Contacts of the strand formed by residues 728 - 737 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1817A N8E 4.4 30.5 - - - -
720B LYS* 3.9 1.2 - - - +
721B PHE* 3.2 52.3 + - + -
725B LEU* 3.2 23.2 + - + +
726B ASP 4.5 1.9 - - - +
727B LYS* 1.3 79.0 - - - +
729B THR* 1.3 78.7 + - - +
730B VAL* 3.9 13.9 - - + -
767B ALA* 4.7 2.5 - - + -
768B ARG 3.2 15.3 - - - +
769B TYR* 3.9 20.8 - - + -
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Residues in contact with THR 729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B ASP* 5.4 1.6 - - - +
718B SER* 4.5 11.9 - - - +
719B TYR 3.4 25.1 - - - +
720B LYS* 3.7 20.0 - - + +
727B LYS 4.6 2.8 + - - -
728B LEU* 1.3 79.3 + - - +
730B VAL* 1.3 64.8 + - - +
766B MET* 4.7 4.9 - - + -
767B ALA* 3.3 5.0 - - - -
768B ARG* 2.7 70.7 + - - +
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Residues in contact with VAL 730 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718B SER* 3.4 1.0 - - - -
719B TYR* 2.9 37.7 + - + +
721B PHE* 3.9 17.7 - - + -
728B LEU* 3.9 27.1 - - + -
729B THR* 1.3 78.4 - - - +
731B GLY* 1.3 64.2 + - - +
766B MET* 3.6 7.9 - - - +
767B ALA* 4.6 6.1 - - + -
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Residues in contact with GLY 731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B PHE* 5.1 0.9 - - - -
717B THR* 3.3 11.4 - - - -
718B SER* 3.9 3.6 - - - -
730B VAL* 1.3 82.5 - - - +
732B GLY* 1.3 59.0 + - - -
765B LEU* 3.6 9.1 - - - +
766B MET* 2.7 50.3 + - - +
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Residues in contact with GLY 732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B PHE* 3.7 13.2 - - - -
716B TYR* 3.5 2.1 - - - -
717B THR* 2.8 41.6 + - - +
731B GLY* 1.3 74.4 - - - -
733B GLY* 1.3 57.9 + - - -
764B ASP 3.1 15.3 - - - -
765B LEU* 4.2 6.7 - - - -
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Residues in contact with GLY 733 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715B LEU* 3.0 17.9 - - - -
716B TYR* 3.4 13.0 - - - -
732B GLY* 1.3 75.4 - - - -
734B ALA* 1.3 60.4 + - - +
763B VAL* 3.4 7.1 - - - +
764B ASP* 2.9 35.1 + - - +
765B LEU* 5.3 0.2 - - - +
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Residues in contact with ALA 734 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713B LEU* 4.9 1.4 - - - +
714B SER* 3.7 1.2 - - - -
715B LEU* 2.9 37.2 + - + +
716B TYR* 4.2 4.7 - - - -
733B GLY* 1.3 75.6 - - - +
735B ARG* 1.3 60.0 + - - +
761B TRP* 4.1 25.8 - - + -
762B LEU 3.3 9.0 - - - +
763B VAL* 4.4 10.5 - - + -
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Residues in contact with ARG 735 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B ARG 4.2 17.4 + - - -
192B THR 5.3 1.8 + - - -
194B GLY 5.4 0.2 - - - +
195B ILE 3.6 13.5 + - - -
196B THR* 3.5 21.2 + - - +
197B VAL 5.3 0.4 - - - +
712B GLN* 2.8 42.5 + - - +
713B LEU 3.5 10.2 + - - +
714B SER* 4.1 17.1 + - - +
716B TYR* 3.8 14.5 + - - +
734B ALA* 1.3 74.8 - - - +
736B TRP* 1.3 64.8 + - - +
737B GLN* 2.7 31.3 + - - +
760B TYR* 4.0 1.5 + - - +
761B TRP* 3.5 5.7 - - - -
762B LEU* 2.8 50.3 + - + +
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Residues in contact with TRP 736 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691B TYR* 4.5 11.9 - + - -
711B ASP* 3.8 32.8 - - + -
712B GLN* 3.5 4.3 - - - +
713B LEU* 3.0 49.2 + - + +
735B ARG* 1.3 76.8 - - - +
737B GLN* 1.3 79.0 + - - +
738B GLY* 3.8 14.4 - - - -
759B ASP* 2.6 30.2 + - + -
760B TYR 3.4 19.1 - - - -
761B TRP* 3.4 50.6 - + + -
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Residues in contact with GLN 737 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B THR* 4.5 6.8 - - - +
707B TRP 5.0 1.0 + - - -
709B PRO* 3.4 32.2 - - + +
711B ASP 3.4 12.8 - - - +
712B GLN* 4.2 3.8 - - + -
735B ARG* 2.7 34.4 + - + -
736B TRP* 1.3 88.0 + - - +
738B GLY* 1.3 64.5 + - - +
740B SER* 4.3 9.7 + - - -
757B GLN* 5.8 0.2 - - - +
759B ASP* 3.0 25.6 - - - +
760B TYR* 3.2 52.3 + - + -
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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