Contacts of the helix formed by residues 94 - 119 (chain B) in PDB entry 3GTU
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 GLU 94 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A HIS* 5.0 5.8 - - + +
78A TYR* 3.3 32.1 - - + +
81A ARG* 2.7 40.5 + - - +
82A LYS* 5.5 1.3 + - - -
92B GLU 4.2 0.2 + - - -
93B THR* 1.3 73.1 - - - +
95B GLU* 1.3 71.5 + - - +
97B LYS* 3.4 11.0 + - - +
98B ILE* 3.0 40.9 + - + +
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A HIS* 3.6 27.0 + - + +
93B THR* 3.1 16.3 + - - +
94B GLU* 1.3 87.7 + - - +
96B GLU* 1.3 62.4 + - + +
98B ILE* 3.5 9.8 + - - +
99B ARG* 3.3 27.3 + - - +
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Residues in contact with GLU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLY* 3.6 14.1 - - - -
92B GLU* 3.0 20.9 + - - +
93B THR* 3.0 29.9 + - - +
95B GLU* 1.3 74.6 - - + +
97B LYS* 1.3 66.6 + - - +
99B ARG* 3.2 7.3 + - - +
100B VAL* 3.0 26.9 + - - +
152B ALA* 3.5 23.7 - - + +
154B GLU 4.9 2.8 + - - -
155B LYS* 3.2 42.9 + - - +
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Residues in contact with LYS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG* 3.2 42.7 - - - +
91B GLY* 3.4 28.5 - - - +
92B GLU* 3.9 13.8 + - - +
93B THR 2.9 16.0 + - - +
94B GLU* 3.6 10.3 + - - +
95B GLU 3.3 0.2 - - - -
96B GLU* 1.3 76.5 - - - +
98B ILE* 1.3 62.5 + - - +
100B VAL* 3.2 7.4 + - - +
101B ASP* 3.0 32.3 + - - +
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A HIS* 3.7 36.1 - - + +
68A LYS 5.6 0.7 - - - +
69A ILE* 3.5 28.3 - - + -
78A TYR* 4.1 25.4 - - + -
81A ARG* 4.5 7.9 - - - +
94B GLU* 3.0 31.4 + - + +
95B GLU* 3.7 7.4 - - - +
97B LYS* 1.3 75.8 - - - +
99B ARG* 1.3 64.4 + - + +
101B ASP* 3.3 3.9 + - - +
102B ILE* 2.9 39.6 + - + +
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Residues in contact with ARG 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP* 5.5 2.4 + - - -
95B GLU* 3.3 12.7 + - - +
96B GLU* 3.2 9.8 + - - +
98B ILE* 1.3 80.9 - - + +
100B VAL* 1.3 56.6 + - - +
102B ILE* 3.2 6.2 + - + +
103B ILE* 2.9 36.7 + - - +
144B PHE* 3.0 63.9 + - + -
145B LEU 4.7 0.8 + - - -
148B PHE* 3.4 33.3 - - - -
151B PHE* 2.7 39.6 + - - +
152B ALA* 4.2 16.8 - - - -
153B GLY* 4.4 0.6 - - - +
159B VAL* 5.7 0.2 - - - -
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 4.6 2.0 - - - +
90B CYS* 5.4 1.1 - - + -
91B GLY 3.9 22.4 - - - +
96B GLU 3.0 17.7 + - - +
97B LYS* 3.2 8.9 + - - +
99B ARG* 1.3 75.7 - - - +
101B ASP* 1.3 65.0 + - - +
103B ILE 3.3 0.2 + - - -
104B GLU* 2.9 30.0 + - - +
152B ALA* 4.2 10.5 - - + +
157B THR* 3.9 20.0 - - - +
158B PHE* 3.6 36.6 - - + -
159B VAL* 3.4 15.7 - - + +
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Residues in contact with ASP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA* 3.8 19.7 - - + +
77A ARG* 3.6 24.0 + - - +
81A ARG* 2.8 32.9 + - - -
81B ARG* 3.1 27.4 + - - +
97B LYS* 3.0 16.7 + - - +
98B ILE* 3.7 5.4 - - - +
100B VAL* 1.3 77.5 - - - +
102B ILE* 1.3 59.7 + - - +
104B GLU* 3.8 1.3 + - - +
105B ASN* 2.7 34.4 + - - +
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP* 5.2 5.6 - - + +
56A PHE* 3.9 31.2 - - + -
68A LYS 4.4 5.8 - - - +
69A ILE* 3.9 37.7 - - + -
70A THR* 4.0 19.7 - - - +
71A GLN* 4.1 7.9 - - + +
74A ALA* 4.1 4.7 - - + -
98B ILE* 2.9 32.0 + - + +
99B ARG* 3.7 7.4 - - + +
101B ASP* 1.3 74.1 - - - +
103B ILE* 1.3 61.9 + - + +
105B ASN* 3.4 2.9 + - - +
106B GLN* 2.8 32.3 + - + +
144B PHE* 5.1 9.0 - - + -
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Residues in contact with ILE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 4.2 18.4 - - + -
99B ARG 2.9 21.5 + - - +
100B VAL 3.8 2.9 - - - +
102B ILE* 1.3 75.7 - - - +
104B GLU* 1.3 66.4 + - - +
106B GLN* 2.9 3.5 + - + -
107B VAL* 2.8 34.4 + - + +
141B PHE* 4.5 8.1 - - + -
144B PHE* 3.6 36.8 - - + -
151B PHE* 3.9 19.5 - - + +
159B VAL* 3.5 22.2 - - + +
162B LEU* 5.6 0.2 - - + -
163B THR* 3.5 23.1 - - - +
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 4.7 1.2 + - - -
100A GLU* 4.3 9.8 - - - +
101A ASN* 6.0 0.2 - - - -
77B ASN* 3.6 35.5 + - - +
81B ARG* 2.7 48.2 + - - -
100B VAL 2.9 18.8 + - - +
101B ASP 3.9 3.7 - - - +
103B ILE* 1.3 75.5 - - - +
105B ASN* 1.3 72.6 + - - +
107B VAL* 3.2 22.0 - - - +
108B MET* 3.5 9.2 + - - +
158B PHE* 3.3 16.4 - - + -
159B VAL* 4.0 8.0 - - + +
162B LEU* 4.3 8.0 - - + +
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Residues in contact with ASN 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN* 3.4 29.4 - - + +
73A ASN* 3.0 44.3 + - - +
74A ALA* 3.7 10.7 - - - +
77A ARG* 5.8 0.8 - - - +
104A MET* 5.5 0.2 - - - +
77B ASN* 5.6 2.4 + - - +
101B ASP* 2.7 24.9 + - - +
102B ILE 3.4 1.2 + - - -
103B ILE 3.2 0.6 - - - -
104B GLU* 1.3 85.8 + - - +
106B GLN* 1.3 64.7 + - - +
108B MET* 3.1 21.7 - - - +
109B ASP* 3.2 14.9 + - - +
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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
----------------------------------------------------------
56A PHE* 3.5 49.4 - - + +
58A ASN* 5.8 1.6 - - - +
70A THR* 6.0 0.2 - - - -
71A GLN* 3.2 23.9 + - - +
102B ILE* 2.8 22.0 + - + +
103B ILE* 2.9 9.3 + - + +
105B ASN* 1.3 73.7 - - - +
107B VAL* 1.3 64.6 + - - +
109B ASP* 3.0 26.9 + - - +
110B PHE* 3.0 12.5 + - - +
137B GLN* 3.6 25.3 + - - +
140B GLN* 5.0 1.6 - - - +
141B PHE* 4.1 12.8 - - + -
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASN* 6.0 0.4 - - - +
103B ILE* 2.8 24.6 + - + +
104B GLU 3.2 19.5 - - - +
106B GLN* 1.3 71.9 - - - +
108B MET* 1.3 57.0 + - - +
110B PHE* 3.6 7.6 - - - +
111B ARG* 2.8 40.1 + - - +
141B PHE* 4.2 13.7 - - + -
162B LEU* 4.0 30.3 - - + +
163B THR* 3.9 34.8 - - - +
166B ILE* 4.3 13.2 - - + +
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Residues in contact with MET 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASN* 4.5 6.3 - - - +
104A MET* 6.4 1.8 - - + -
16B LEU* 5.9 2.9 - - + -
76B SER* 5.7 4.9 - - - -
77B ASN* 3.2 37.0 - - - +
104B GLU 3.7 8.3 - - - +
105B ASN* 3.1 16.1 + - - +
106B GLN 3.1 0.2 - - - -
107B VAL* 1.3 82.6 - - - +
109B ASP* 1.3 61.1 + - - +
111B ARG* 3.9 24.2 - - - +
112B THR* 2.8 41.3 + - - +
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Residues in contact with ASP 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASN* 4.7 6.4 + - - -
71A GLN* 3.1 26.6 + - - +
105B ASN 3.2 12.0 + - - +
106B GLN* 3.0 18.7 + - - +
108B MET* 1.3 79.3 - - - +
110B PHE* 1.3 64.7 + - - +
112B THR* 3.6 6.2 + - - -
113B GLN* 3.4 26.4 + - - +
137B GLN* 6.2 0.2 - - - -
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Residues in contact with PHE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLN* 3.0 12.8 + - - +
107B VAL* 3.6 10.1 - - - +
109B ASP* 1.3 76.7 - - - +
111B ARG* 1.3 63.2 + - - +
113B GLN* 3.1 26.8 + - - +
114B LEU* 3.3 10.6 + - - +
130B TYR* 3.5 20.9 - + - -
134B LEU* 3.6 21.3 - - + -
137B GLN* 3.6 33.6 - - + +
138B LEU* 3.9 16.2 - - + -
141B PHE* 3.7 26.2 - + + -
166B ILE* 3.7 21.8 - - + -
167B LEU* 4.8 4.0 - - + -
170B ASN* 3.3 21.5 - - - -
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Residues in contact with ARG 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.8 33.6 + - - +
19B ALA* 5.4 1.4 - - - +
76B SER* 6.0 1.2 - - - -
77B ASN* 5.1 2.2 + - - -
107B VAL* 2.8 31.6 + - - +
108B MET* 3.9 32.9 - - - +
110B PHE* 1.3 71.9 - - - +
112B THR* 1.3 57.3 + - - +
114B LEU* 3.1 4.5 + - + +
115B ILE* 2.8 47.6 + - + +
162B LEU* 3.4 39.8 + - - +
165B ASP* 3.5 25.6 + - - +
166B ILE* 3.7 26.0 - - + +
169B GLN* 5.0 6.0 + - - +
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Residues in contact with THR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B MET* 2.8 32.6 + - - +
109B ASP* 3.7 8.0 - - - -
110B PHE 3.2 0.2 - - - -
111B ARG* 1.3 76.0 - - - +
113B GLN* 1.3 66.0 + - + +
115B ILE* 3.3 10.4 + - - +
116B ARG* 2.9 50.1 + - + +
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Residues in contact with GLN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASP* 3.4 14.3 + - - +
110B PHE* 3.1 27.8 + - - +
112B THR* 1.3 77.8 - - + +
114B LEU* 1.3 58.8 + - - +
116B ARG* 3.4 10.8 + - - +
117B LEU* 2.9 29.8 + - - +
130B TYR* 4.1 16.9 - - + -
133B GLU* 5.6 2.1 - - - +
137B GLN* 4.6 11.5 - - - +
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE 3.3 5.6 + - - +
111B ARG* 3.1 9.5 + - + +
113B GLN* 1.3 76.4 - - - +
115B ILE* 1.3 56.0 + - + +
117B LEU* 3.1 9.1 + - + +
118B CYS* 2.8 64.3 + - - -
130B TYR* 3.5 38.5 - - + +
166B ILE* 3.7 24.2 - - + -
169B GLN* 3.7 32.3 - - + +
170B ASN* 4.3 9.6 - - - +
173B PHE* 5.0 10.1 - - + -
218B TRP* 5.3 3.6 - - + -
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Residues in contact with ILE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 5.3 7.6 - - + -
111B ARG* 2.8 49.0 + - + +
112B THR* 3.7 8.5 - - + +
114B LEU* 1.3 72.8 - - + +
116B ARG* 1.3 59.0 + - - +
118B CYS* 3.2 3.3 + - - +
119B TYR* 2.8 59.0 + - + +
169B GLN* 6.0 3.6 - - - +
212B ASN* 5.7 4.5 - - - +
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Residues in contact with ARG 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LYS* 4.8 17.6 - - - +
112B THR* 2.9 41.1 + - - +
113B GLN* 3.4 9.1 - - - +
115B ILE* 1.3 78.5 - - - +
117B LEU* 1.3 57.6 + - - +
119B TYR* 5.0 2.2 - - - -
120B SER* 2.9 38.4 + - - -
126B LEU* 6.0 4.0 - - + -
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLN 2.9 17.9 + - - +
114B LEU* 3.4 11.2 - - + +
116B ARG* 1.3 76.9 - - - +
118B CYS* 1.3 66.0 + - - +
120B SER* 4.0 4.3 + - - -
123B HIS* 2.8 73.2 + - + +
126B LEU* 3.7 20.4 - - + +
127B LYS* 3.5 17.0 - - - +
130B TYR* 3.9 20.6 - - + -
173B PHE* 3.7 21.5 - - + -
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Residues in contact with CYS 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LEU* 2.8 45.7 + - - +
115B ILE* 3.8 4.5 - - - +
117B LEU* 1.3 81.0 - - - +
119B TYR* 1.3 55.4 + - + +
123B HIS* 3.8 6.5 - - - -
169B GLN* 6.1 0.2 - - - -
173B PHE* 5.0 0.9 - - - -
212B ASN* 3.8 19.7 - - - +
216B ALA 4.8 0.4 - - - -
217B GLN* 2.8 41.6 + - - +
218B TRP* 3.3 36.6 - - + -
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Residues in contact with TYR 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ILE* 2.8 48.5 + - + +
116B ARG* 4.4 2.0 - - - +
118B CYS* 1.3 74.8 - - + +
120B SER* 1.3 69.3 + - - +
121B SER 3.5 1.2 + - - -
212B ASN* 4.1 14.7 - - + +
213B ASN* 3.1 29.5 + - - +
215B MET* 3.7 39.9 - - + +
216B ALA* 3.7 27.1 - - + -
217B GLN* 4.0 13.4 + - - +
----------------------------------------------------------
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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