Contacts of the helix formed by residues 735 - 740 (chain A) in PDB entry 2WSC
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 VAL 735 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599A PHE* 2.6 64.8 - - + +
602A LEU* 4.3 24.5 - - + -
603A PHE* 3.3 28.2 - - + -
693A LEU* 3.1 9.5 - - + +
731A ARG 2.8 11.4 - - - +
732A ALA* 4.5 1.8 - - - +
734A GLY* 1.3 64.2 - - - -
736A THR* 1.3 67.2 + - - +
737A HIS 3.1 0.2 - - - -
738A TYR* 3.8 4.4 - - - +
739A LEU* 2.7 33.5 + - + +
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Residues in contact with THR 736 (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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602A LEU* 6.1 0.7 - - - +
732A ALA 3.5 12.8 + - - -
734A GLY 2.4 7.7 + - - -
735A VAL* 1.3 79.8 - - - +
737A HIS* 1.3 56.3 + - - +
739A LEU* 3.3 10.9 + - - +
740A LEU* 3.0 25.7 + - - +
1762A CLA 4.8 10.9 - - - +
1785A CLA 3.6 32.9 - - + +
1796A CLA 3.1 45.3 - - + +
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Residues in contact with HIS 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A VAL* 4.1 22.6 - - + +
686A TRP* 4.9 0.4 - - - -
688A PHE* 4.1 18.0 - + - -
689A SER* 3.7 15.3 - - - +
733A VAL* 3.3 36.9 + - + +
734A GLY 2.6 13.8 + - - +
736A THR* 1.3 66.7 - - - +
738A TYR* 1.3 51.7 + - - +
739A LEU 2.8 8.6 + - - -
740A LEU* 2.9 17.0 + - + +
741A GLY* 2.5 35.7 + - - -
1796A CLA 3.0 65.2 + + - -
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Residues in contact with TYR 738 (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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603A PHE* 3.7 25.8 - + + -
606A TYR* 4.4 12.2 - + - -
686A TRP* 3.0 53.2 - + - -
689A SER* 3.1 22.1 + - - +
690A LEU* 3.2 23.8 - - + -
693A LEU* 3.1 22.4 - - + -
734A GLY 3.9 0.4 + - - -
735A VAL 3.5 14.5 - - - +
737A HIS* 1.3 75.8 - - - +
739A LEU* 1.3 57.5 + - + +
742A GLY* 3.2 7.7 + - - -
1811A CLA 4.4 4.5 - - - -
661B PHE* 3.7 16.7 - + - -
665B ILE* 4.8 3.6 - - + -
1786B CLA 4.1 37.5 - - + +
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Residues in contact with LEU 739 (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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405A PHE* 4.0 25.6 - - + -
602A LEU* 4.6 18.2 - - + -
603A PHE* 4.7 14.4 - - + -
605A MET* 5.8 1.8 - - + -
606A TYR* 3.4 36.6 - - + -
735A VAL* 2.7 41.5 + - + +
736A THR* 3.6 8.5 - - - +
737A HIS 2.8 4.2 + - - -
738A TYR* 1.3 76.6 - - + +
740A LEU* 1.3 57.6 + - - +
741A GLY 3.0 4.3 - - - -
743A ILE* 2.7 55.2 + - + +
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Residues in contact with LEU 740 (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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682A ALA* 4.3 3.5 - - - +
685A VAL* 3.9 10.9 - - + +
736A THR 3.0 11.3 + - - +
737A HIS* 2.9 54.4 + - + +
739A LEU* 1.3 75.8 - - - +
741A GLY* 1.3 62.5 + - - +
743A ILE* 4.8 3.8 - - - -
744A ALA* 3.9 17.6 + - - +
1785A CLA 3.9 35.2 - - + -
1796A CLA 3.3 33.7 - - + -
1807A BCR 4.1 30.5 - - + +
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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