Contacts of the helix formed by residues 116 - 145 (chain A) in PDB entry 1VJX
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 ASN 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 3.2 33.7 + - - +
61A GLU* 2.9 7.9 + - - +
115A VAL* 1.3 82.5 + - + +
117A SER* 1.3 62.1 + - - +
118A ASP* 2.6 22.4 + - - +
119A ALA* 3.5 12.4 + - + +
120A GLN* 3.1 27.6 + - - +
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL 3.4 4.6 + - - -
116A ASN* 1.3 73.6 + - - +
118A ASP* 1.3 63.8 + - - -
120A GLN* 3.9 15.5 - - - +
121A LYS* 3.1 26.9 + - - +
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Residues in contact with ASP 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASN* 2.6 20.9 + - - +
117A SER* 1.3 76.0 + - - +
119A ALA* 1.3 58.9 + - - +
121A LYS* 3.2 8.0 + - - +
122A THR* 2.9 35.2 + - - +
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A MSE 4.1 13.9 - - - -
57A GLU* 3.5 34.3 - - - +
114A LEU* 3.9 22.0 - - + -
116A ASN* 3.4 13.2 + - + +
118A ASP* 1.3 78.0 - - - +
120A GLN* 1.3 62.8 + - - +
122A THR* 3.1 3.4 + - - -
123A VAL* 3.0 27.2 + - - +
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Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 3.1 51.8 + - + +
112A ASP* 4.7 5.1 + - - +
114A LEU* 3.1 24.6 + - + +
115A VAL* 4.5 5.2 - - - +
116A ASN 3.1 16.1 + - - +
117A SER* 3.9 18.1 - - - +
119A ALA* 1.3 77.1 - - - +
121A LYS* 1.3 62.4 + - - +
123A VAL* 3.4 0.7 + - - -
124A LYS* 3.0 21.0 + - - +
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Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER 3.1 19.2 + - - +
118A ASP* 3.2 9.4 + - - +
120A GLN* 1.3 75.2 - - - +
122A THR* 1.3 64.7 + - - +
124A LYS* 3.4 7.3 + - - +
125A LYS* 3.1 22.7 + - + +
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Residues in contact with THR 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 3.5 26.5 - - + -
53A MSE 3.4 23.1 - - + +
118A ASP* 2.9 20.2 + - - +
119A ALA* 3.1 9.3 + - - -
121A LYS* 1.3 77.8 - - - +
123A VAL* 1.3 60.4 + - - +
125A LYS* 3.4 11.8 - - + +
126A ILE* 3.4 21.0 + - - +
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PHE* 4.1 18.2 - - + -
53A MSE 3.7 20.4 - - + -
107A TYR* 3.8 23.8 - - + +
110A LEU* 4.2 11.2 - - + -
111A LYS* 4.0 12.6 - - + -
114A LEU* 3.4 23.1 - - + -
119A ALA 3.0 19.1 + - - +
120A GLN 4.0 3.1 - - - +
122A THR* 1.3 75.6 - - - +
124A LYS* 1.3 60.0 + - - +
126A ILE* 3.3 7.6 + - - +
127A ILE* 3.0 30.2 + - + +
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Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A TYR* 6.3 3.1 - - - -
111A LYS* 3.7 27.2 - - + +
120A GLN 3.0 16.9 + - - +
121A LYS* 3.4 8.2 + - - +
123A VAL* 1.3 73.4 - - - +
125A LYS* 1.3 59.6 + - - +
127A ILE* 3.4 8.1 + - + +
128A ASP* 3.0 49.4 + - - +
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Residues in contact with LYS 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 6.4 2.0 - - - -
121A LYS* 3.1 12.1 + - + +
122A THR* 3.4 14.1 - - + +
123A VAL 3.3 0.2 - - - -
124A LYS* 1.3 76.5 - - - +
126A ILE* 1.3 57.9 + - + +
128A ASP* 3.4 9.2 + - - +
129A GLN* 3.0 56.4 + - - +
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Residues in contact with ILE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 3.8 22.9 - - - +
46A HIS* 3.7 32.3 - - + +
49A ILE* 3.7 34.1 - - + -
50A PHE* 3.6 39.7 - - + -
107A TYR* 4.9 4.3 - - + -
122A THR* 3.4 13.2 + - + +
123A VAL* 3.3 10.1 + - - +
125A LYS* 1.3 74.5 - - + +
127A ILE* 1.3 55.0 + - + +
129A GLN* 3.2 4.0 + - - +
130A GLU* 2.8 43.2 + - + +
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Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ILE* 5.0 4.7 - - + +
107A TYR* 3.6 43.3 - - + +
108A TYR* 3.5 55.0 - - + +
111A LYS* 3.9 20.2 - - + -
123A VAL* 3.0 21.2 + - + +
124A LYS* 3.6 7.9 - - + +
126A ILE* 1.3 76.2 - - + +
128A ASP* 1.3 58.0 + - - +
130A GLU* 3.2 8.5 + - - +
131A LYS* 2.8 37.4 + - + +
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Residues in contact with ASP 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LYS* 3.0 48.7 + - - +
125A LYS* 3.5 8.7 - - + +
127A ILE* 1.3 75.7 - - - +
129A GLN* 1.3 63.4 + - + +
131A LYS* 3.3 28.0 + - - +
132A GLU* 3.1 26.0 + - - +
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Residues in contact with GLN 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 5.7 2.5 - - + +
45A ILE* 6.0 0.5 - - - +
46A HIS* 2.9 37.2 + - + +
125A LYS* 3.0 55.1 + - - +
126A ILE* 3.2 7.1 + - - +
128A ASP* 1.3 74.4 - - + +
130A GLU* 1.3 64.8 + - - +
132A GLU* 3.3 9.6 + - + +
133A HIS* 3.0 34.1 + - - +
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 2.5 26.5 - - - +
43A GLU* 2.6 26.6 - - - +
46A HIS* 2.8 10.3 + - + -
100A GLU* 2.5 46.9 - - - +
104A ILE* 3.9 12.3 - - + +
107A TYR* 3.7 24.0 - - + -
126A ILE* 2.8 30.3 + - + +
127A ILE* 3.5 7.0 - - - +
129A GLN* 1.3 72.3 - - - +
131A LYS* 1.3 57.3 + - - +
133A HIS* 3.2 8.5 + - - +
134A LEU* 3.1 24.1 + - - +
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Residues in contact with LYS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ILE* 4.2 17.3 - - + -
108A TYR* 3.5 27.5 + - + +
127A ILE* 2.8 23.6 + - + +
128A ASP* 3.6 29.1 + - - +
129A GLN 3.2 0.2 - - - -
130A GLU* 1.3 78.7 - - - +
132A GLU* 1.3 58.0 + - + +
134A LEU* 3.6 12.0 - - + +
135A ARG* 3.1 24.9 + - - +
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Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ASP 3.1 17.1 + - - +
129A GLN* 3.3 12.1 + - + +
131A LYS* 1.3 75.9 - - - +
133A HIS* 1.3 66.7 + - + +
135A ARG* 3.0 39.9 + - - +
136A LYS* 3.0 22.5 + - - +
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Residues in contact with HIS 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 4.7 7.7 - - - +
39A LEU* 3.6 33.5 + - + +
42A GLN* 2.5 46.2 + - + +
43A GLU* 3.1 31.3 + - - +
46A HIS* 4.3 7.1 - + - -
100A GLU* 4.4 6.7 + - - +
129A GLN* 3.0 32.3 + - + +
130A GLU* 3.2 17.7 + - - +
132A GLU* 1.3 76.6 - - + +
134A LEU* 1.3 59.5 + - - +
136A LYS* 3.1 6.2 + - - +
137A LEU* 2.9 32.9 + - + +
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ILE* 4.0 35.4 - - + +
100A GLU* 4.0 16.3 - - + +
101A LYS* 4.0 28.5 - - + -
104A ILE* 4.1 13.2 - - + -
130A GLU 3.1 9.9 + - - +
131A LYS* 3.6 13.0 - - + +
133A HIS* 1.3 77.4 - - - +
135A ARG* 1.3 65.7 + - - +
137A LEU* 3.2 5.1 + - + +
138A LEU* 2.9 40.3 + - + +
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Residues in contact with ARG 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LYS 3.1 18.4 + - - +
132A GLU* 3.0 34.1 + - - +
133A HIS 3.4 0.4 - - - -
134A LEU* 1.3 75.2 - - - +
136A LYS* 1.3 78.1 + - - +
138A LEU* 3.3 11.3 + - - +
139A GLU* 2.9 67.8 + - + +
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Residues in contact with LYS 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A THR* 3.7 36.1 + - + -
39A LEU* 5.1 8.5 - - + -
132A GLU 3.0 15.1 + - - +
133A HIS* 3.1 10.7 + - - +
135A ARG* 1.3 87.9 - - - +
137A LEU* 1.3 59.9 + - - +
139A GLU* 2.9 32.2 + - - +
140A MSE 2.9 48.8 + - - +
143A GLU* 5.4 2.0 + - - -
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TYR* 3.6 25.1 - - + +
36A PHE* 4.6 4.7 - - + -
39A LEU* 4.0 22.9 - - + -
93A LEU* 3.7 27.7 - - + +
96A ALA* 3.7 31.2 - - + +
97A ILE* 3.6 21.2 - - + +
100A GLU* 4.3 9.2 - - + -
133A HIS* 2.9 19.1 + - + +
134A LEU* 3.5 10.8 - - - +
136A LYS* 1.3 76.6 - - - +
138A LEU* 1.3 57.1 + - - +
140A MSE 3.5 5.9 + - - +
141A LYS* 3.0 27.5 + - - +
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ILE* 3.7 29.6 - - + -
101A LYS* 5.7 4.5 - - + +
134A LEU* 2.9 42.3 + - + +
135A ARG* 3.8 8.1 - - - +
137A LEU* 1.3 72.6 - - - +
139A GLU* 1.3 59.5 + - - +
141A LYS* 3.6 11.6 - - + +
142A ARG* 2.9 32.5 + - - +
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Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ARG* 2.9 44.4 + - - +
136A LYS* 2.9 37.0 + - - +
138A LEU* 1.3 73.8 - - - +
140A MSE 1.3 59.9 + - - +
142A ARG* 3.4 9.2 + - - +
143A GLU* 3.0 60.4 + - - +
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Residues in contact with MSE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ILE* 3.6 47.1 - - + -
35A THR* 3.5 26.9 - - + -
36A PHE* 3.7 22.0 - - + -
89A LEU* 3.9 8.9 - - + +
93A LEU* 3.6 21.3 - - + +
136A LYS* 2.9 36.7 + - - +
137A LEU* 3.8 5.2 - - - +
139A GLU* 1.3 71.1 - - + +
141A LYS* 1.3 67.9 + - - +
143A GLU* 4.7 2.5 - - - +
144A SER* 2.9 37.0 + - - +
145A THR* 3.8 2.3 + - - -
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LYS* 4.1 20.3 - - - +
93A LEU* 3.4 15.8 - - + +
94A ASP* 2.9 33.4 + - - +
97A ILE* 4.1 16.6 - - + -
137A LEU 3.0 17.7 + - - +
138A LEU* 3.6 13.9 - - + +
140A MSE 1.3 75.8 - - - +
142A ARG* 1.3 65.1 + - - +
145A THR* 2.9 40.9 + - + +
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Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU 2.9 19.6 + - - +
139A GLU* 3.7 8.8 + - - +
140A MSE 3.3 0.2 - - - -
141A LYS* 1.3 79.8 - - - +
143A GLU* 1.3 94.6 + - - +
145A THR* 4.1 6.4 - - - +
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Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LYS* 5.4 2.1 + - - -
139A GLU* 3.0 44.3 + - - +
140A MSE 4.7 2.1 + - - +
142A ARG* 1.3 107.6 + - - +
144A SER* 1.3 66.3 + - - +
145A THR* 3.3 6.6 + - - +
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Residues in contact with SER 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 4.7 13.2 - - - +
89A LEU* 3.7 21.8 - - - +
140A MSE 2.9 23.1 + - - +
143A GLU* 1.3 80.3 + - - +
145A THR* 1.3 62.6 + - - +
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Residues in contact with THR 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 3.9 10.7 - - - +
90A LYS* 3.4 61.5 + - + +
93A LEU* 4.4 0.3 - - - +
141A LYS* 2.9 42.7 + - + +
142A ARG 4.1 7.6 - - - +
143A GLU 3.3 3.2 + - - +
144A SER* 1.3 82.5 + - - +
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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