Contacts of the strand formed by residues 561 - 565 (chain B) in PDB entry 6V3O
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 VAL 561 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B TYR* 3.5 8.7 - - + +
534B ILE* 3.5 29.6 - - + -
543B VAL* 3.5 29.1 - - + +
546B VAL* 4.4 14.1 - - + -
547B GLU* 3.5 35.9 + - + +
550B GLN* 4.0 8.3 - - - +
559B LEU 3.9 5.8 - - - +
560B PRO* 1.3 73.7 - - - +
562B VAL* 1.3 66.0 + - - +
563B PRO* 4.1 0.9 - - - +
587B TYR* 4.0 5.9 + - - +
595B GLN* 3.1 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 562 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B PRO* 3.3 33.0 - - + -
532B TYR 2.9 9.2 + - - +
533B ILE* 3.3 11.8 - - + +
534B ILE* 2.9 26.6 + - - -
560B PRO* 3.8 5.4 - - + +
561B VAL* 1.3 82.7 - - - +
563B PRO* 1.3 62.5 - - - +
596B GLN* 3.2 53.2 - - + +
597B VAL 3.8 2.5 - - - +
598B MET* 3.8 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 563 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ILE* 4.1 4.9 - - + +
537B ALA* 3.7 19.7 - - + -
543B VAL* 4.2 21.1 - - + -
561B VAL 4.1 1.6 - - - +
562B VAL* 1.3 84.8 - - - +
564B LEU* 1.3 59.7 + - - +
565B PHE* 3.8 30.0 + - + -
581B LEU* 5.9 4.0 - - + -
595B GLN* 3.9 10.3 - - - +
596B GLN 3.4 15.3 - - - +
597B VAL* 4.0 9.4 - - + +
598B MET* 2.9 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 564 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ARG* 4.0 14.6 - - - +
533B ILE* 4.2 9.4 - - + -
534B ILE 3.0 20.7 + - - +
535B SER* 3.9 15.0 - - - +
536B MET 3.7 2.9 + - - -
537B ALA* 3.1 23.0 + - - +
563B PRO* 1.3 72.3 - - - +
565B PHE* 1.3 61.3 + - - +
566B GLU* 3.3 35.3 + - + +
598B MET* 3.5 46.0 - - + +
600B GLY* 4.0 17.9 - - - +
603B ASP* 4.6 6.5 - - - +
1001B SO4 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 565 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B ALA* 3.3 28.5 - - + -
538B THR 4.5 10.5 - - - -
539B ALA 5.0 0.9 - - - -
563B PRO* 3.8 33.7 - - + -
564B LEU* 1.3 70.1 - - - +
566B GLU* 1.3 62.3 + - - +
567B ARG 3.9 1.6 - - - -
570B ASP* 3.9 22.0 - - + +
571B LEU* 4.0 26.0 - - + +
574B ALA* 3.6 34.3 - - + -
577B SER* 4.4 13.9 - - - -
578B VAL* 5.7 3.6 - - + -
597B VAL* 4.0 24.2 - - + -
598B MET 3.4 8.1 + - - +
599B VAL* 4.3 2.5 - - + -
600B GLY 3.9 17.2 + - - -
604B SER* 4.2 0.9 + - - -
624B MET* 4.9 5.2 - - + -
----------------------------------------------------------
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