Contacts of the helix formed by residues 132 - 155 (chain J) 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 J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127J LEU 4.6 0.9 + - - -
128J GLU* 4.5 28.5 - - + +
130J LEU 4.3 0.8 + - - -
131J ASP* 1.3 72.4 + - - +
133J VAL* 1.3 66.2 + - + +
135J GLN* 3.1 39.1 + - - +
136J ASP* 3.1 10.2 + - - +
121L ARG* 4.7 2.5 - - - +
124L ILE* 4.6 18.8 - - + -
125L GLU* 4.6 24.0 - - - +
128L GLU* 4.8 15.9 - - - +
135L GLN* 5.0 7.4 - - - +
139L ILE* 4.4 21.7 - - + +
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Residues in contact with VAL 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71J ARG* 3.4 31.4 - - - +
131J ASP* 3.2 9.6 + - - +
132J LEU* 1.3 73.2 - - + +
134J SER* 1.3 56.3 + - - +
135J GLN 2.6 15.2 + - - -
136J ASP* 3.2 3.8 + - - +
137J LEU* 3.2 23.4 + - + +
121L ARG* 3.9 7.4 - - - +
124L ILE* 5.0 7.2 - - + -
139L ILE* 4.1 16.7 - - + +
142L ALA* 3.8 15.5 - - + -
143L GLY* 3.9 22.0 - - - +
146L GLU* 3.8 18.2 - - - +
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Residues in contact with SER 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J VAL* 3.9 25.5 - - - +
21J LEU* 4.5 7.7 - - - +
71J ARG* 3.0 26.3 + - - +
75J LEU* 4.8 1.7 - - - +
127J LEU* 3.3 18.7 - - - +
131J ASP* 2.5 34.7 + - - -
133J VAL* 1.3 70.8 - - - +
135J GLN* 1.3 57.1 + - - +
137J LEU* 4.0 11.8 - - - +
138J LEU* 3.6 16.1 + - - +
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Residues in contact with GLN 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124J ILE* 3.4 35.8 + - + +
125J GLU* 5.1 0.2 - - - +
127J LEU* 4.3 8.5 - - + -
128J GLU* 3.3 46.1 - - - +
131J ASP 3.4 10.2 + - - +
132J LEU* 3.1 27.9 - - - +
133J VAL 2.6 6.7 + - - -
134J SER* 1.3 73.9 - - - +
136J ASP* 1.3 65.6 + - - +
137J LEU 2.7 5.5 + - - -
138J LEU* 2.7 14.2 + - - +
139J ILE* 2.8 23.5 + - + +
132K LEU* 5.0 7.6 - - - +
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Residues in contact with ASP 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132J LEU 3.1 4.7 + - - +
133J VAL 3.2 1.3 + - - +
135J GLN* 1.3 78.6 + - - +
137J LEU* 1.3 65.7 + - - +
139J ILE* 3.6 11.5 - - - +
140J ALA* 3.1 24.4 + - - +
136K ASP* 2.5 21.6 - - - +
136L ASP* 2.4 34.0 - - - +
139L ILE* 3.9 30.0 - - + +
140L ALA* 5.2 6.6 - - - +
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Residues in contact with LEU 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J LEU* 6.1 0.2 - - + -
67J GLU* 4.7 26.9 - - + +
68J VAL* 4.4 9.4 - - + +
71J ARG* 4.7 21.5 - - + -
133J VAL* 3.2 17.5 + - + +
134J SER* 4.0 9.0 - - - +
135J GLN 2.7 0.6 + - - -
136J ASP* 1.3 80.8 - - - +
138J LEU* 1.3 79.2 + - + +
139J ILE 3.2 0.3 + - - -
140J ALA* 3.3 8.0 + - - +
141J HIS* 3.1 50.5 - - + +
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Residues in contact with LEU 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J LEU* 4.0 21.8 - - + -
24J GLN* 3.1 41.5 - - + +
28J TYR* 3.9 8.5 - - - +
68J VAL* 4.9 2.9 - - + -
120J THR* 3.6 20.8 - - + +
123J SER* 5.1 5.6 - - - -
124J ILE* 4.1 15.4 - - + +
127J LEU* 4.5 11.4 - - + -
134J SER 3.6 13.2 + - - +
135J GLN 2.7 11.5 + - - +
137J LEU* 1.3 93.5 - - + +
139J ILE* 1.3 63.7 + - - +
141J HIS* 3.3 9.2 + - + +
142J ALA* 3.3 15.4 + - - +
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Residues in contact with ILE 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124J ILE* 3.8 28.9 - - + -
135J GLN* 2.8 36.4 + - + +
136J ASP* 3.6 15.5 - - - +
138J LEU* 1.3 67.9 - - - +
140J ALA* 1.3 72.8 + - - +
142J ALA* 2.6 23.7 + - - +
143J GLY 3.2 2.8 + - - -
132K LEU* 4.4 27.4 - - + +
133K VAL* 4.1 22.9 - - + -
136K ASP* 4.0 26.2 - - + -
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Residues in contact with ALA 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64J TYR* 4.6 5.0 + - + -
136J ASP* 3.1 12.0 + - - +
137J LEU* 3.5 11.4 - - - +
139J ILE* 1.3 83.0 - - - +
141J HIS* 1.3 68.9 + - + +
143J GLY* 3.1 13.4 + - - +
144J GLU* 3.6 5.9 + - - +
136K ASP* 5.3 7.6 + - - +
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Residues in contact with HIS 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J TYR* 2.7 33.1 + + - +
64J TYR* 3.2 46.8 - + + -
67J GLU* 3.0 20.7 + - - -
68J VAL* 3.9 7.0 - - + -
120J THR* 5.8 0.9 - - + -
137J LEU* 3.1 40.9 - - + +
138J LEU* 3.5 9.0 - - + +
139J ILE 2.8 3.4 + - - -
140J ALA* 1.3 75.9 - - + +
142J ALA* 1.3 52.1 + - - +
144J GLU* 2.9 5.0 + - - +
145J LEU* 2.7 52.7 + - + +
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Residues in contact with ALA 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117J ILE* 5.7 2.5 - - + -
120J THR* 4.5 11.6 - - + +
121J ARG* 5.4 1.3 - - - +
124J ILE* 4.4 9.2 - - + -
138J LEU 3.3 7.6 + - - +
139J ILE* 2.6 20.0 + - - +
141J HIS* 1.3 73.6 - - - +
143J GLY* 1.3 54.4 + - - +
145J LEU* 4.1 7.9 - - - -
146J GLU* 2.7 56.8 + - - +
133K VAL* 3.9 13.2 - - + -
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Residues in contact with GLY 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139J ILE 3.2 3.0 + - - -
140J ALA* 3.1 11.2 + - - -
142J ALA* 1.3 78.5 - - - +
144J GLU* 1.3 59.7 + - - +
146J GLU* 4.1 1.4 - - - +
147J LYS* 3.2 27.0 + - - +
71K ARG* 4.3 8.0 + - - -
133K VAL* 3.8 21.5 - - - +
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Residues in contact with GLU 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57J GLN* 4.7 4.0 - - - +
60J LEU* 3.5 28.6 - - + +
64J TYR* 3.4 24.1 + - + +
140J ALA 3.6 6.0 + - - +
141J HIS 2.9 2.8 + - - +
143J GLY* 1.3 74.7 - - - +
145J LEU* 1.3 69.0 + - - +
147J LYS* 3.6 21.1 + - + +
148J PHE* 2.8 26.2 + - - +
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Residues in contact with LEU 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J TYR* 4.6 10.1 - - + +
31J LEU* 4.0 18.6 - - + -
57J GLN* 3.6 13.7 - - - +
61J VAL* 4.6 3.6 - - + -
64J TYR* 4.1 15.3 - - + -
113J TYR* 3.5 33.7 - - + -
116J VAL* 4.7 14.4 - - + -
117J ILE* 4.6 12.3 - - + -
120J THR* 5.7 3.8 - - + +
141J HIS* 2.7 53.1 + - + +
142J ALA* 3.6 6.7 - - - +
144J GLU* 1.3 74.6 - - - +
146J GLU* 1.3 63.5 + - - +
148J PHE* 3.2 2.8 + - - +
149J GLN 3.0 16.8 + - - -
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Residues in contact with GLU 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117J ILE* 3.6 33.6 - - + +
121J ARG* 2.9 35.7 + - - -
142J ALA* 2.7 37.4 + - - +
145J LEU* 1.3 72.7 - - - +
147J LYS* 1.3 62.4 + - - +
149J GLN* 3.2 7.8 + - - +
150J TRP 3.1 15.9 + - - -
6K ILE* 3.5 17.4 - - + +
71K ARG* 3.0 37.1 + - - +
74K THR* 3.6 13.8 - - + +
133K VAL* 3.8 1.4 - - - +
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Residues in contact with LYS 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143J GLY 3.2 18.9 + - - +
144J GLU* 3.6 24.8 + - + +
145J LEU 3.2 0.2 - - - -
146J GLU* 1.3 75.5 - - - +
148J PHE* 1.3 69.8 + - - +
150J TRP* 2.8 31.2 + - + +
151J PHE* 3.2 27.1 + - + -
66K ASP 5.2 0.4 + - - -
67K GLU* 5.1 10.7 + - - +
70K GLU* 2.8 43.6 + - - +
71K ARG* 5.2 1.5 - - - +
74K THR* 4.2 18.8 - - - +
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Residues in contact with PHE 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J LEU* 4.2 11.9 - - + -
53J MET* 4.1 32.8 - - + -
54J ILE* 4.7 5.8 - - + -
57J GLN* 3.0 50.0 - - + +
109J LEU* 4.3 8.1 - - + -
113J TYR* 3.4 37.9 - + - -
144J GLU* 2.8 14.3 + - + +
145J LEU 3.6 2.9 - - - +
147J LYS* 1.3 73.7 - - - +
149J GLN* 1.3 65.0 + - - +
151J PHE* 2.8 39.9 + + + +
152J VAL* 3.0 28.9 + - + -
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Residues in contact with GLN 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110J ASP* 3.5 8.1 + - - +
113J TYR* 3.4 23.7 - - + +
114J ASN* 3.0 29.5 + - - +
117J ILE* 3.4 28.6 - - + +
145J LEU 3.0 12.4 + - - +
146J GLU* 3.2 11.6 - - - +
148J PHE* 1.3 78.2 - - - +
150J TRP* 1.3 66.3 + - - +
152J VAL* 2.7 23.2 + - + +
153J ARG* 2.8 49.4 + - + +
6K ILE* 5.0 3.3 - - - +
7K PRO* 3.9 5.9 - - - +
74K THR* 5.9 1.0 - - - +
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Residues in contact with TRP 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H HIS 5.0 0.2 - - - -
40H TRP* 3.7 17.7 - - - -
42H VAL 5.2 1.8 - - - -
43H VAL* 5.7 3.5 - - + +
47H PHE* 4.1 18.2 - + - -
51H HIS* 4.5 9.4 - + - -
99H ARG* 4.8 3.6 - - - +
146J GLU 3.1 2.2 + - - -
147J LYS* 2.8 23.8 + - + +
149J GLN* 1.3 78.6 + - - +
151J PHE* 1.3 86.9 + + - -
153J ARG* 3.0 10.3 + - - +
154J ALA* 2.6 47.1 + - + +
157J GLU* 5.5 1.0 + - - -
4K PHE* 4.4 16.3 - + - -
70K GLU* 4.3 32.5 - - + -
73K ALA* 3.5 36.7 + - + +
74K THR* 3.7 37.7 - - + +
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Residues in contact with PHE 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H PHE* 3.2 28.7 - + + -
48H ILE* 4.1 11.4 - - + -
51H HIS* 3.8 26.9 - + - -
53J MET* 4.0 21.8 - - + -
147J LYS* 3.2 30.3 + - + -
148J PHE* 2.8 40.2 + + + +
150J TRP* 1.3 88.6 - + - +
152J VAL* 1.3 63.1 + - - +
154J ALA* 3.4 5.7 + - - +
155J HIS* 2.8 23.7 + - - -
70K GLU* 5.1 0.7 - - - -
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Residues in contact with VAL 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53J MET* 4.7 2.2 - - + -
106J LEU* 3.1 55.8 - - + +
109J LEU* 4.3 8.1 - - + -
110J ASP* 4.2 14.8 - - + +
113J TYR* 5.5 2.2 - - + -
148J PHE* 3.3 45.5 - - + +
149J GLN* 2.7 16.1 + - + +
151J PHE* 1.3 75.9 - - - +
153J ARG* 1.3 62.8 + - + +
155J HIS* 3.1 19.3 + - - +
156J LEU* 3.9 5.9 - - + +
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Residues in contact with ARG 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110J ASP* 2.8 32.2 + - + +
114J ASN* 3.1 32.1 + - - +
149J GLN* 2.8 44.2 + - + +
150J TRP* 3.4 10.5 - - - +
152J VAL* 1.3 68.6 - - + +
154J ALA* 1.3 54.1 + - - +
155J HIS 2.8 5.4 - - - -
156J LEU* 2.6 38.4 + - + +
157J GLU* 3.5 10.5 + - + +
4K PHE* 3.8 47.6 - - + +
5K THR 3.6 22.6 + - - -
6K ILE* 4.5 1.4 - - - +
7K PRO* 3.9 7.7 - - - +
74K THR 5.2 2.0 + - - -
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Residues in contact with ALA 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H VAL* 3.7 22.0 - - + +
44H GLY 3.0 27.1 + - - +
47H PHE* 3.7 34.3 - - + -
150J TRP* 2.6 32.3 + - + +
151J PHE 3.8 0.2 - - - +
153J ARG* 1.3 71.5 - - - +
155J HIS* 1.3 58.6 + - - +
156J LEU 3.2 1.2 + - - -
157J GLU* 4.1 10.1 + - - -
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Residues in contact with HIS 155 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H GLY 2.9 16.4 - - - +
45H PRO* 3.1 36.2 + - - +
46H ASN* 4.9 0.8 - - - -
47H PHE* 3.3 27.1 + + + -
48H ILE* 3.6 30.1 + - + +
46J ASN* 4.4 1.3 + - - -
49J GLY* 5.5 0.4 - - - -
50J VAL* 4.0 17.6 + - + +
53J MET* 3.8 9.1 - - - -
103J GLN* 4.0 10.6 + - - +
106J LEU* 3.4 28.5 - - + +
151J PHE 2.8 21.3 + - - -
152J VAL 3.1 12.0 + - - +
153J ARG 2.8 0.8 + - - -
154J ALA* 1.3 76.5 - - - +
156J LEU* 1.3 63.3 + - - +
157J GLU 5.4 0.2 - - - +
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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