Contacts of the helix formed by residues 728 - 735 (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 ASP 728 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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703A VAL* 3.0 15.2 + - + +
704A LEU 3.5 22.8 - - - +
705A LYS* 3.4 15.4 - - - +
706A GLY 4.4 3.5 + - - -
710A ILE* 3.4 40.9 - - - +
711A GLY 4.4 0.4 + - - -
727A TYR* 1.3 70.0 - - - +
729A ALA* 1.3 64.6 + - - +
730A GLU* 3.3 10.2 + - - +
731A TYR* 3.0 29.3 + - + +
732A TYR* 3.3 15.4 + - - -
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Residues in contact with ALA 729 (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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650A LEU* 3.2 32.9 - - + +
651A SER* 4.0 10.8 - - - +
653A TYR* 4.5 12.0 + - + +
727A TYR* 3.2 19.1 + - + -
728A ASP* 1.3 71.3 + - - +
730A GLU* 1.3 57.3 + - - +
732A TYR* 3.0 6.2 + - - +
733A ILE* 2.9 35.2 + - + +
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Residues in contact with GLU 730 (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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651A SER* 5.5 0.2 + - - -
710A ILE* 3.8 17.7 - - + -
728A ASP* 3.3 10.4 + - - +
729A ALA* 1.3 78.4 - - - +
731A TYR* 1.3 56.7 + - - +
733A ILE* 4.4 4.3 - - - +
734A GLU* 2.9 38.3 + - - +
756A ARG* 2.7 46.6 + - - -
761A ARG* 3.5 11.3 - - - +
763A VAL* 3.2 42.9 - - + +
769A LEU* 4.1 12.3 - - + +
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Residues in contact with TYR 731 (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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614A ASP* 4.2 10.6 + - - -
662A ILE* 3.6 27.3 - - + +
678A PRO* 4.6 15.2 - - + +
701A TYR* 5.0 0.7 + - - -
703A VAL* 3.7 30.5 - - + -
710A ILE* 3.8 14.5 - - + +
711A GLY* 3.7 26.2 - - - -
728A ASP* 3.0 15.0 + - - +
730A GLU* 1.3 75.8 - - - +
732A TYR* 1.3 66.8 + + - +
735A ASN* 2.9 78.4 + - + +
736A GLN* 3.4 2.8 + - + -
769A LEU* 4.2 15.9 - - + -
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Residues in contact with TYR 732 (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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616A SER* 4.7 2.0 - - - -
618A ILE* 4.1 7.2 - - + -
650A LEU* 3.9 24.2 - - + -
660A LEU* 2.6 59.2 + - + -
662A ILE* 4.1 19.8 - - + +
702A ILE* 3.4 3.8 - - - +
703A VAL* 3.0 52.3 + - + +
727A TYR* 4.3 13.7 - + + -
728A ASP 3.3 15.5 + - - -
729A ALA 3.0 8.0 + - - +
731A TYR* 1.3 77.6 - + - +
733A ILE* 1.3 53.6 + - - +
736A GLN* 3.3 17.7 - - + +
737A VAL* 2.8 35.5 + - - +
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Residues in contact with ILE 733 (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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647A THR* 3.4 44.6 - - + +
650A LEU* 3.7 24.0 - - + -
651A SER* 4.0 14.8 - - - +
729A ALA* 2.9 24.6 + - + +
730A GLU* 3.9 5.8 - - - +
732A TYR* 1.3 77.2 - - - +
734A GLU* 1.3 59.3 + - - +
737A VAL* 4.5 3.1 - - - -
738A LEU* 2.9 46.6 + - + +
756A ARG* 3.6 37.5 - - - +
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Residues in contact with GLU 734 (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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730A GLU* 2.9 38.6 + - + +
733A ILE* 1.3 72.2 - - - +
735A ASN* 1.3 61.1 + - - +
738A LEU* 3.4 24.2 - - - +
739A PRO* 3.2 19.2 - - - +
752A LYS* 5.9 1.4 - - - +
756A ARG* 2.6 28.5 + - - +
763A VAL 4.8 1.7 - - - +
766A GLY* 3.4 30.1 + - - +
769A LEU* 3.8 26.4 - - + +
770A LYS* 3.8 7.4 - - - +
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Residues in contact with ASN 735 (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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612A ARG* 2.8 44.3 + - - +
614A ASP* 5.0 0.8 + - - -
731A TYR* 2.9 61.0 + - + +
734A GLU* 1.3 80.7 - - - +
736A GLN* 1.3 63.5 + - - +
739A PRO* 3.3 10.9 - - - +
769A LEU* 3.2 23.6 + - + +
770A LYS 4.7 0.4 - - - -
771A PRO* 3.9 11.3 - - - +
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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
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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