Contacts of the helix formed by residues 8 - 25 (chain A) in PDB entry 2VMO
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 ASP 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LEU* 2.8 36.9 + - + +
7A GLN* 1.3 82.8 + - + +
9A PRO* 1.3 67.4 - - - +
10A GLN* 3.6 10.6 + - - +
11A VAL* 3.0 41.0 + - + +
12A PHE* 2.9 18.4 + - - +
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Residues in contact with PRO 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 PRO 3.8 16.3 - - - +
6A GLN 3.9 8.3 - - - +
7A GLN 3.7 6.3 - - - +
8A ASP* 1.3 87.3 - - - +
10A GLN* 1.3 59.2 + - + +
12A PHE* 3.8 4.2 - - + +
13A ALA* 2.9 33.4 + - - +
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Residues in contact with GLN 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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8A ASP* 3.2 8.4 + - - +
9A PRO* 1.3 82.7 - - + +
11A VAL* 1.3 64.3 + - + +
13A ALA* 3.5 4.9 + - - +
14A ALA* 3.2 21.7 + - - +
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Residues in contact with VAL 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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4A LEU* 4.4 11.0 - - + -
8A ASP* 3.0 35.6 + - + +
10A GLN* 1.3 76.8 - - + +
12A PHE* 1.3 65.5 + - - +
14A ALA* 3.2 7.0 + - - +
15A ILE* 3.0 43.1 + - + +
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Residues in contact with PHE 12 (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* 3.9 33.4 - - + -
4A LEU* 4.2 8.9 - - + +
5A PRO* 3.7 49.1 - - + -
8A ASP 2.9 17.4 + - - +
9A PRO* 3.8 4.3 - - + +
11A VAL* 1.3 77.1 - - - +
13A ALA* 1.3 65.7 + - + +
15A ILE* 3.2 5.9 + - + +
16A GLU* 2.9 59.7 + - + +
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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 PRO 2.9 21.6 + - - +
10A GLN* 3.8 5.4 - - - +
11A VAL 3.4 0.2 - - - -
12A PHE* 1.3 76.2 - - - +
14A ALA* 1.3 57.1 + - - +
16A GLU* 3.4 6.2 + - - +
17A GLN* 3.0 37.1 + - + +
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Residues in contact with ALA 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 GLN 3.2 11.2 + - - +
11A VAL* 3.7 9.2 - - - +
13A ALA* 1.3 75.6 - - - +
15A ILE* 1.3 61.1 + - + +
17A GLN* 3.3 19.9 + - - +
18A GLU* 3.0 27.0 + - - +
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Residues in contact with ILE 15 (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 24.2 - - + -
4A LEU* 3.7 28.9 - - + -
11A VAL* 3.0 30.0 + - + +
12A PHE* 3.7 4.9 - - + +
14A ALA* 1.3 75.8 - - + +
16A GLU* 1.3 65.9 + - + +
18A GLU* 3.2 8.7 + - + +
19A ARG* 2.8 29.9 + - + +
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Residues in contact with GLU 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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1A MET* 5.6 2.1 - - - +
12A PHE* 2.9 59.9 + - + +
13A ALA* 3.7 6.5 - - - +
15A ILE* 1.3 78.8 - - - +
17A GLN* 1.3 64.2 + - - +
19A ARG* 2.8 47.2 + - - +
20A LYS* 3.0 45.3 + - - +
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Residues in contact with GLN 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* 3.0 18.0 + - - +
14A ALA* 3.3 27.4 + - - +
16A GLU* 1.3 76.6 - - - +
18A GLU* 1.3 56.6 + - - +
20A LYS* 3.3 7.7 + - - +
21A ARG* 2.9 30.1 + - - +
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Residues in contact with GLU 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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14A ALA 3.0 12.6 + - - +
15A ILE* 3.2 12.3 + - + +
17A GLN* 1.3 73.7 - - - +
19A ARG* 1.3 61.6 + - - +
21A ARG* 2.8 41.4 + - - +
22A GLN* 2.8 54.8 + - - +
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Residues in contact with ARG 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 ILE* 2.8 18.6 + - + +
16A GLU* 2.8 44.1 + - - +
17A GLN 3.3 0.2 - - - -
18A GLU* 1.3 76.9 - - - +
20A LYS* 1.3 84.7 + - - +
22A GLN* 3.4 11.9 + - - +
23A HIS* 3.3 19.1 + - - +
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Residues in contact with LYS 20 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLU* 3.0 31.5 + - - +
17A GLN* 3.8 5.8 - - - +
19A ARG* 1.3 98.6 - - - +
21A ARG* 1.3 59.7 - - - +
23A HIS* 3.2 9.1 + - - +
24A ALA* 3.0 29.8 + - - +
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Residues in contact with ARG 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 GLN 2.9 17.7 + - - +
18A GLU* 2.8 43.1 + - - +
19A ARG 3.3 0.2 - - - -
20A LYS* 1.3 77.1 - - - +
22A GLN* 1.3 74.6 + - - +
24A ALA* 3.1 15.7 + - - +
25A LYS* 3.1 57.6 + - + +
27A GLU* 4.3 19.0 + - - -
32A GLU* 5.2 3.6 + - - -
337A THR* 4.5 8.7 + - - +
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Residues in contact with GLN 22 (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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18A GLU* 2.8 51.5 + - - +
19A ARG* 3.7 10.1 - - - +
20A LYS 3.4 0.2 - - - -
21A ARG* 1.3 87.8 - - - +
23A HIS* 1.3 60.0 + - - +
25A LYS* 4.1 4.7 - - - +
27A GLU* 5.7 1.0 - - - +
34A PHE* 3.8 44.1 - - + -
366A ARG* 3.4 13.2 + - - -
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Residues in contact with HIS 23 (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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19A ARG 3.3 9.8 + - - +
20A LYS* 3.2 11.3 + - - +
21A ARG 3.1 0.6 - - - -
22A GLN* 1.3 80.0 - - - +
24A ALA* 1.3 65.8 + - + +
366A ARG* 2.7 41.6 + - - +
404A THR* 3.2 29.5 + - - -
405A ASP* 4.2 18.2 + - + -
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Residues in contact with ALA 24 (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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20A LYS 3.0 18.3 + - - +
21A ARG* 3.1 5.8 + - - +
23A HIS* 1.3 85.9 - - + +
25A LYS* 1.3 66.8 + - + +
26A ILE 4.1 0.3 + - - -
400A VAL* 4.3 8.0 - - - +
401A ALA* 5.4 0.7 - - - -
404A THR* 3.0 26.3 + - - +
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Residues in contact with LYS 25 (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 ARG* 3.1 49.1 + - + +
22A GLN* 4.1 4.2 - - - +
24A ALA* 1.3 86.2 - - + +
26A ILE* 1.3 63.4 - - - +
27A GLU* 3.6 6.0 + - + +
332A ASP* 4.7 7.8 + - - -
335A GLY* 3.4 32.1 - - - +
337A THR* 4.0 14.8 - - - +
366A ARG* 3.3 23.0 + - - -
404A THR* 3.6 1.2 - - - +
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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
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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