Contacts of the helix formed by residues 15 - 22 (chain A) in PDB entry 1VPW
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 THR 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ILE* 3.5 36.8 - - + +
5A LYS* 3.6 20.9 - - + -
8A ALA* 3.4 23.2 - - + +
14A SER* 1.3 72.1 - - - +
16A THR* 1.3 59.0 + - - +
18A VAL* 2.9 8.1 + - - +
19A SER* 2.6 36.5 + - - -
704B A 5.0 4.3 + - - -
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Residues in contact with THR 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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14A SER* 3.3 11.8 + - - -
15A THR* 1.3 81.4 + - - +
17A THR* 1.3 65.3 + - - +
19A SER* 3.2 8.3 + - - -
20A HIS* 2.9 42.7 + - + +
702B G 4.4 14.4 - - + +
703B C 3.1 40.4 + - - +
704B A 3.3 15.4 + - - +
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Residues in contact with THR 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 VAL* 3.8 15.9 - - + +
14A SER* 2.8 16.8 + - - -
16A THR* 1.3 74.7 - - - +
18A VAL* 1.3 58.6 + - - +
20A HIS* 2.6 32.0 + - - +
21A VAL* 3.0 25.6 + - + +
26A ARG* 5.1 4.1 + - - +
28A VAL* 4.6 6.3 - - + -
32A THR* 4.0 22.0 - - + -
36A VAL* 4.2 2.2 - - + -
701B C 3.6 15.1 - - - +
702B G 2.6 24.8 + - - -
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Residues in contact with VAL 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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4A ILE* 3.7 20.4 - - + -
7A VAL* 4.4 15.7 - - + -
8A ALA* 3.5 32.3 - - + +
13A VAL* 3.7 8.5 - - + -
14A SER 3.3 13.5 - - - +
15A THR* 2.9 8.7 + - - +
17A THR* 1.3 78.3 - - - +
19A SER* 1.3 65.5 + - - +
21A VAL* 3.2 2.6 + - - +
22A ILE* 2.9 35.8 + - + +
36A VAL* 3.9 24.5 - - + -
40A ILE* 5.0 0.2 - - + -
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Residues in contact with SER 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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4A ILE* 4.2 15.4 - - - +
15A THR 2.6 15.9 + - - -
16A THR* 3.5 11.6 + - - -
18A VAL* 1.3 73.8 - - - +
20A HIS* 1.3 67.2 + - - +
22A ILE* 3.0 4.5 + - - -
23A ASN* 2.7 38.8 + - - +
25A THR* 4.9 3.5 - - - +
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Residues in contact with HIS 20 (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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16A THR* 2.9 36.2 + - + +
17A THR* 2.6 15.0 + - - +
19A SER* 1.3 75.3 - - - +
21A VAL* 1.3 56.0 + - - +
24A LYS* 2.7 25.6 + - - -
25A THR* 2.7 42.3 + - + +
26A ARG* 3.1 68.5 + - + +
28A VAL* 4.3 11.2 - - + -
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Residues in contact with VAL 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 THR* 3.0 31.4 + - + +
18A VAL* 3.7 7.0 - - - +
20A HIS* 1.3 73.2 - - - +
22A ILE* 1.3 68.7 + - - +
24A LYS* 3.6 16.7 + - - +
28A VAL* 4.1 21.5 - - + -
33A ARG* 4.5 13.9 - - + +
36A VAL* 3.3 34.1 - - + -
37A TRP* 3.9 27.1 + - + +
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Residues in contact with ILE 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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4A ILE* 5.6 1.8 - - + -
18A VAL* 2.9 24.7 + - + +
19A SER* 4.4 2.2 - - - -
21A VAL* 1.3 81.0 - - + +
23A ASN* 1.3 79.2 + - - +
24A LYS* 3.5 4.7 - - - +
37A TRP* 4.3 16.5 - - + -
40A ILE* 3.2 35.7 - - + -
45A TYR* 3.5 24.2 - - + -
47A PRO* 4.2 18.4 - - + -
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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