Contacts of the helix formed by residues 132 - 155 (chain L) in PDB entry 1VEQ
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 LEU 132 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121K ARG* 4.8 2.5 - - - +
124K ILE* 4.5 20.6 - - + -
125K GLU* 4.6 22.4 - - - +
128K GLU* 4.7 17.0 - - - +
135K GLN* 4.8 7.9 - - - +
139K ILE* 4.3 20.9 - - + +
127L LEU 5.0 0.4 - - - -
128L GLU* 4.5 29.6 + - + +
130L LEU 4.2 0.4 - - - -
131L ASP* 1.3 72.0 + - - +
133L VAL* 1.3 63.2 + - + +
135L GLN* 3.0 42.5 + - - +
136L ASP* 3.1 10.0 + - - +
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Residues in contact with VAL 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121K ARG* 4.0 7.2 - - - +
124K ILE* 4.9 7.4 - - + -
139K ILE* 4.0 18.1 - - + +
142K ALA* 3.8 23.8 - - + -
143K GLY* 3.9 21.5 - - - +
146K GLU* 3.9 10.3 - - - +
71L ARG* 3.5 31.0 - - - +
131L ASP* 3.2 9.1 + - - +
132L LEU* 1.3 73.3 - - + +
134L SER* 1.3 55.9 + - - +
135L GLN 2.6 14.8 + - - -
136L ASP* 3.2 4.3 + - - +
137L LEU* 3.2 22.9 + - + +
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Residues in contact with SER 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L VAL* 4.0 25.8 - - - +
21L LEU* 4.8 7.5 - - - +
71L ARG* 3.0 25.9 + - - +
75L LEU* 4.9 1.7 - - - +
127L LEU* 3.2 19.3 - - - +
131L ASP* 2.5 34.7 + - - -
132L LEU 3.5 0.4 - - - -
133L VAL* 1.3 70.5 - - - +
135L GLN* 1.3 57.4 + - - +
137L LEU* 4.1 10.9 - - - +
138L LEU* 3.7 15.8 + - - +
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Residues in contact with GLN 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132J LEU* 5.0 9.2 - - - +
124L ILE* 3.5 34.7 + - + +
125L GLU* 5.1 0.2 - - - +
127L LEU* 4.2 8.7 - - + -
128L GLU* 3.3 46.0 - - - +
131L ASP 3.4 10.0 + - - +
132L LEU* 3.0 31.3 + - - +
133L VAL 2.6 2.8 + - - -
134L SER* 1.3 78.7 - - - +
136L ASP* 1.3 63.2 + - - +
137L LEU 2.6 5.7 + - - -
138L LEU* 2.7 13.4 + - - +
139L ILE* 2.8 24.1 + - + +
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Residues in contact with ASP 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136J ASP* 2.4 37.9 - - - +
136K ASP* 2.4 19.3 - - - +
139K ILE* 4.0 28.4 - - + +
140K ALA* 5.3 6.4 - - - +
132L LEU 3.1 5.3 + - - +
133L VAL 4.1 1.6 - - - +
135L GLN* 1.3 78.8 + - - +
137L LEU* 1.3 63.5 - - - +
139L ILE* 3.7 11.7 - - - +
140L ALA* 3.1 23.2 + - - +
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Residues in contact with LEU 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L LEU* 6.1 0.9 - - + -
67L GLU* 4.7 27.6 - - + +
68L VAL* 4.5 8.7 - - + -
71L ARG* 4.7 22.2 - - + -
133L VAL* 3.2 19.6 + - + +
134L SER* 4.1 7.9 - - - -
135L GLN 2.6 0.8 + - - -
136L ASP* 1.3 81.3 - - - +
138L LEU* 1.3 78.0 + - + +
139L ILE 3.2 0.2 + - - -
140L ALA* 3.3 6.7 + - - +
141L HIS* 3.1 50.9 - - + +
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Residues in contact with LEU 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L LEU* 4.0 24.7 - - + -
24L GLN* 3.2 41.5 - - + +
28L TYR* 4.0 5.2 - - - +
68L VAL* 4.9 2.5 - - + -
120L THR* 3.6 22.2 - - + +
123L SER* 5.0 6.3 - - - -
124L ILE* 4.0 15.3 - - + -
127L LEU* 4.5 10.8 - - + -
134L SER 3.9 10.5 - - - +
135L GLN 2.7 11.2 + - - +
137L LEU* 1.3 93.5 - - + +
139L ILE* 1.3 63.4 + - - +
141L HIS* 3.3 12.0 + - + +
142L ALA* 3.2 15.1 + - - +
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Residues in contact with ILE 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132J LEU* 4.4 25.1 - - + +
133J VAL* 4.1 21.8 - - + -
136J ASP* 3.9 29.8 - - + +
124L ILE* 3.8 31.2 - - + +
135L GLN* 2.8 36.0 + - + +
136L ASP* 3.7 14.6 - - - +
138L LEU* 1.3 69.0 - - - +
140L ALA* 1.3 73.2 + - - +
142L ALA* 2.6 22.9 + - - +
143L GLY 3.2 3.1 + - - -
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Residues in contact with ALA 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136J ASP* 5.2 7.4 + - - +
64L TYR* 4.5 5.0 + - + -
136L ASP* 3.1 13.3 + - - +
137L LEU* 3.5 11.0 - - - +
139L ILE* 1.3 81.8 - - - +
141L HIS* 1.3 68.0 + - + +
143L GLY* 3.1 15.1 + - - +
144L GLU* 3.6 5.7 + - - +
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Residues in contact with HIS 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L TYR* 2.7 32.7 + + - +
64L TYR* 3.3 47.3 - + + -
67L GLU* 3.0 20.5 + - - -
68L VAL* 3.9 7.2 - - + -
120L THR* 5.7 0.9 - - + -
137L LEU* 3.1 39.1 - - + +
138L LEU* 3.4 9.7 - - + +
139L ILE 2.9 3.6 + - - -
140L ALA* 1.3 72.6 - - + +
142L ALA* 1.3 67.6 + - - +
144L GLU* 2.9 5.2 + - - +
145L LEU* 2.7 41.3 + - + +
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Residues in contact with ALA 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133J VAL* 3.8 13.9 - - + -
117L ILE* 5.6 3.1 - - + -
120L THR* 4.4 15.7 - - + +
121L ARG* 5.4 1.3 - - - +
124L ILE* 4.5 3.8 - - + -
138L LEU 3.2 7.6 + - - +
139L ILE* 2.6 16.8 + - - +
141L HIS* 1.3 73.8 - - - +
143L GLY* 1.3 57.4 + - - +
145L LEU* 4.1 8.1 - - - -
146L GLU* 2.7 56.7 + - - +
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Residues in contact with GLY 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71J ARG* 4.3 7.3 + - - -
133J VAL* 3.9 20.0 - - - +
139L ILE 3.2 3.4 + - - -
140L ALA* 3.1 10.8 + - - -
142L ALA* 1.3 79.6 - - - +
144L GLU* 1.3 58.5 + - - +
146L GLU* 4.1 1.7 - - - +
147L LYS* 3.2 26.3 + - - +
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Residues in contact with GLU 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57L GLN* 4.2 5.1 - - - +
60L LEU* 3.5 28.2 - - + +
64L TYR* 3.4 24.2 + - + +
140L ALA 3.6 5.4 + - - +
141L HIS 2.9 2.8 + - - +
143L GLY* 1.3 75.5 - - - +
145L LEU* 1.3 60.7 + - - +
147L LYS* 3.6 21.6 + - + +
148L PHE* 2.8 32.7 + - - +
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Residues in contact with LEU 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L TYR* 4.6 9.2 - - + +
31L LEU* 4.0 18.8 - - + -
57L GLN* 3.6 13.7 - - - +
61L VAL* 4.6 3.4 - - + -
64L TYR* 4.1 15.3 - - + -
113L TYR* 3.6 33.5 - - + -
116L VAL* 4.7 14.8 - - + -
117L ILE* 4.5 12.1 - - + -
120L THR* 5.7 4.3 - - + +
141L HIS* 2.7 52.7 + - + +
142L ALA* 3.6 7.4 - - - +
144L GLU* 1.3 74.4 - - - +
146L GLU* 1.3 63.7 + - - +
148L PHE* 3.2 2.6 + - - +
149L GLN 3.0 18.5 + - - -
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Residues in contact with GLU 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J ILE* 3.5 16.9 - - + +
71J ARG* 2.9 39.3 + - - +
74J THR* 3.4 15.0 - - + +
133J VAL* 3.8 1.5 - - - +
117L ILE* 3.5 34.0 - - + +
121L ARG* 2.9 35.1 + - - -
142L ALA* 2.7 36.2 + - - +
143L GLY 4.1 0.2 - - - +
145L LEU* 1.3 72.9 - - - +
147L LYS* 1.3 62.6 + - - +
149L GLN* 3.3 7.4 - - - +
150L TRP 3.2 15.8 + - - -
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Residues in contact with LYS 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66J ASP 5.0 0.2 + - - -
67J GLU* 5.0 10.9 + - - +
70J GLU* 2.7 46.3 + - - +
71J ARG* 5.2 1.3 - - - +
74J THR* 4.2 18.8 - - - +
143L GLY 3.2 18.2 + - - +
144L GLU* 3.6 23.9 + - + +
145L LEU 3.2 0.2 - - - -
146L GLU* 1.3 77.9 - - - +
148L PHE* 1.3 59.7 + - - +
150L TRP* 2.8 36.0 + - + +
151L PHE* 3.2 27.3 + - + -
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Residues in contact with PHE 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L LEU* 4.2 11.7 - - + -
53L MET* 4.1 33.0 - - + -
54L ILE* 4.7 5.4 - - + -
57L GLN* 3.1 50.5 - - + +
109L LEU* 4.2 7.4 - - + -
113L TYR* 3.4 38.4 - + - -
144L GLU* 2.8 16.0 + - + +
145L LEU 3.6 2.7 - - - +
147L LYS* 1.3 72.5 - - - +
149L GLN* 1.3 66.6 + - - +
151L PHE* 2.8 40.5 + + + +
152L VAL* 3.1 28.4 + - + -
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Residues in contact with GLN 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J ILE* 5.0 3.8 - - - +
7J PRO* 4.0 5.5 - - - +
74J THR* 5.7 1.7 - - - +
110L ASP* 3.4 16.3 + - - +
113L TYR* 3.4 23.0 - - + +
114L ASN* 3.0 32.9 + - - +
117L ILE* 3.5 19.3 - - + +
145L LEU 3.0 13.0 + - - +
146L GLU* 3.3 11.2 - - - +
148L PHE* 1.3 77.2 - - - +
150L TRP* 1.3 65.2 + - - +
152L VAL* 2.8 15.3 + - + +
153L ARG* 2.8 55.6 + - + +
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Residues in contact with TRP 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A HIS 5.0 0.2 - - - -
40A TRP* 3.7 19.7 - - - -
42A VAL 5.2 1.8 - - - -
43A VAL* 6.1 1.1 - - + -
47A PHE* 4.2 17.3 - + - -
51A HIS* 4.5 9.2 - + - -
99A ARG* 4.8 5.3 - - - +
4J PHE* 4.4 13.4 - + - -
70J GLU* 4.3 33.0 - - + -
73J ALA* 3.5 47.4 + - + +
74J THR* 3.7 26.2 - - + -
146L GLU 3.2 3.0 + - - -
147L LYS* 2.8 23.2 + - + +
149L GLN* 1.3 78.5 + - - +
151L PHE* 1.3 83.9 + + - -
153L ARG* 3.0 9.7 + - - +
154L ALA* 2.7 47.2 + - + +
157L GLU* 5.4 1.4 + - - -
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Residues in contact with PHE 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 3.3 24.5 - + - -
48A ILE* 4.2 11.2 - - + -
51A HIS* 3.8 30.3 - + - -
70J GLU* 5.0 1.3 - - - -
53L MET* 4.0 22.2 - - + -
147L LYS* 3.2 30.7 + - + -
148L PHE* 2.8 41.5 + + + +
150L TRP* 1.3 89.7 - + - +
152L VAL* 1.3 64.3 + - - +
154L ALA* 3.3 5.4 + - - +
155L HIS* 2.9 23.7 + - - -
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Residues in contact with VAL 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L MET* 4.7 2.0 - - + +
106L LEU* 3.1 57.1 - - + +
109L LEU* 4.3 7.6 - - + -
110L ASP* 4.2 14.1 - - + +
113L TYR* 5.5 2.0 - - + -
148L PHE* 3.3 44.4 - - + +
149L GLN* 2.8 15.8 + - + +
151L PHE* 1.3 76.4 - - - +
153L ARG* 1.3 63.2 + - + +
155L HIS* 3.0 19.3 + - - +
156L LEU* 3.9 5.7 - - + +
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Residues in contact with ARG 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J PHE* 3.5 54.1 - - + +
5J THR 3.6 22.8 + - - +
6J ILE* 4.4 1.4 - - - +
7J PRO* 4.1 3.2 - - - +
74J THR* 5.0 2.6 + - - +
110L ASP* 2.7 33.2 + - + +
114L ASN* 3.1 31.7 + - - +
149L GLN* 2.8 42.9 + - + +
150L TRP* 3.4 10.8 - - - +
152L VAL* 1.3 69.0 - - - +
154L ALA* 1.3 53.1 + - - +
155L HIS 2.7 5.7 + - - -
156L LEU* 2.6 40.4 + - + +
157L GLU* 3.5 9.5 + - + +
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Residues in contact with ALA 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL 4.6 0.2 - - - +
43A VAL* 3.7 24.6 - - + +
44A GLY 3.1 25.3 + - - -
47A PHE* 3.8 33.8 - - + +
150L TRP* 2.7 32.5 + - + +
151L PHE 3.3 0.4 + - - +
153L ARG* 1.3 70.9 - - - +
155L HIS* 1.3 59.5 + - - +
156L LEU 3.2 0.6 + - - -
157L GLU* 4.0 10.9 + - - -
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Residues in contact with HIS 155 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLY 3.0 15.3 - - - +
45A PRO* 3.1 36.3 + - - +
46A ASN* 4.8 0.6 - - - -
47A PHE* 3.2 26.9 + + + -
48A ILE* 3.6 29.8 + - + +
46L ASN* 4.4 1.3 + - - -
49L GLY* 5.5 0.4 - - - -
50L VAL* 4.0 17.5 + - + +
53L MET* 3.8 9.6 - - - -
103L GLN* 4.0 10.5 + - - +
106L LEU* 3.4 28.7 - - + +
151L PHE 2.9 20.7 + - - -
152L VAL* 3.0 12.0 + - - +
153L ARG 2.7 0.8 + - - -
154L ALA* 1.3 78.0 - - - +
156L LEU* 1.3 61.7 + - - +
157L GLU 3.8 0.6 - - - +
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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