Contacts of the strand formed by residues 711 - 720 (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 ASP 711 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673B TYR* 5.2 1.0 + - - -
691B TYR* 2.9 26.4 + - - +
692B THR 3.3 4.5 - - - -
693B HIS* 2.9 25.1 + - - +
709B PRO* 3.3 5.5 - - - +
710B GLN* 1.3 95.5 + - - +
712B GLN* 1.3 63.7 + - - +
736B TRP* 3.8 19.1 - - + -
737B GLN* 3.4 1.0 - - - -
738B GLY* 3.0 29.8 + - - +
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Residues in contact with GLN 712 (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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194B GLY* 3.5 31.9 + - - +
195B ILE 3.4 12.8 + - - +
196B THR* 3.7 12.2 + - - -
691B TYR* 3.4 10.9 - - - -
692B THR* 3.0 49.1 + - - +
694B LYS* 6.2 1.8 - - - +
708B GLU* 5.0 6.5 + - - +
709B PRO* 4.7 8.6 + - + +
711B ASP* 1.3 78.8 - - - +
713B LEU* 1.3 60.9 + - - +
735B ARG* 2.8 42.2 + - - +
736B TRP* 3.5 13.7 - - - +
737B GLN* 4.2 3.4 - - + +
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Residues in contact with LEU 713 (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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689B ALA* 6.5 0.2 - - + -
690B GLY 3.5 12.6 - - - +
691B TYR* 4.0 21.1 - - + -
712B GLN* 1.3 77.2 - - - +
714B SER* 1.3 73.4 + - - +
715B LEU* 5.4 7.0 - - + +
734B ALA 5.6 1.1 - - - +
735B ARG* 3.5 6.8 + - - +
736B TRP* 3.0 43.2 + - + +
761B TRP* 3.5 39.3 - - + -
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Residues in contact with SER 714 (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 5.5 0.7 + - - -
191B HIS 5.2 1.2 - - - -
192B THR 5.0 1.4 - - - -
193B PRO* 4.3 24.8 - - - +
688B GLN 4.3 0.4 - - - -
689B ALA* 2.8 28.8 - - - +
690B GLY 3.0 18.3 + - - +
713B LEU* 1.3 80.1 + - - +
715B LEU* 1.3 61.7 + - - +
716B TYR* 4.2 18.2 - - - -
734B ALA 3.7 5.8 - - - -
735B ARG* 4.1 18.9 + - - +
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Residues in contact with LEU 715 (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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687B VAL* 4.8 9.9 - - + -
688B GLN 3.5 3.1 - - - -
689B ALA* 4.0 14.8 - - + -
713B LEU* 5.4 8.3 - - + +
714B SER* 1.3 76.4 - - - +
716B TYR* 1.3 67.3 + - - +
717B THR* 4.1 25.1 - - + -
732B GLY 5.9 0.2 - - - -
733B GLY* 3.0 7.2 - - - -
734B ALA* 2.9 41.0 + - + +
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Residues in contact with TYR 716 (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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147B TYR* 4.1 5.7 - - + -
176B ASN* 5.2 6.1 - - - +
180B PHE* 4.1 22.0 - + + -
190B ARG 4.2 5.0 + - - -
191B HIS* 3.5 66.4 + + + -
193B PRO* 6.0 0.4 - - + -
687B VAL* 3.3 2.8 - - - +
688B GLN* 2.9 53.2 + - + +
714B SER* 4.2 17.9 - - - -
715B LEU* 1.3 80.6 - - - +
717B THR* 1.3 62.2 - - - +
732B GLY 3.5 1.6 - - - -
733B GLY* 3.4 16.2 - - - -
734B ALA 4.3 3.4 - - - -
735B ARG* 3.8 20.8 + - - +
762B LEU 5.3 1.0 + - - -
764B ASP* 3.7 17.5 + - - -
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Residues in contact with THR 717 (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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147B TYR* 4.5 3.4 - - - -
180B PHE* 3.9 4.6 - - - -
685B TRP* 2.7 29.9 + - + +
686B GLN 2.7 18.4 + - - -
687B VAL* 3.8 13.2 - - - +
715B LEU* 4.1 15.9 - - + -
716B TYR* 1.3 76.1 - - - +
718B SER* 1.3 61.6 + - - +
731B GLY* 3.3 1.5 - - - -
732B GLY 2.8 42.6 + - - +
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Residues in contact with SER 718 (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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147B TYR* 2.9 29.6 + - - -
179B ASP* 3.5 13.3 + - - -
180B PHE* 5.1 1.6 - - - -
684B GLY 3.7 1.9 + - - +
685B TRP* 3.4 5.5 - - - -
686B GLN* 2.9 35.3 + - - +
717B THR* 1.3 76.1 + - - +
719B TYR* 1.3 63.0 + - - +
729B THR* 4.5 10.8 - - - +
730B VAL 3.4 9.6 - - - -
731B GLY* 3.9 5.2 - - - -
766B MET* 5.1 2.0 - - - -
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Residues in contact with TYR 719 (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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682B ALA* 6.0 1.6 - - + -
684B GLY* 3.4 23.8 - - - -
685B TRP* 3.8 27.1 - + + +
718B SER* 1.3 77.7 - - - +
720B LYS* 1.3 77.4 + - - +
721B PHE* 3.7 42.9 + + - -
722B LYS* 5.1 5.7 + - - +
728B LEU 4.1 0.2 - - - +
729B THR* 3.4 8.2 - - - +
730B VAL* 2.9 40.9 + - + +
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Residues in contact with LYS 720 (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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684B GLY* 3.0 25.6 + - - +
719B TYR* 1.3 84.7 + - - +
721B PHE* 1.3 69.1 + - - +
722B LYS* 5.1 1.0 - - - +
726B ASP* 3.8 23.3 - - - +
727B LYS 5.8 0.4 - - - -
728B LEU 3.9 4.3 - - - +
729B THR* 3.7 24.2 - - + +
768B ARG* 5.9 1.3 - - - +
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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