Contacts of the helix formed by residues 120 - 143 (chain B) in PDB entry 2H6C
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 120 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ARG* 3.7 31.3 - - + +
116A PHE* 6.1 3.6 - - + -
117A ARG* 2.8 51.5 + - - +
116B PHE 3.5 14.0 - - - +
117B ARG 4.7 3.9 + - - +
119B ASP* 1.3 69.7 + - - +
121B ASP* 1.4 65.3 + - - +
122B MET 3.2 2.0 - - - -
123B ILE* 3.1 35.8 + - + +
124B PHE* 3.6 10.3 - - + -
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Residues in contact with ASP 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ARG* 3.2 30.9 + - - +
119B ASP* 3.1 12.1 + - - +
120B GLU* 1.4 79.1 - - - +
122B MET* 1.3 65.1 + - + +
123B ILE 3.3 0.2 - - - -
124B PHE* 3.4 11.8 + - - +
125B GLU* 3.7 14.2 + - - +
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Residues in contact with MET 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 5.8 1.6 - - + -
24B LYS* 3.5 42.6 - - + +
25B LEU* 3.9 10.5 - - + -
27B ASN* 5.7 0.2 - - - +
28B TYR* 3.4 29.2 - - + +
115B ILE* 4.7 6.7 - - + -
116B PHE* 4.1 9.2 - - + -
119B ASP* 3.3 33.5 + - - +
120B GLU 3.2 1.2 - - - -
121B ASP* 1.3 79.2 - - + +
123B ILE* 1.3 67.0 + - - +
124B PHE 3.1 2.4 + - - -
125B GLU* 3.3 14.3 + - + -
126B ILE* 3.2 32.3 + - + +
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PHE* 4.0 26.2 - - + -
123A ILE* 3.8 24.0 - - + -
116B PHE* 3.6 54.4 - - + +
120B GLU* 3.1 36.7 + - + +
122B MET* 1.3 79.6 - - - +
124B PHE* 1.3 73.3 + - + +
126B ILE* 3.4 2.9 + - - +
127B PHE* 3.0 42.8 + - + -
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Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 3.9 18.4 - - + -
88A TYR* 3.2 22.5 + - + +
109A GLU* 3.8 18.4 - - + +
112A LEU* 4.0 21.1 - - + -
113A ARG* 3.8 46.7 - - + +
116A PHE* 3.8 30.1 - + - -
120B GLU* 3.6 20.0 - - + -
121B ASP 3.4 6.1 + - - +
122B MET 3.1 0.8 - - - -
123B ILE* 1.3 83.9 - - + +
125B GLU* 1.3 51.6 + - - +
127B PHE* 3.1 15.2 - + - +
128B LYS* 2.5 36.4 + - - +
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 3.8 25.5 - - + +
24B LYS* 4.7 11.3 - - + +
121B ASP 3.7 12.8 + - - +
122B MET* 3.6 28.5 - - + +
123B ILE 3.2 0.2 - - - -
124B PHE* 1.3 74.9 - - - +
126B ILE* 1.3 66.3 + - - +
128B LYS* 3.2 10.2 + - - +
129B ASN* 2.9 24.3 + - - +
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Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE* 3.8 32.3 - - + -
22B ILE* 5.5 4.3 - - + -
25B LEU* 4.7 13.9 - - + -
83B LEU* 4.2 20.0 - - + -
112B LEU* 4.7 11.9 - - + -
116B PHE* 3.7 26.9 - - + -
122B MET* 3.2 28.3 + - + +
123B ILE 3.8 5.2 - - - +
125B GLU* 1.3 78.4 - - + +
127B PHE* 1.3 66.5 + - + +
129B ASN* 3.3 5.8 - - + +
130B TYR* 3.2 39.1 + - + +
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Residues in contact with PHE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A MET* 5.8 3.6 - - + -
87A LEU* 4.9 9.0 - - + -
88A TYR* 5.7 2.9 - - + -
112A LEU* 4.8 5.2 - - + -
116A PHE* 3.8 24.0 - + - -
123A ILE* 4.1 13.7 - - + -
126A ILE* 2.8 52.3 - - + -
127A PHE* 4.4 8.3 - + + -
130A TYR* 4.3 21.4 - + + -
123B ILE* 3.0 28.3 + - + +
124B PHE* 3.1 28.7 + + + +
126B ILE* 1.3 80.2 - - + +
128B LYS* 1.4 68.8 + - - +
129B ASN 3.0 0.3 + - - -
130B TYR* 3.9 0.7 - - - +
131B LEU* 2.9 26.9 + - + +
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Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A TYR* 4.5 32.0 - - + -
124B PHE 2.5 18.8 + - - +
125B GLU* 3.8 13.0 - - - +
127B PHE* 1.4 71.4 - - - +
129B ASN* 1.3 57.7 + - - +
131B LEU* 3.3 8.8 + - - +
132B THR* 2.8 32.6 + - - -
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Residues in contact with ASN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 2.8 33.5 + - - +
21B PRO 3.7 4.9 + - - -
22B ILE* 2.8 25.2 - - + +
83B LEU* 4.7 0.2 - - - +
125B GLU 2.9 13.4 + - - +
126B ILE* 3.3 12.6 - - - +
127B PHE 3.0 0.2 - - - -
128B LYS* 1.3 79.0 - - - +
130B TYR* 1.3 66.9 + - + +
132B THR* 3.0 10.1 + - - -
133B LYS* 3.0 56.6 + - - +
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Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE* 3.6 26.7 - + + -
130A TYR* 4.3 20.6 - - + -
131A LEU* 3.6 25.6 - - + -
134A VAL* 3.9 17.9 - - + -
53B MET* 2.7 29.5 - - + +
83B LEU* 3.5 26.6 + - + +
85B GLY 4.0 2.9 + - - -
126B ILE* 3.2 27.2 + - + +
127B PHE* 4.1 1.6 - - - +
129B ASN* 1.3 88.3 - - - +
131B LEU* 1.3 53.0 + - - +
133B LYS* 3.1 29.5 + - + +
134B VAL* 2.6 41.2 + - - +
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A MET* 4.4 3.8 - - + -
85A GLY 3.9 13.5 - - - +
86A ARG* 3.9 3.6 - - - -
87A LEU* 3.9 24.0 - - + +
88A TYR* 4.1 9.6 - - + +
90A THR* 3.4 30.6 - - + +
130A TYR* 3.6 41.1 - - + +
127B PHE* 2.9 19.4 + - + +
128B LYS* 3.3 9.0 - - - +
130B TYR* 1.3 77.9 - - - +
132B THR* 1.3 59.1 + - - +
134B VAL* 4.0 6.9 - - + +
135B ALA* 3.1 23.0 + - - +
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Residues in contact with THR 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A THR* 5.0 8.5 - - - +
20B PHE* 3.7 25.4 - - + -
128B LYS* 2.8 21.2 + - - +
129B ASN* 3.0 9.3 + - - -
131B LEU* 1.3 69.2 - - - +
133B LYS* 1.3 60.1 + - - +
135B ALA* 3.1 9.1 + - + +
136B TYR* 2.6 36.3 + - + +
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A VAL* 4.0 17.5 - - + -
19B PHE 5.3 0.9 - - - -
20B PHE* 3.6 49.8 - - + -
76B TYR* 5.2 13.3 + - - +
83B LEU* 2.4 35.1 + - - +
129B ASN* 3.0 33.9 + - - +
130B TYR* 3.4 33.9 - - + +
132B THR* 1.3 78.6 - - - +
134B VAL* 1.3 64.2 + - - +
136B TYR* 2.9 10.7 + - - -
137B TYR* 3.0 25.6 + - + -
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TYR* 5.4 9.9 - - + +
130A TYR* 4.1 7.0 - - + +
133A LYS* 3.7 20.6 - - + -
134A VAL* 3.2 40.2 - - + +
137A TYR* 4.2 24.5 - - + -
130B TYR 2.6 20.3 + - - +
131B LEU* 4.0 7.4 - - + +
132B THR 3.2 0.2 - - - -
133B LYS* 1.3 71.4 - - - +
135B ALA* 1.3 63.6 + - - +
137B TYR* 3.4 3.6 + - - +
138B ALA* 3.1 25.6 + - + +
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A THR* 3.7 30.1 - - + +
92A ASN* 3.5 25.1 + - - +
131B LEU 3.1 12.8 + - - +
132B THR* 3.3 10.8 - - + +
134B VAL* 1.3 78.6 - - - +
136B TYR* 1.3 64.9 + - - +
138B ALA* 4.8 2.2 - - - -
139B ARG* 3.2 19.6 + - - +
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Residues in contact with TYR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A VAL* 6.4 0.4 - - + -
20B PHE* 4.0 27.4 - + + -
132B THR* 2.6 19.7 + - + +
133B LYS 2.9 8.6 + - - +
135B ALA* 1.3 74.9 - - - +
137B TYR* 1.3 97.7 + + - +
139B ARG* 3.6 3.7 + - - +
140B GLN* 3.3 53.6 + - + +
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Residues in contact with TYR 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A VAL* 4.1 23.1 - - + -
137A TYR* 3.7 21.8 - - + -
138A ALA* 3.8 28.5 - - + -
141A VAL* 3.8 23.9 - - + +
20B PHE* 4.5 12.8 - + - -
75B LEU* 5.3 5.8 - - + -
76B TYR* 3.4 33.6 - + - +
133B LYS* 3.0 37.5 + - + +
134B VAL* 4.3 2.0 - - - +
136B TYR* 1.3 100.1 - + - +
138B ALA* 1.3 63.9 + - - +
140B GLN* 3.2 7.9 + - - +
141B VAL* 3.1 18.7 + - - +
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 3.7 27.3 - - + +
76A TYR* 5.0 5.2 - - + -
92A ASN* 5.6 0.7 - - - +
137A TYR* 4.4 25.3 - - + +
134B VAL* 3.1 19.8 + - + +
135B ALA* 4.2 3.6 - - - +
137B TYR* 1.3 75.5 - - - +
139B ARG* 1.3 67.5 + - - +
141B VAL* 2.8 10.1 + - - +
142B ALA* 2.8 21.5 + - - +
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Residues in contact with ARG 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ILE* 3.8 16.9 - - + +
66A ILE 4.6 2.4 + - - -
67A PHE* 3.4 38.9 - - + +
68A GLU* 2.5 41.3 + - - +
75A LEU* 4.5 1.5 - - - +
91A GLY 2.6 31.1 + - - -
92A ASN* 3.1 19.3 + - - +
93A ASN 5.2 1.2 - - - +
135B ALA 3.2 16.1 + - - +
136B TYR* 3.7 6.7 - - - +
138B ALA* 1.3 75.9 - - - +
140B GLN* 1.3 63.5 + - - +
142B ALA* 3.0 7.5 + - - +
143B GLU* 2.9 48.3 + - - +
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Residues in contact with GLN 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A VAL* 3.8 21.5 - - + -
144A ILE* 5.0 3.3 - - + +
190A HIS* 3.3 40.7 + - + +
191A HIS* 3.8 6.4 - - - -
192A VAL* 4.0 6.2 - - + +
136B TYR* 3.3 57.4 + - + +
137B TYR 3.2 11.6 + - - +
138B ALA 3.0 0.4 - - - -
139B ARG* 1.3 87.8 - - - +
141B VAL* 1.4 62.7 + - - +
143B GLU* 3.0 32.0 + - - +
144B ILE* 4.2 1.6 - - - +
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Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 5.9 3.6 - - + +
137A TYR* 4.2 22.9 - - + +
140A GLN* 3.9 41.5 - - + +
141A VAL* 4.4 6.5 - - + -
144A ILE* 5.5 2.5 - - + -
137B TYR 3.1 13.8 + - - +
138B ALA* 2.8 11.3 + - - +
140B GLN* 1.4 74.9 - - - +
142B ALA* 1.3 51.8 + - - +
144B ILE* 2.3 47.5 - - + +
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ILE* 3.8 24.5 - - + -
67A PHE* 4.4 2.7 - - + -
73A LYS* 2.8 40.1 + - + +
74A LEU 3.5 24.9 - - - +
75A LEU* 4.4 7.4 - - + +
138B ALA 2.8 15.3 + - - +
139B ARG 3.0 8.0 + - - +
141B VAL* 1.3 75.9 - - - +
143B GLU* 1.3 53.3 + - - +
144B ILE* 3.6 0.8 - - - +
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Residues in contact with GLU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 3.2 36.8 - - + -
68A GLU* 5.3 1.9 - - - +
73A LYS* 5.2 0.9 - - - +
190A HIS* 3.0 25.9 + - - +
191A HIS* 2.9 38.4 + - + +
139B ARG* 2.9 28.2 + - - +
140B GLN* 3.0 26.9 + - - +
141B VAL 3.1 1.6 - - - -
142B ALA* 1.3 73.6 - - - +
144B ILE* 1.3 62.9 + - - +
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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