - + -
114A VAL* 4.5 8.2 - - + +
66B LEU* 4.4 17.3 - - + -
76B MET* 4.7 3.1 - - + +
77B ILE* 3.6 14.6 - - + -
80B ILE* 3.4 41.3 - - + -
92B PHE* 4.6 9.4 - - + -
97B ILE* 4.6 2.5 - - + -
99B THR* 4.9 2.2 - - + -
107B VAL* 2.9 20.3 + - + +
108B VAL* 3.1 13.5 - - + +
110B ILE* 1.3 78.7 - - - +
112B SER* 1.3 63.4 + - - +
113B ALA 3.1 0.2 + - - -
114B VAL* 3.2 4.9 - - - +
115B ALA* 3.1 22.0 + - - +
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Residues in contact with SER 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 3.6 16.7 - - - +
81B LYS* 4.0 24.0 - - - +
108B VAL* 2.9 27.5 + - - +
109B THR* 4.0 6.9 - - - -
111B LEU* 1.3 72.5 - - - +
113B ALA* 1.3 53.4 + - - +
115B ALA* 3.7 1.7 - - - +
116B GLN* 2.7 35.3 + - - +
119B ARG* 5.6 0.7 + - - -
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.4 22.9 - - + -
95A ASP* 4.5 10.1 - - + +
97A ILE* 3.6 13.7 - - + -
109B THR 3.2 12.4 + - - +
110B ILE 2.8 15.8 + - - +
112B SER* 1.3 69.5 - - - +
114B VAL* 1.3 66.5 + - - +
115B ALA 3.0 0.9 - - - -
116B GLN* 2.8 26.5 + - - +
117B ALA* 2.9 12.5 + - - +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 4.3 14.4 - - + -
73A THR* 5.4 6.7 - - + +
76A MET* 6.5 0.9 - - - -
107A VAL* 5.7 0.4 - - + -
110A ILE* 3.6 18.4 - - + +
111A LEU* 3.2 35.9 - - + -
114A VAL* 3.5 34.3 - - + +
110B ILE* 2.9 21.4 + - + +
111B LEU 3.2 11.9 - - - +
113B ALA* 1.3 73.0 - - - +
115B ALA* 1.3 65.0 + - - +
117B ALA* 3.6 4.8 + - - +
118B GLU* 3.2 22.2 + - - +
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A VAL* 5.2 0.9 - - + -
73B THR* 3.8 18.8 - - + -
76B MET* 5.3 0.2 - - + -
77B ILE* 3.8 24.5 - - + -
111B LEU 3.1 13.2 + - - +
112B SER* 3.7 3.4 - - - +
113B ALA 3.0 0.6 - - - -
114B VAL* 1.3 82.2 - - + +
116B GLN* 1.3 66.4 + - - +
118B GLU* 3.1 13.5 - - - +
119B ARG* 3.1 34.9 + - - +
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Residues in contact with GLN 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LYS* 5.3 9.6 - - - +
66A LEU* 4.2 8.5 - - - +
67A ASP* 4.5 4.1 - - - +
94A ASP 5.3 0.4 + - - -
95A ASP* 3.5 24.2 + - - +
112B SER 2.7 23.2 + - - +
113B ALA* 3.1 18.4 - - - +
115B ALA* 1.3 74.6 - - - +
117B ALA* 1.3 74.4 + - - +
119B ARG* 3.4 18.7 + - - +
120B GLN* 3.4 24.2 + - + +
----------------------------------------------------------
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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
----------------------------------------------------------
66A LEU* 4.9 8.1 - - + -
67A ASP* 3.5 35.3 - - + +
76A MET* 5.6 6.5 - - + -
113B ALA 2.9 10.4 + - - +
114B VAL* 3.7 10.3 - - - +
116B GLN* 1.3 82.8 - - - +
118B GLU* 1.3 66.9 + - - +
120B GLN* 2.9 9.7 + - - +
121B ARG* 2.9 21.0 + - - +
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Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A THR* 5.4 11.0 - - + +
114A VAL* 3.9 17.0 - - - +
115A ALA* 5.9 0.7 - - - -
118A GLU* 3.2 34.7 - - - +
73B THR* 3.6 17.9 - - - +
74B ALA 5.5 0.3 + - - -
114B VAL 3.2 7.7 + - - +
115B ALA* 3.1 21.1 - - - +
117B ALA* 1.3 77.0 - - - +
119B ARG* 1.3 72.3 + - + +
121B ARG* 3.0 19.9 + - - +
122B ILE* 2.9 40.0 + - + +
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B THR* 5.6 0.8 - - - +
74B ALA* 3.5 36.0 - - - +
77B ILE* 5.5 7.9 - - - +
81B LYS* 5.9 3.0 - - - +
112B SER 5.6 0.6 + - - -
115B ALA* 3.1 21.8 + - - +
116B GLN* 3.6 22.6 - - - +
118B GLU* 1.3 80.6 + - + +
120B GLN* 1.3 74.9 + - - +
122B ILE* 3.7 4.3 + - - +
123B LEU* 3.0 25.4 + - + +
----------------------------------------------------------
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Residues in contact with GLN 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 5.5 4.0 - - - +
116B GLN* 3.4 17.5 + - + +
117B ALA* 2.9 9.0 + - - +
119B ARG* 1.3 94.4 + - - +
121B ARG* 1.3 68.5 + - - +
123B LEU* 2.8 20.5 + - - +
124B GLU* 2.7 47.4 + - - +
----------------------------------------------------------
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 6.6 0.7 - - + -
71A ARG 4.4 17.5 - - - -
72A ASP* 3.7 24.7 + - - +
73A THR* 5.4 9.4 + - - +
117B ALA 2.9 13.3 + - - +
118B GLU* 3.3 20.5 + - - +
120B GLN* 1.3 77.8 - - - +
122B ILE* 1.3 84.9 + - - +
124B GLU* 3.6 5.5 + - - +
125B ARG* 3.2 38.4 + - + +
19E T 4.6 11.7 + - - -
20E A 3.2 27.3 + - - -
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLU* 2.9 39.8 + - + +
119B ARG* 4.2 4.3 - - - +
121B ARG* 1.3 108.1 - - - +
123B LEU* 1.3 67.8 + - - +
125B ARG* 3.4 5.8 + - - +
126B THR* 3.0 27.7 + - - +
18E A 4.6 3.0 - - - +
19E T 3.8 41.1 - - - +
----------------------------------------------------------
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ARG* 3.0 19.3 + - + +
120B GLN* 2.8 30.9 + - - +
122B ILE* 1.3 72.7 - - - +
124B GLU* 1.3 71.0 + - - +
126B THR* 2.8 21.5 + - + -
127B ASN* 2.9 39.7 + - - +
22C A 6.2 0.2 - - - +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLN* 2.7 48.5 + - - +
121B ARG* 3.7 6.1 - - - +
123B LEU* 1.3 78.9 - - - +
125B ARG* 1.3 58.8 + - + +
127B ASN* 3.3 12.3 + - - +
128B GLU* 2.8 33.9 + - - +
----------------------------------------------------------
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Residues in contact with ARG 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ARG* 3.2 32.8 + - + +
122B ILE* 3.8 4.7 - - - +
123B LEU 3.1 0.6 - - - -
124B GLU* 1.3 80.8 - - + +
126B THR* 1.3 57.7 + - - +
128B GLU* 3.7 20.0 + - - +
129B GLY* 2.8 27.4 + - - -
18E A 4.0 17.4 + - - +
19E T 2.7 40.2 + - - +
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Residues in contact with THR 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 3.0 20.1 + - - +
123B LEU* 2.8 19.9 + - + -
125B ARG* 1.3 69.1 - - - +
127B ASN* 1.3 64.3 + - - +
129B GLY 3.2 1.0 + - - -
130B ARG* 2.8 50.6 + - - +
20C A 6.3 1.3 - - + -
21C A 6.3 0.7 - - - +
22C A 6.3 0.2 - - - -
17E T 4.1 17.0 - - - +
18E A 3.0 27.5 + - - +
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Residues in contact with ASN 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 2.9 46.5 + - - +
124B GLU* 3.6 11.7 + - - +
126B THR* 1.3 78.1 - - - +
128B GLU* 1.3 65.9 + - - +
130B ARG* 2.9 33.7 + - - +
131B GLN* 2.9 20.4 + - + +
----------------------------------------------------------
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLU 2.8 22.3 + - - +
125B ARG* 3.7 22.7 + - - +
127B ASN* 1.3 74.5 - - - +
129B GLY* 1.3 59.5 + - - +
131B GLN* 3.4 16.0 + - - +
132B GLU* 3.4 33.9 + - + +
----------------------------------------------------------
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Residues in contact with GLY 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ARG 2.8 21.7 + - - -
126B THR 3.6 0.9 - - - -
128B GLU* 1.3 72.1 + - - +
130B ARG* 1.3 63.7 + - - +
132B GLU* 4.1 9.3 - - - +
133B ALA* 3.2 23.4 + - - +
17E T 3.8 10.5 - - - +
18E A 3.8 17.1 + - - -
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Residues in contact with ARG 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B THR* 2.8 35.3 + - - +
127B ASN* 3.1 28.8 - - - +
129B GLY* 1.3 71.6 - - - +
131B GLN* 1.3 76.8 + - - +
133B ALA* 3.3 3.4 + - - +
134B MET* 2.9 47.4 + - - +
140B PHE* 4.3 26.4 - - + -
21C A 5.4 1.6 + - - -
22C A 3.3 54.2 + - - -
23D T 4.7 9.5 + - - -
16E T 5.4 2.0 + - - -
17E T 4.1 22.3 + - - +
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Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASN* 2.9 23.7 + - + +
128B GLU* 3.4 10.1 - - - +
130B ARG* 1.3 88.5 - - - +
132B GLU* 1.3 53.5 + - + +
134B MET* 2.9 19.7 + - - +
135B ALA* 2.8 32.9 + - - +
----------------------------------------------------------
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLU* 3.4 36.3 + - + +
129B GLY* 4.1 7.3 - - - +
130B ARG 3.4 0.2 - - - -
131B GLN* 1.3 75.1 - - + +
133B ALA* 1.3 64.4 + - - +
135B ALA* 2.9 9.6 + - - +
136B LYS* 2.8 45.8 + - + +
----------------------------------------------------------
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLY 3.2 17.6 + - - +
130B ARG 3.4 4.7 - - - +
131B GLN 3.2 0.2 - - - -
132B GLU* 1.3 78.6 - - - +
134B MET* 1.3 61.7 + - - +
136B LYS* 3.3 9.4 + - - +
138B VAL* 2.9 40.7 + - + +
140B PHE* 4.0 4.3 - - + -
17E T 3.4 36.6 - - - +
----------------------------------------------------------
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Residues in contact with MET 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ARG* 2.9 37.6 + - - +
131B GLN* 2.9 21.7 + - - +
133B ALA* 1.3 76.3 - - - +
135B ALA* 1.3 55.1 + - - +
137B GLY* 2.8 25.8 + - - -
138B VAL 4.4 7.2 - - - +
140B PHE* 3.3 29.4 - - + -
23D T 5.5 12.3 - - - +
24D T 6.0 1.3 - - - +
----------------------------------------------------------
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B GLN 2.8 15.6 + - - +
132B GLU* 2.9 12.1 + - - +
134B MET* 1.3 72.8 - - - +
136B LYS* 1.3 61.9 + - + +
137B GLY* 3.0 2.0 + - - -
----------------------------------------------------------
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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