Contacts of the helix formed by residues 688 - 694 (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 PHE 688 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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684A PHE* 3.8 17.7 - + + +
685A VAL* 3.0 14.4 - - - +
686A TRP 2.6 2.0 + - - -
687A ALA* 1.3 74.7 - - - +
689A SER* 1.4 70.0 + - - +
690A LEU 3.3 2.6 - - - +
691A MET* 3.2 29.7 + - + +
692A PHE* 3.6 27.3 + + - -
737A HIS* 4.1 25.8 - + - -
1796A CLA 3.4 56.8 - + + -
1813A CLA 3.3 50.7 - + + -
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Residues in contact with SER 689 (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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685A VAL 3.2 4.4 + - - -
686A TRP* 2.2 32.1 + - - -
688A PHE* 1.4 77.7 - - - +
690A LEU* 1.3 55.0 + - - +
691A MET 3.0 1.8 - - - -
692A PHE* 2.8 9.5 + - - +
693A LEU* 2.5 41.3 + - - +
733A VAL 4.8 0.2 - - - -
734A GLY 4.8 1.6 - - - -
737A HIS* 4.2 7.0 - - - -
738A TYR* 3.1 51.2 + - - -
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Residues in contact with LEU 690 (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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686A TRP* 4.1 25.4 - - + +
687A ALA* 5.2 2.9 - - - -
688A PHE 3.3 1.3 - - - +
689A SER* 1.3 76.6 - - - +
691A MET* 1.3 53.4 + - - +
693A LEU* 3.4 11.0 - - + -
694A PHE* 2.4 58.2 + - + +
738A TYR* 3.2 24.7 - - + -
1812A CLA 4.9 9.0 - - + -
1813A CLA 3.7 19.5 - - + -
657B TRP* 4.5 7.2 - - + -
661B PHE* 3.0 45.3 - - + -
713B PHE* 5.5 2.2 - - + -
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Residues in contact with MET 691 (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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688A PHE* 3.2 21.0 + - + +
689A SER 3.0 0.6 - - - -
690A LEU* 1.3 78.3 - - - +
692A PHE* 1.3 58.0 - - + +
695A SER* 3.4 15.1 - - - -
700A TRP* 3.9 11.0 - - + -
1796A CLA 4.3 19.3 - - + -
1802A PQN 2.2 56.8 - - + +
1813A CLA 3.0 92.4 - - + +
1778B BCR 4.5 2.0 - - + -
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Residues in contact with PHE 692 (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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688A PHE* 3.6 23.3 + + - -
689A SER 2.8 12.5 + - - +
691A MET* 1.3 80.0 - - + +
693A LEU* 1.3 60.8 + - - +
695A SER 4.5 0.2 + - - -
725A LEU* 3.4 33.7 - - + -
730A GLY* 3.6 14.0 - - - +
731A ARG* 5.2 0.3 - - - -
733A VAL* 3.0 44.2 - - + +
734A GLY 3.9 0.2 - - - +
1796A CLA 3.0 52.0 - - + -
1802A PQN 3.4 57.0 - + + -
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Residues in contact with LEU 693 (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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599A PHE* 4.2 7.6 - - + -
603A PHE* 3.0 34.1 - - + -
689A SER* 2.5 21.6 + - - +
690A LEU* 3.4 18.4 - - + +
692A PHE* 1.3 74.5 - - - +
694A PHE* 1.3 66.1 + - + +
695A SER 3.6 2.4 + - - +
730A GLY 5.2 0.2 - - - -
731A ARG* 5.9 1.1 - - - +
734A GLY* 3.3 11.2 - - - -
735A VAL* 3.1 17.7 - - + +
738A TYR* 3.1 36.1 - - + -
664B LEU 3.8 8.8 - - - +
665B ILE* 3.6 19.0 - - + +
667B TRP* 4.3 7.3 - - - -
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Residues in contact with PHE 694 (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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690A LEU* 2.4 50.9 + - + +
692A PHE 3.5 0.4 - - - -
693A LEU* 1.3 71.1 - - + +
695A SER* 1.3 57.2 + - - +
1813A CLA 3.5 28.0 - - + -
569B ASP* 4.5 1.6 - - - +
577B TYR* 2.9 28.5 + - - +
578B LEU* 4.1 1.6 - - - +
581B PHE* 3.9 16.4 - + - -
661B PHE* 3.1 46.0 - + - -
664B LEU* 3.6 42.0 - - + -
665B ILE* 3.6 16.4 - - + -
667B TRP* 4.6 7.1 - - - -
713B PHE* 4.5 9.6 - + - -
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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