Contacts of the helix formed by residues 340 - 345 (chain A) in PDB entry 2VWK
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 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A LEU 4.0 7.6 - - - -
4A ASP* 3.3 33.4 + - - -
5A THR 5.2 0.2 - - - -
121A LEU* 4.4 5.7 - - - +
128A PRO* 3.8 11.9 - - - +
339A GLN* 1.3 79.3 + - - +
341A LEU* 1.3 60.9 + - - +
342A TRP* 3.5 8.3 + - - +
343A ASP* 2.6 36.3 + - - +
344A VAL* 3.0 22.0 + - - +
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Residues in contact with LEU 341 (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 LEU 4.5 4.8 + - - -
129A MET* 4.3 13.4 - - + +
256A ILE* 3.5 30.5 - - + -
258A PHE* 4.1 20.2 - - + -
327A PHE* 3.6 32.8 - - + -
330A GLU* 3.7 16.6 - - + +
331A ALA* 3.6 33.7 - - + +
334A SER* 3.7 18.7 + - - +
339A GLN 3.7 1.0 + - - -
340A SER* 1.3 68.7 - - - +
342A TRP* 1.3 65.3 + - - +
344A VAL* 4.3 0.9 - - - -
345A SER* 2.9 28.2 + - - +
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Residues in contact with TRP 342 (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 ASP* 4.3 8.5 - - - +
242A GLN* 4.6 16.4 - - + -
249A ALA* 3.8 32.8 - - + -
250A VAL 3.0 30.5 + - - -
251A GLU* 3.4 40.4 - - + +
255A ARG 5.9 0.7 - - - -
256A ILE* 4.5 12.2 - - + +
257A HIS* 3.6 21.8 - - + -
340A SER* 3.5 8.0 + - - +
341A LEU* 1.3 81.7 - - - +
343A ASP* 1.3 85.4 + - - +
345A SER* 3.1 7.6 + - - -
346A ARG* 3.0 49.7 + - + +
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Residues in contact with ASP 343 (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 ASP* 4.7 2.1 - - - +
118A LYS* 2.8 32.7 + - - +
339A GLN* 4.6 5.6 - - + +
340A SER* 2.6 30.7 + - - +
342A TRP* 1.3 97.6 - - - +
344A VAL* 1.3 62.6 + - - +
346A ARG* 3.0 15.2 + - - +
347A SER* 3.1 13.5 + - - -
355A TRP* 3.7 23.4 - - + -
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Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLU* 3.5 20.5 - - + +
333A LEU* 3.7 7.2 - - + -
334A SER* 3.6 40.6 - - - +
337A VAL* 4.2 9.9 - - + -
339A GLN* 3.7 18.8 - - + +
340A SER 3.0 16.6 + - - +
341A LEU 4.1 0.7 - - - +
343A ASP* 1.3 78.8 - - - +
345A SER* 1.3 61.1 + - - +
346A ARG 3.3 1.0 + - - -
347A SER* 3.4 11.2 + - - +
352A LEU* 3.5 34.8 - - + +
355A TRP* 4.4 2.2 - - + -
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Residues in contact with SER 345 (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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258A PHE* 4.0 22.4 - - - -
259A ASP 5.2 2.2 + - - +
262A PRO* 3.8 18.0 - - - +
263A VAL* 3.9 12.4 + - - +
266A ARG* 6.0 1.2 - - - -
330A GLU* 3.5 29.1 - - - -
341A LEU* 2.9 22.2 + - - +
342A TRP* 3.1 9.9 + - - -
344A VAL* 1.3 76.3 - - - +
346A ARG* 1.3 71.6 + - - +
347A SER 3.5 1.8 - - - +
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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