Contacts of the helix formed by residues 0 - 21 (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 SER 0 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 1.3 63.8 + - - +
2A THR* 3.3 14.3 + - - -
3A ASP* 2.9 59.2 + - - +
4A CYS* 3.5 12.0 + - - -
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Residues in contact with MET 1 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A SER* 1.3 73.6 - - - +
2A THR* 1.3 58.2 + - - +
4A CYS* 3.4 7.4 + - - +
5A GLU* 2.9 47.3 + - - +
135A ARG* 4.0 10.8 - - - +
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Residues in contact with THR 2 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A SER* 3.2 10.9 + - - -
1A MET* 1.3 76.3 - - - +
3A ASP* 1.3 56.2 + - - +
5A GLU* 3.7 7.6 + - - -
6A PHE* 2.7 35.9 + - + +
127A MET* 3.9 31.6 - - + -
128A ASN* 5.8 1.3 - - - +
135A ARG* 4.7 11.3 + - - +
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Residues in contact with ASP 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A SER* 2.9 38.5 + - - +
2A THR* 1.3 76.3 - - - +
4A CYS* 1.3 60.2 + - - +
6A PHE* 3.3 7.7 + - - +
7A GLY* 3.1 23.6 + - - -
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Residues in contact with CYS 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A SER 3.5 10.2 + - - +
1A MET* 3.4 8.6 + - - +
2A THR 3.3 0.4 - - - -
3A ASP* 1.3 76.9 - - - +
5A GLU* 1.3 64.1 + - + +
7A GLY* 3.4 2.2 + - - -
8A TYR* 3.1 24.3 + - - +
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Residues in contact with GLU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 2.9 30.7 + - + +
2A THR* 3.8 3.4 - - - +
4A CYS* 1.3 76.8 - - + +
6A PHE* 1.3 61.8 + - - +
8A TYR* 3.4 8.1 + - - +
9A ILE* 3.2 28.1 + - + +
127A MET* 3.8 26.2 - - + +
131A GLY 4.6 0.5 - - - +
135A ARG* 2.9 56.3 + - - +
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Residues in contact with PHE 6 (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* 2.7 22.0 + - + +
3A ASP* 3.6 7.9 - - - +
4A CYS 3.3 0.2 - - - -
5A GLU* 1.3 73.2 - - - +
7A GLY* 1.3 60.9 + - - +
9A ILE* 3.3 5.7 + - - +
10A TYR* 2.9 35.7 + + + +
120A TYR* 3.4 50.3 - + - -
123A ALA* 3.6 21.5 - - + -
124A GLU* 3.5 34.1 - - + -
127A MET* 3.7 20.1 - - + -
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Residues in contact with GLY 7 (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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3A ASP 3.1 13.8 + - - -
4A CYS* 3.4 3.3 + - - -
5A GLU 3.4 0.2 - - - -
6A PHE* 1.3 75.5 - - - +
8A TYR* 1.3 63.8 + - - +
10A TYR* 3.6 10.7 - - - +
11A ARG* 3.0 26.2 + - - +
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Residues in contact with TYR 8 (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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4A CYS 3.1 16.8 + - - +
5A GLU* 3.6 8.7 - - - +
6A PHE 3.3 0.2 - - - -
7A GLY* 1.3 74.2 - - - +
9A ILE* 1.3 59.8 + - + +
11A ARG* 3.3 8.1 + - - +
12A LEU* 3.0 41.8 + - + +
31A SER* 5.5 0.8 + - - -
33A THR* 3.4 19.1 - - + +
140A TRP* 3.5 38.6 - + + +
141A GLU* 2.6 37.4 + - + -
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Residues in contact with ILE 9 (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* 3.2 17.6 + - + +
6A PHE 3.3 6.3 + - - +
8A TYR* 1.3 74.0 - - + +
10A TYR* 1.3 61.4 + - - +
12A LEU* 3.3 9.7 + - - +
13A ALA* 2.9 26.8 + - + +
93A PHE* 4.8 4.3 - - + -
123A ALA* 3.7 23.6 - - + -
126A ILE* 3.8 40.8 - - + -
127A MET* 3.9 31.0 - - + -
131A GLY* 5.5 0.2 - - - -
134A ILE* 4.8 4.7 - - + -
140A TRP* 3.9 26.0 - - + +
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Residues in contact with TYR 10 (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* 2.9 26.2 + + + +
7A GLY* 3.6 11.0 - - - +
9A ILE* 1.3 75.9 - - - +
11A ARG* 1.3 64.2 + - + +
13A ALA* 3.3 2.0 + - - +
14A GLN* 2.9 45.1 + - + +
116A LYS* 3.2 39.7 + - - +
119A SER* 3.7 9.2 - - - -
120A TYR* 3.5 50.6 - + + -
123A ALA* 3.7 12.9 - - + +
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Residues in contact with ARG 11 (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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7A GLY 3.0 17.9 + - - +
8A TYR* 3.6 6.7 - - - +
10A TYR* 1.3 81.7 - - + +
12A LEU* 1.3 56.5 + - + +
14A GLN* 3.8 30.4 + - - +
15A ASP* 2.7 84.1 + - - +
18A GLN* 3.7 19.2 + - - +
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Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR* 3.0 31.2 + - + +
9A ILE* 3.4 9.9 - - - +
11A ARG* 1.3 77.2 - - + +
13A ALA* 1.3 55.9 + - - +
15A ASP* 3.5 5.2 + - - +
16A TYR* 3.0 28.4 + - - +
31A SER* 5.2 1.1 - - - +
33A THR* 4.3 9.0 - - + -
34A SER* 3.8 38.1 + - - +
37A LEU* 4.1 11.6 - - + +
38A GLN* 5.9 0.3 - - - +
93A PHE* 3.9 11.4 - - + -
140A TRP* 3.7 50.9 - - + -
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Residues in contact with ALA 13 (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 2.9 16.7 + - - +
10A TYR 3.7 4.7 - - - +
11A ARG 3.3 0.2 - - - -
12A LEU* 1.3 73.4 - - - +
14A GLN* 1.3 64.2 + - - +
17A LEU* 3.2 13.9 + - - +
93A PHE* 3.6 11.6 - - + -
96A GLU* 2.9 33.4 - - - +
119A SER* 3.2 32.1 + - - +
122A VAL* 4.4 7.6 - - + -
123A ALA* 4.9 1.3 - - - +
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Residues in contact with GLN 14 (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* 2.9 38.7 + - + +
11A ARG* 3.7 25.3 + - - +
13A ALA* 1.3 73.0 - - - +
15A ASP* 1.3 66.6 + - - +
17A LEU* 3.2 11.2 + - - +
18A GLN* 3.0 42.7 + - - +
115A TYR 3.6 13.5 + - - -
116A LYS* 3.0 39.2 - - - +
119A SER* 3.1 31.6 + - - +
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Residues in contact with ASP 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ARG* 2.7 59.6 + - - +
12A LEU 3.6 2.7 - - - +
14A GLN* 1.3 73.0 - - - +
16A TYR* 1.3 63.0 + - - +
18A GLN* 3.3 10.6 + - - +
19A CYS* 2.9 23.9 + - - +
31A SER* 5.0 4.0 + - - -
34A SER* 2.5 35.9 + - - +
38A GLN* 3.5 11.6 + - + +
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Residues in contact with TYR 16 (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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12A LEU 3.0 17.7 + - - +
14A GLN 3.2 0.4 - - - -
15A ASP* 1.3 77.3 - - - +
17A LEU* 1.3 58.3 + - - +
19A CYS* 3.2 10.7 + - - +
20A VAL* 2.9 51.5 + - + +
37A LEU* 5.1 3.4 - - + -
38A GLN* 4.0 35.4 - - + +
41A ALA* 3.3 35.1 + - + -
42A PHE* 3.3 11.6 + - + +
45A GLN* 2.7 22.5 + - - +
93A PHE* 3.1 42.2 - - + -
96A GLU* 3.6 18.6 - - + +
97A GLY* 4.0 2.9 - - - -
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Residues in contact with LEU 17 (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 3.2 11.0 + - - +
14A GLN* 3.5 10.8 - - - +
16A TYR* 1.3 81.0 - - - +
18A GLN* 1.3 60.8 + - + +
20A VAL* 3.3 6.3 + - - +
21A LEU* 3.0 47.5 + - + +
23A ILE* 5.4 2.9 - - + -
96A GLU* 3.7 22.4 - - - +
97A GLY* 5.9 0.7 - - - -
100A ILE* 3.7 36.6 - - + -
112A VAL* 5.8 0.4 - - + -
115A TYR* 3.7 35.0 - - + +
118A ILE* 4.0 12.6 - - + -
119A SER* 3.9 11.0 - - - +
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Residues in contact with GLN 18 (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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11A ARG* 3.7 21.9 + - - +
14A GLN* 3.0 39.2 + - - +
15A ASP* 3.7 10.3 - - - +
16A TYR 3.3 0.2 - - - -
17A LEU* 1.3 76.7 - - + +
19A CYS* 1.3 57.2 + - - +
22A GLN* 3.0 6.9 + - - -
23A ILE* 2.8 68.1 + - + +
24A PRO 6.2 0.2 - - - -
116A LYS* 5.5 3.4 - - - +
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Residues in contact with CYS 19 (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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15A ASP 2.9 14.5 + - - +
16A TYR* 3.3 15.5 - - - +
18A GLN* 1.3 75.2 - - - +
20A VAL* 1.3 67.2 + - - +
22A GLN* 3.3 16.6 + - - +
38A GLN* 3.7 37.9 - - + +
42A PHE* 4.3 25.5 - - - -
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Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 2.9 55.6 + - + +
17A LEU* 3.3 7.6 + - - +
19A CYS* 1.3 78.0 - - - +
21A LEU* 1.3 61.6 + - + +
22A GLN* 3.5 10.6 + - - +
42A PHE* 5.0 13.1 - - + -
45A GLN* 3.7 11.0 - - - +
97A GLY* 3.9 22.9 - - - +
100A ILE* 4.1 7.9 - - + -
101A LYS* 4.0 23.1 - - + +
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Residues in contact with LEU 21 (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* 3.0 35.0 + - + +
20A VAL* 1.3 77.8 - - + +
22A GLN* 1.3 73.3 + - - +
23A ILE* 3.7 31.3 - - + +
100A ILE* 4.0 20.0 - - + +
101A LYS* 5.0 5.4 - - + -
104A LEU* 3.5 42.0 - - + -
112A VAL* 4.5 2.2 - - + -
115A TYR* 4.0 8.3 - - + -
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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) + - + + + + + -
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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