Contacts of the strand formed by residues 685 - 698 (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 TRP 685 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680B GLU* 3.6 4.3 - - - +
681B LEU* 3.0 51.6 + - + +
682B ALA* 3.0 36.1 + - + +
683B PRO 3.8 0.4 + - - -
684B GLY* 1.3 73.7 - - - +
686B GLN* 1.3 62.0 + - - +
717B THR* 2.7 34.8 + - + +
718B SER 3.4 11.2 - - - -
719B TYR* 3.8 23.8 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 686 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLY 4.1 12.6 + - - +
146B SER* 3.4 18.5 + - - +
147B TYR* 2.6 56.2 + - + +
628B ARG 4.9 0.2 + - - -
679B GLY* 3.6 8.7 - - - -
680B GLU* 3.5 32.1 - - - +
681B LEU* 4.9 0.2 - - - -
683B PRO 5.8 0.6 + - - -
684B GLY 5.1 2.9 - - - +
685B TRP* 1.3 78.2 - - - +
687B VAL* 1.3 56.3 + - - +
717B THR* 2.7 35.3 + - - -
718B SER* 2.9 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 687 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B TYR* 3.5 10.0 - - - +
677B ILE* 4.2 22.9 - - + -
678B SER* 3.3 1.9 - - - -
679B GLY 2.9 36.9 + - - +
681B LEU* 3.1 47.6 - - + -
686B GLN* 1.3 70.8 - - - +
688B GLN* 1.3 65.7 + - - +
689B ALA* 4.8 2.7 - - + +
715B LEU* 4.8 16.4 - - + -
716B TYR 3.3 5.8 - - - +
717B THR* 3.8 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 688 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B TYR* 3.9 16.7 + - + +
170B THR* 3.8 20.3 - - - +
171B VAL 3.1 28.6 + - - +
172B VAL* 4.3 6.6 - - - +
173B THR 4.9 0.6 - - - +
176B ASN* 3.2 27.2 + - - +
191B HIS 5.2 2.3 + - - +
193B PRO* 3.8 21.9 - - + +
676B GLU* 5.3 0.7 - - - +
677B ILE 3.5 7.0 - - - +
678B SER* 4.7 7.4 - - - -
687B VAL* 1.3 74.4 - - - +
689B ALA* 1.3 64.9 + - - +
714B SER* 3.8 0.9 - - - +
715B LEU* 3.5 1.0 - - - -
716B TYR* 2.9 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 689 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PRO* 4.4 4.7 - - - +
676B GLU* 3.1 5.6 - - - +
677B ILE* 2.8 55.9 + - + +
687B VAL* 5.0 3.4 - - + -
688B GLN* 1.3 78.4 - - - +
690B GLY* 1.3 56.9 + - - +
714B SER* 2.8 16.6 - - - +
715B LEU* 4.0 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 690 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PRO* 3.8 20.6 - - - +
194B GLY 6.0 0.4 - - - -
675B ALA 3.1 11.0 - - - -
676B GLU* 3.6 8.7 - - - -
689B ALA* 1.3 74.9 - - - +
691B TYR* 1.3 61.2 + - - +
692B THR* 5.3 1.1 - - - -
713B LEU* 3.5 6.1 - - - +
714B SER 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 691 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B TYR* 4.2 27.1 + + - -
674B GLU* 3.1 7.0 - - - +
675B ALA* 2.6 43.8 + - + +
690B GLY* 1.3 75.0 - - - +
692B THR* 1.3 75.7 + - - +
693B HIS* 4.3 0.9 - - + -
711B ASP* 2.9 31.3 + - + +
712B GLN 3.4 21.1 - - - -
713B LEU* 4.0 21.3 - - + -
736B TRP* 4.5 13.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 692 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PRO* 4.9 0.3 - - - +
194B GLY* 3.5 13.6 + - - +
210B ARG* 5.6 7.0 - - + +
636B PHE* 4.7 8.1 - - + -
673B TYR 3.5 7.4 - - - +
674B GLU* 2.4 36.9 + - + +
690B GLY 5.3 0.2 - - - -
691B TYR* 1.3 79.2 + - - +
693B HIS* 1.3 72.5 + - - +
694B LYS* 5.3 5.4 - - + -
710B GLN 3.5 0.9 - - - +
711B ASP* 3.3 5.5 - - - -
712B GLN* 3.0 57.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 693 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636B PHE* 3.8 4.9 - - - -
671B LYS 4.6 2.0 + - - -
672B GLY* 3.3 8.3 - - - -
673B TYR* 2.8 77.3 + + + +
691B TYR* 4.3 2.2 - - + -
692B THR* 1.3 75.8 - - - +
694B LYS* 1.3 69.9 + - - +
695B ILE* 4.1 16.9 - - + +
710B GLN* 3.2 26.0 + - - -
711B ASP* 2.9 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 694 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ARG* 4.7 7.2 - - - -
211B GLY* 4.2 12.1 - - - +
636B PHE* 4.8 3.6 - - + -
670B THR* 4.3 13.0 - - + -
671B LYS 3.5 9.6 - - - +
692B THR* 5.3 5.2 - - + -
693B HIS* 1.3 79.7 - - - +
695B ILE* 1.3 72.3 + - - +
696B ILE* 4.1 13.0 - - + +
704B VAL 5.1 0.9 - - - -
705B SER 4.2 7.6 + - - -
708B GLU* 2.7 51.3 + - - +
709B PRO 2.7 33.6 + - - +
710B GLN* 2.8 49.8 + - - +
712B GLN* 6.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 695 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B LYS 3.7 1.9 - - - +
670B THR* 3.6 0.8 - - - -
671B LYS* 3.0 35.1 + - + +
693B HIS* 4.1 15.7 - - + +
694B LYS* 1.3 83.1 - - - +
696B ILE* 1.3 62.3 + - - +
697B ARG* 4.0 30.3 + - + +
703B LYS* 3.8 36.1 - - + +
710B GLN* 3.7 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 696 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B GLY* 3.8 35.2 - - - +
212B PHE* 3.8 18.6 - - + -
643B ARG* 4.2 5.4 - - - +
668B ALA* 4.5 9.2 - - + -
669B LYS 3.2 17.0 - - - +
670B THR* 3.4 26.2 - - + +
694B LYS* 4.1 5.8 - - + +
695B ILE* 1.3 74.7 - - - +
697B ARG* 1.3 64.7 + - - +
703B LYS* 3.7 4.3 - - - +
704B VAL* 3.1 60.6 + - + +
705B SER* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 697 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B ALA* 3.3 7.8 - - - +
669B LYS* 2.9 35.4 + - + +
671B LYS* 6.3 3.8 - - + +
695B ILE* 4.0 32.1 - - + +
696B ILE* 1.3 78.4 - - - +
698B ASP* 1.3 68.0 + - - +
701B GLY* 3.1 29.2 + - - +
702B LYS 3.4 9.6 - - - +
703B LYS* 3.6 29.7 - - + +
704B VAL* 5.1 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 698 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643B ARG* 4.9 4.3 - - - -
645B GLU* 3.7 9.6 - - - +
666B ILE* 3.4 25.2 - - - +
667B LYS 4.0 3.5 - - - +
668B ALA* 4.6 2.2 - - - +
697B ARG* 1.3 76.9 - - - +
699B ASP* 1.3 62.3 + - - +
700B SER* 3.1 30.2 + - - +
701B GLY* 2.9 14.6 + - - +
702B LYS* 2.9 40.4 + - - +
704B VAL* 4.1 11.9 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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