Contacts of the helix formed by residues 115 - 137 (chain A) in PDB entry 2VM6
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 TYR 115 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLN* 3.6 10.1 + - - -
17A LEU* 3.7 17.5 - - + +
21A LEU* 4.0 4.7 - - + -
64A VAL* 4.9 0.4 - - + -
100A ILE* 3.4 24.5 - - + -
103A LEU* 3.5 27.1 - - + -
104A LEU* 2.9 41.9 - - + +
107A GLN* 2.6 25.2 + - - -
110A PRO* 5.1 0.9 - - - +
111A ASP 2.9 19.0 + - - -
112A VAL* 2.9 42.3 + - + +
113A ASP 2.8 1.4 + - - -
114A THR* 1.3 80.4 - - - +
116A LYS* 1.3 65.4 + - - +
117A GLU 2.9 0.8 + - - -
118A ILE* 3.5 9.7 + - + +
119A SER* 3.4 15.9 + - - -
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Residues in contact with LYS 116 (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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10A TYR* 3.2 20.3 - - - +
11A ARG* 6.2 0.2 - - - +
14A GLN* 3.0 32.8 - - - +
18A GLN* 5.5 3.1 - - - +
112A VAL 4.4 0.9 + - - +
113A ASP* 2.6 47.0 + - - +
114A THR* 4.5 1.6 - - - -
115A TYR* 1.3 75.3 - - - +
117A GLU* 1.3 60.2 + - + +
119A SER* 3.2 5.2 + - - -
120A TYR* 2.9 28.6 + - - +
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Residues in contact with GLU 117 (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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64A VAL* 3.4 31.1 - - + +
68A ARG* 4.6 12.6 + - - +
114A THR* 3.1 33.4 + - - +
115A TYR 2.9 1.0 - - - -
116A LYS* 1.3 78.5 - - + +
118A ILE* 1.3 62.7 + - - +
120A TYR* 3.4 8.6 + - - +
121A PHE* 3.1 28.1 + - - +
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Residues in contact with ILE 118 (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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17A LEU* 4.0 7.4 - - + -
64A VAL* 4.7 12.6 - - + -
67A ALA* 4.8 7.6 - - + -
96A GLU* 4.0 30.5 - - + +
99A LEU* 4.8 6.5 - - + +
100A ILE* 3.5 41.5 - - + +
103A LEU* 4.0 15.5 - - + -
115A TYR* 3.5 11.3 + - + +
116A LYS 3.3 0.2 - - - -
117A GLU* 1.3 73.9 - - - +
119A SER* 1.3 68.6 + - - +
120A TYR 3.2 0.2 + - - -
121A PHE* 3.3 32.2 + - + -
122A VAL* 3.0 27.3 + - + +
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Residues in contact with SER 119 (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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10A TYR* 3.7 11.7 - - - -
13A ALA* 3.2 30.0 + - - +
14A GLN* 3.1 36.9 + - - -
17A LEU* 3.9 6.8 - - - +
96A GLU* 4.0 3.4 - - - -
115A TYR 3.4 4.2 + - - -
116A LYS 3.2 9.8 + - - -
118A ILE* 1.3 79.9 - - - +
120A TYR* 1.3 56.4 + - - +
122A VAL* 3.4 2.3 + - - +
123A ALA* 2.9 29.5 + - - +
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Residues in contact with TYR 120 (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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6A PHE* 3.4 32.0 - + - -
10A TYR* 3.5 18.6 - + + -
116A LYS 2.9 14.1 + - - +
117A GLU* 3.5 12.6 - - - +
119A SER* 1.3 74.5 - - - +
121A PHE* 1.3 61.1 + - + +
123A ALA* 3.3 2.8 + - - +
124A GLU* 3.0 62.6 + - + +
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Residues in contact with PHE 121 (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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64A VAL* 3.9 9.9 - - + -
67A ALA* 3.9 7.6 - - + -
68A ARG* 3.6 64.4 - - + +
71A PHE* 3.4 46.1 - + + -
72A ASN* 5.2 3.1 - - - +
99A LEU* 4.6 2.5 - - + -
117A GLU 3.1 21.7 + - - +
118A ILE* 3.3 37.4 + - + -
120A TYR* 1.3 76.7 - - + +
122A VAL* 1.3 72.3 + - + +
124A GLU* 3.7 17.1 - - - +
125A PHE* 3.1 17.7 + - - +
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Residues in contact with VAL 122 (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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13A ALA* 4.4 8.7 - - + -
71A PHE* 3.8 20.4 - - + -
92A ILE* 3.7 15.5 - - + -
93A PHE* 4.9 2.5 - - + -
96A GLU* 3.6 40.2 - - + +
118A ILE* 3.0 22.1 + - + +
119A SER* 3.7 4.0 - - - +
121A PHE* 1.3 82.9 - - + +
123A ALA* 1.3 64.8 - - - +
125A PHE* 3.2 3.1 + - - +
126A ILE* 3.0 43.3 + - + +
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Residues in contact with ALA 123 (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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6A PHE* 3.6 19.5 - - + -
9A ILE* 3.7 15.3 - - + +
10A TYR* 3.7 33.9 - - + +
13A ALA* 4.9 0.4 - - + +
119A SER 2.9 17.8 + - - +
120A TYR 3.3 2.2 + - - +
122A VAL* 1.3 76.6 - - - +
124A GLU* 1.3 57.5 + - - +
126A ILE* 3.9 0.5 - - - +
127A MET* 2.9 33.8 + - - +
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Residues in contact with GLU 124 (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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6A PHE* 3.5 13.9 - - + -
68A ARG* 5.7 1.0 + - - -
120A TYR* 3.0 47.7 + - + +
121A PHE* 3.7 17.9 - - + +
122A VAL 3.3 0.2 - - - -
123A ALA* 1.3 77.4 - - - +
125A PHE* 1.3 63.1 + - - +
127A MET* 4.6 0.9 - - - -
128A ASN* 3.0 44.6 + - - +
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Residues in contact with PHE 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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71A PHE* 3.6 24.0 - + + -
72A ASN* 5.2 8.1 - - - +
75A MET* 3.4 54.1 - - + -
76A GLU* 4.9 1.3 - - - -
79A PHE* 3.9 22.0 - + + -
92A ILE* 4.0 19.1 - - + -
121A PHE 3.1 6.7 + - - +
122A VAL 3.2 2.4 + - - +
124A GLU* 1.3 80.3 - - - +
126A ILE* 1.3 60.0 + - + +
129A ASN* 2.9 70.7 + - + +
130A THR* 4.6 5.6 - - + -
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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
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9A ILE* 3.8 30.7 - - + -
89A ILE* 5.0 3.6 - - + -
92A ILE* 3.8 30.3 - - + -
93A PHE* 3.5 36.8 - - + -
122A VAL* 3.0 35.4 + - + +
125A PHE* 1.3 77.6 - - - +
127A MET* 1.3 55.0 + - - +
130A THR* 2.6 47.8 + - - +
131A GLY 3.0 4.7 + - - -
134A ILE* 3.9 11.4 - - + -
140A TRP* 4.4 5.2 - - + -
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Residues in contact with MET 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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2A THR* 3.9 26.9 - - + -
5A GLU* 3.8 30.7 - - + +
6A PHE* 3.7 42.4 - - + -
9A ILE* 3.9 13.7 - - + -
123A ALA 2.9 18.9 + - - +
124A GLU* 4.0 2.7 - - - +
126A ILE* 1.3 78.4 - - - +
128A ASN* 1.3 66.3 + - - +
131A GLY* 3.2 36.4 + - - +
132A GLU 4.7 0.3 + - - -
135A ARG* 5.5 3.1 - - - +
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Residues in contact with ASN 128 (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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2A THR* 5.8 1.2 - - - +
124A GLU* 3.0 34.9 + - - +
127A MET* 1.3 86.2 - - - +
129A ASN* 1.3 71.3 + - - +
131A GLY 4.8 0.2 - - - -
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Residues in contact with ASN 129 (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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84A ILE* 3.5 16.6 - - - +
125A PHE* 2.9 60.0 + - + +
128A ASN* 1.3 93.3 - - - +
130A THR* 1.3 59.4 - - + +
131A GLY 3.7 0.4 - - - -
132A GLU 5.5 0.2 - - - -
133A TRP 5.6 0.2 + - - -
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Residues in contact with THR 130 (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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79A PHE* 4.6 12.3 - - + -
84A ILE* 3.9 35.2 - - + -
89A ILE* 4.1 15.0 - - + +
92A ILE* 4.6 3.6 - - + -
125A PHE* 4.6 16.4 - - + -
126A ILE* 2.6 41.1 + - - +
129A ASN* 1.3 78.2 - - + +
131A GLY* 1.3 59.1 + - - +
132A GLU 3.3 2.7 - - - -
133A TRP* 3.1 5.4 + - - +
134A ILE* 2.9 33.2 + - - +
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Residues in contact with GLY 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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5A GLU* 4.6 1.4 - - - +
9A ILE* 5.5 0.4 - - - -
126A ILE 3.0 8.7 + - - -
127A MET* 3.2 35.3 + - - -
128A ASN 4.8 0.2 - - - -
129A ASN 3.7 0.8 - - - -
130A THR* 1.3 77.0 - - - +
132A GLU* 1.3 61.3 + - - +
134A ILE* 3.4 11.6 + - - +
135A ARG* 3.2 31.0 + - - +
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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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127A MET 4.7 0.4 + - - -
129A ASN 5.5 0.6 - - - -
130A THR 3.3 0.4 - - - -
131A GLY* 1.3 74.3 - - - +
133A TRP* 1.3 66.2 + - - +
135A ARG* 3.0 38.9 + - - +
136A GLN* 3.1 46.9 + - + +
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Residues in contact with TRP 133 (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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84A ILE* 3.4 64.8 + - + -
85A ASN* 3.7 5.2 - - + -
86A TRP* 3.6 52.0 - + - -
89A ILE* 3.7 21.3 - - + -
129A ASN 5.6 0.2 + - - -
130A THR 3.1 8.6 + - - +
132A GLU* 1.3 77.3 - - - +
134A ILE* 1.3 68.7 + - - +
136A GLN* 3.0 4.6 + - - +
137A ASN* 2.9 64.2 + - + +
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Residues in contact with ILE 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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9A ILE* 4.8 3.6 - - + -
86A TRP* 3.8 20.8 - - + -
89A ILE* 4.0 15.5 - - + -
126A ILE* 3.9 9.6 - - + -
130A THR* 2.9 37.1 + - - +
131A GLY* 3.6 12.6 - - - +
132A GLU 3.3 0.2 - - - -
133A TRP* 1.3 78.3 - - - +
135A ARG* 1.3 60.9 + - + +
137A ASN 3.2 7.8 + - - -
138A GLY 3.4 0.5 + - - -
139A GLY* 2.9 42.4 + - - -
140A TRP* 3.9 40.2 - - + +
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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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1A MET* 4.0 13.7 - - - +
2A THR* 4.7 12.1 + - - +
5A GLU* 2.9 41.5 + - - +
127A MET* 5.5 3.0 - - - +
131A GLY 3.2 14.4 + - - +
132A GLU* 3.0 37.3 + - - +
133A TRP 3.2 0.2 - - - -
134A ILE* 1.3 74.8 - - + +
136A GLN* 1.3 60.6 + - + +
137A ASN 3.1 5.9 + - - -
138A GLY* 4.0 5.4 + - - -
139A GLY* 4.7 4.7 + - - +
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Residues in contact with GLN 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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132A GLU* 3.1 38.9 + - - +
133A TRP* 3.0 7.9 + - - +
135A ARG* 1.3 77.7 - - + +
137A ASN* 1.3 68.9 + - - +
138A GLY 3.7 1.6 + - - -
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Residues in contact with ASN 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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86A TRP* 3.5 18.7 + - + +
133A TRP* 2.9 78.8 + - + +
134A ILE 3.5 1.8 - - - +
135A ARG 3.1 1.0 - - - -
136A GLN* 1.3 90.1 + - - +
138A GLY* 1.3 58.0 + - - +
139A GLY 3.5 2.6 + - - -
143A GLY* 3.5 6.9 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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