Contacts of the strand formed by residues 657 - 664 (chain V) in PDB entry 5IY6
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 ALA 657 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503V ALA* 4.3 8.5 - - + -
504V LYS 3.4 8.3 + - - +
505V VAL* 3.5 19.7 - - + -
506V GLN* 3.1 22.3 + - - +
621V ASN* 3.2 15.5 - - - +
644V LEU* 4.3 8.1 - - + -
645V ARG 3.8 14.6 - - - +
655V TYR* 4.3 0.3 - - - +
656V ASN* 1.3 82.0 + - - +
658V PHE* 1.3 70.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 658 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505V VAL* 4.3 0.7 - - - -
506V GLN* 3.6 23.1 - - + -
550V PHE* 6.3 1.8 - + - -
551V HIS* 3.8 21.3 - + + -
556V ASP* 5.7 2.7 - - - -
621V ASN 3.0 10.5 + - - +
622V VAL* 3.2 6.5 - - + +
623V LEU 2.8 31.5 + - - +
644V LEU* 3.7 6.0 - - - +
655V TYR* 3.7 33.4 - + - -
656V ASN* 4.8 4.3 - - - -
657V ALA* 1.3 97.6 - - - +
659V PHE* 1.3 52.9 - - - +
660V TYR* 3.1 39.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 659 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505V VAL* 3.9 8.9 - - + +
506V GLN 3.1 9.1 + - - +
507V CYS* 4.1 15.0 - - + -
508V ALA* 2.9 32.5 + - - +
623V LEU* 3.4 26.9 - - + +
625V GLN* 3.2 32.1 - - + -
636V GLU* 4.5 15.9 - - + -
640V LEU* 3.5 37.0 - - + -
644V LEU* 4.3 3.4 - - + -
658V PHE* 1.3 73.7 - - - +
660V TYR* 1.3 71.8 + - - +
661V SER* 3.1 26.2 - - - -
676V ARG* 4.9 4.3 - - - -
680V LEU* 5.4 6.1 - - + -
687V PHE* 4.7 13.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 660 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506V GLN* 6.5 0.2 - - + -
508V ALA* 3.4 21.5 - - + -
510V VAL* 4.4 7.9 - - + -
547V LEU* 3.9 31.8 - - + +
550V PHE* 5.8 0.3 - - - -
551V HIS* 2.8 31.5 + + - -
622V VAL* 3.9 7.4 - - + -
623V LEU 2.8 18.6 + - - +
624V ILE* 3.3 19.5 - - + -
625V GLN* 2.8 33.8 + - - +
658V PHE* 3.1 42.0 - + + -
659V PHE* 1.3 83.7 - - - +
661V SER* 1.3 57.4 + - - +
662V LEU* 4.1 15.7 - - + -
690V ILE* 4.5 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 661 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508V ALA 3.0 11.5 + - - -
509V GLU* 3.4 9.2 - - - +
510V VAL* 2.8 31.6 + - - +
625V GLN* 3.0 33.7 + - - -
627V SER 5.4 0.9 - - - -
659V PHE* 3.1 14.9 - - - -
660V TYR* 1.3 68.5 - - - +
662V LEU* 1.3 61.8 + - - +
663V VAL* 4.7 0.7 - - - -
676V ARG* 3.6 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 662 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510V VAL* 3.7 20.2 - - + -
512V CYS* 4.8 4.3 - - - -
540V LYS* 3.5 43.2 + - + +
543V ALA* 5.1 0.7 - - + -
544V CYS* 3.6 39.9 - - + +
547V LEU* 4.4 8.3 - - + -
571V TYR* 5.3 0.4 - - - +
624V ILE* 4.1 14.6 - - + -
625V GLN 3.0 20.1 + - - +
626V ILE* 4.1 7.2 - - + -
627V SER* 3.7 14.6 - - - +
660V TYR* 4.1 14.6 - - + -
661V SER* 1.3 79.1 - - - +
663V VAL* 1.4 59.9 + - - +
669V GLU* 3.6 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 663 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509V GLU* 3.5 37.7 - - + +
510V VAL 2.9 11.8 + - - +
511V TRP* 3.6 14.4 - - + +
512V CYS* 2.9 30.2 + - - +
540V LYS* 4.5 3.8 - - - -
628V SER* 3.9 14.6 - - - +
661V SER 4.2 1.1 - - - +
662V LEU* 1.4 75.9 - - - +
664V SER* 1.3 62.9 + - - +
665V GLN 3.6 0.2 + - - -
669V GLU* 3.3 6.7 - - - +
670V MET* 3.5 43.1 - - + +
673V SER* 4.4 2.0 - - - +
676V ARG* 4.3 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 664 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512V CYS 3.6 5.2 - - - -
514V MET* 3.4 24.2 - - - -
534V TYR* 2.7 27.9 + - - -
537V ASN* 3.1 19.3 + - - +
540V LYS* 3.3 4.6 - - - +
663V VAL* 1.3 73.4 - - - +
665V GLN* 1.3 61.0 - - - +
667V THR* 2.8 27.6 + - - -
669V GLU* 2.8 11.1 + - - -
670V MET* 3.4 10.0 - - - +
----------------------------------------------------------
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