Contacts of the strand formed by residues 728 - 737 (chain A) in PDB entry 2W77
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 LEU 728 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720A LYS* 3.9 2.1 - - - +
721A PHE* 3.3 56.4 + - + -
725A LEU* 3.0 27.5 + - + +
727A LYS* 1.3 78.3 - - - +
729A THR* 1.3 62.9 + - - +
730A VAL* 4.3 18.2 - - + -
767A ALA* 4.9 6.5 - - + -
768A ARG 3.5 14.6 - - - +
769A TYR* 3.9 23.3 - - + -
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Residues in contact with THR 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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179A ASP* 5.3 1.3 - - - +
718A SER* 4.2 19.1 - - - +
719A TYR 3.4 16.4 - - - +
720A LYS* 3.3 27.4 + - + +
727A LYS 4.0 1.4 + - - -
728A LEU* 1.3 72.1 - - - +
730A VAL* 1.3 65.5 + - - +
766A MET* 4.1 7.1 - - + +
767A ALA* 3.3 4.3 - - - +
768A ARG* 2.8 71.4 + - - +
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Residues in contact with VAL 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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718A SER* 3.1 3.3 - - - -
719A TYR* 2.8 40.0 + - + +
721A PHE* 4.2 22.9 - - + -
728A LEU* 4.3 17.9 - - + -
729A THR* 1.3 77.9 - - - +
731A GLY* 1.3 61.4 + - - +
766A MET* 3.6 6.3 - - - +
767A ALA* 4.2 15.9 - - + -
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Residues in contact with GLY 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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180A PHE* 4.7 1.1 - - - -
717A THR* 3.2 12.1 - - - -
718A SER* 3.9 2.0 - - - -
730A VAL* 1.3 82.3 - - - +
732A GLY* 1.3 59.1 + - - -
765A LEU* 3.4 6.2 - - - +
766A MET* 2.8 50.6 + - - +
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Residues in contact with GLY 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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180A PHE* 3.7 10.2 - - - -
717A THR* 2.9 39.0 + - - +
731A GLY* 1.3 76.9 - - - -
733A GLY* 1.3 58.7 + - - -
764A ASP 3.1 14.6 - - - -
765A LEU* 4.0 8.5 - - - -
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Residues in contact with GLY 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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715A LEU* 3.1 16.2 - - - -
716A TYR* 3.5 16.4 - - - -
732A GLY* 1.3 75.0 - - - -
734A ALA* 1.3 59.8 + - - +
763A VAL* 3.3 7.3 - - - +
764A ASP* 2.6 39.5 + - - +
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Residues in contact with ALA 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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713A LEU* 4.3 1.3 - - - +
714A SER* 3.7 0.7 - - - -
715A LEU* 2.9 38.3 + - + +
716A TYR* 4.1 6.6 - - - -
733A GLY* 1.3 74.9 - - - +
735A ARG* 1.3 62.3 + - - +
761A TRP* 4.0 25.8 - - + -
762A LEU 3.1 9.6 - - - +
763A VAL* 4.4 9.9 - - + -
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Residues in contact with ARG 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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190A ARG 4.7 14.4 + - - +
192A THR 4.2 7.1 + - - -
194A GLY 4.6 1.4 - - - +
195A ILE 2.9 20.7 + - - -
196A THR* 3.7 10.9 - - - +
712A GLN* 2.6 41.3 + - - +
713A LEU 3.3 21.9 + - - +
714A SER* 3.5 21.9 + - - +
716A TYR* 4.0 14.4 - - + +
734A ALA* 1.3 76.9 - - - +
736A TRP* 1.3 68.7 + - - +
737A GLN* 3.4 27.3 + - + +
760A TYR* 3.9 2.4 - - + +
761A TRP* 3.4 4.7 - - - -
762A LEU* 2.8 50.6 + - + +
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Residues in contact with TRP 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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691A TYR* 4.9 8.7 - + - -
711A ASP* 3.9 30.3 - - + -
712A GLN* 3.5 1.4 - - - -
713A LEU* 2.9 51.0 + - + +
735A ARG* 1.3 78.8 - - - +
737A GLN* 1.3 73.6 + - - +
738A GLY* 3.8 11.4 - - - -
759A ASP* 3.0 38.2 + - + +
760A TYR 3.3 23.1 - - - -
761A TRP* 3.5 53.9 - + + +
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Residues in contact with GLN 737 (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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196A THR* 3.5 10.4 - - - +
707A TRP 4.8 1.4 + - - -
709A PRO* 3.2 34.6 - - + +
711A ASP 3.5 7.2 - - - +
712A GLN* 4.3 2.2 - - + -
735A ARG* 3.4 29.8 + - + +
736A TRP* 1.3 86.2 - - - +
738A GLY* 1.3 60.6 + - - +
740A SER* 4.0 11.7 + - - -
757A GLN* 5.7 0.2 - - - +
759A ASP* 2.9 25.5 - - - +
760A TYR* 3.1 52.8 + - + -
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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