Contacts of the strand formed by residues 643 - 648 (chain B) in PDB entry 3WOO
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 PRO 643 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B PHE* 3.6 15.5 - - + -
601B THR 3.4 7.0 - - - +
634B LEU 4.0 10.8 - - - +
636B ASP* 4.4 3.1 - - + -
639B ILE* 3.6 19.4 - - + -
641B SER 3.8 6.3 - - - +
642B VAL* 1.3 97.0 - - + +
644B VAL* 1.3 60.7 + - - +
697B ASP* 3.4 30.4 - - + +
699B ARG* 3.4 24.0 - - + +
700B TYR* 3.5 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 644 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B HIS* 3.7 34.5 - - - +
601B THR* 2.9 18.6 + - - +
602B THR 3.4 29.6 - - - +
603B LEU* 3.5 8.7 - - + +
606B VAL* 4.0 5.8 - - + -
642B VAL 3.9 1.3 - - - +
643B PRO* 1.3 74.5 - - - +
645B ASN* 1.3 69.0 + - - +
696B VAL* 3.8 0.7 - - - +
697B ASP* 2.9 26.0 + - - +
700B TYR* 3.8 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 645 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B TRP* 3.8 11.7 - - + -
220B ARG* 3.0 40.7 + - - +
222B THR 2.9 43.7 + - - +
600B PHE* 3.4 4.2 - - - -
601B THR* 3.0 27.0 + - - +
644B VAL* 1.3 89.9 - - - +
646B TYR* 1.3 67.2 + - - +
673B PHE* 3.4 12.2 - - - -
694B ILE* 4.3 1.8 - - + -
695B ALA 3.1 7.9 - - - +
696B VAL* 3.6 7.6 - - - -
697B ASP 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 646 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B TRP* 3.8 6.7 - - - -
261B LEU* 3.5 19.1 - - + -
267B VAL* 4.8 1.3 - - + -
586B VAL* 4.3 11.0 - - + -
599B PRO 2.9 13.7 - - - +
600B PHE* 3.7 20.9 - + + -
645B ASN* 1.3 76.7 - - - +
647B LEU* 1.3 69.5 + - - +
648B SER* 4.9 2.0 - - - -
661B VAL* 3.5 26.5 - - + +
669B VAL* 3.0 38.9 + - - +
670B GLY* 3.7 1.7 + - - -
693B MET* 3.5 6.0 - - + +
694B ILE* 3.5 3.5 - - - -
695B ALA* 2.9 50.2 + - + +
696B VAL 4.4 0.2 - - - -
697B ASP* 3.6 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 647 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B TRP* 3.4 57.0 - - + +
586B VAL* 3.5 11.4 - - - +
587B MET 3.1 30.4 + - - +
588B GLY* 4.0 7.9 - - - -
589B TYR* 3.8 24.9 - - + -
597B TYR* 4.1 1.8 - - + -
598B THR 3.7 9.9 - - - +
599B PRO 2.8 9.5 + - - +
646B TYR* 1.3 74.1 - - - +
648B SER* 1.3 63.5 + - - +
676B ASN* 4.8 1.1 - - + -
692B ARG* 3.9 16.6 - - + -
693B MET 3.2 11.2 - - - +
694B ILE* 3.9 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 648 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B VAL* 3.9 17.4 - - - +
585B ASN 3.4 17.0 - - - -
586B VAL* 3.9 3.4 - - - -
587B MET 3.9 3.4 - - - -
646B TYR* 4.9 2.6 - - - -
647B LEU* 1.3 78.4 - - - +
649B ASP* 1.3 58.8 + - - +
650B LEU* 3.1 6.9 + - - +
692B ARG* 3.2 10.6 - - - -
693B MET* 2.9 62.1 + - - +
----------------------------------------------------------
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