Contacts of the strand formed by residues 693 - 701 (chain B) in PDB entry 2YA6
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 LYS 693 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689B MET* 3.5 5.6 - - - -
690B HIS 3.1 32.6 + - - +
691B GLU* 4.2 14.4 + - + +
692B GLY* 1.3 80.9 - - - +
694B GLU* 1.3 59.4 + - - +
695B TYR* 3.2 33.2 - - + +
715B ARG* 3.8 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 694 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B LEU* 3.5 2.3 - - - +
639B ASN* 2.6 49.6 + - - +
640B ASN 4.9 0.7 + - - -
687B HIS* 2.7 32.9 + - - +
689B MET* 3.6 12.1 - - + +
692B GLY 4.3 0.6 + - - -
693B LYS* 1.3 72.1 - - - +
695B TYR* 1.3 60.3 + - - +
715B ARG* 3.0 27.0 + - - +
716B VAL* 3.0 54.3 + - + +
717B GLU 5.1 0.7 - - - +
718B GLU* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 695 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687B HIS* 3.7 6.9 - - - -
688B THR* 2.8 49.0 + - + +
690B HIS* 3.6 24.0 + - + -
693B LYS* 3.2 53.7 - - + +
694B GLU* 1.3 75.7 - - - +
696B ILE* 1.3 69.0 + - - +
713B LEU* 3.9 17.7 - - + -
714B ALA 3.3 15.7 - - - +
715B ARG* 3.7 18.0 - - - -
716B VAL* 3.8 3.6 - - - -
725B LEU* 3.9 16.4 - - + -
771B TRP* 3.5 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
----------------------------------------------------------
636B VAL* 4.1 17.9 - - + -
638B LEU* 3.6 29.6 - - + -
644B LYS* 5.0 1.1 - - + -
646B PHE* 4.1 22.0 - - + -
685B ALA* 4.2 15.0 - - + -
686B ILE 3.3 13.5 - - - +
687B HIS* 4.5 0.9 - - + -
695B TYR* 1.3 80.0 - - - +
697B ILE* 1.3 75.1 + - - +
698B LEU* 4.5 4.5 - - + +
712B HIS 3.8 0.5 - - - +
713B LEU* 3.7 2.9 - - - +
714B ALA* 2.9 40.6 + - + +
716B VAL* 4.1 4.6 - - + +
722B LEU* 3.8 20.6 - - + -
724B TRP* 4.5 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 697 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B ALA* 3.1 3.6 - - - +
686B ILE* 2.9 40.3 + - + -
688B THR* 3.8 17.0 - - + -
696B ILE* 1.3 76.2 - - - +
698B LEU* 1.3 62.3 + - - +
711B VAL* 3.5 29.8 - - + -
712B HIS 3.2 6.3 - - - +
713B LEU* 4.4 5.2 - - + -
740B LEU* 3.5 21.4 - - + +
748B TYR* 3.6 45.8 - - + -
769B PHE* 4.5 1.8 - - + -
774B LEU* 3.7 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 698 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B PHE* 3.5 42.6 - - + -
654B LEU* 3.9 18.2 - - + -
676B VAL* 4.2 9.2 - - + -
683B MET* 4.2 10.8 - - - -
684B SER 3.3 12.6 - - - +
685B ALA* 4.1 6.5 - - + +
696B ILE* 4.1 1.5 + - + -
697B ILE* 1.3 75.2 - - - +
699B SER* 1.3 63.4 + - - +
700B ASN* 3.8 26.9 - - - +
711B VAL* 4.6 0.7 - - - -
712B HIS* 2.7 49.8 + - + +
724B TRP* 4.0 15.7 - - + -
740B LEU* 4.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 699 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683B MET* 3.5 1.9 - - - +
684B SER 2.9 20.9 + - - -
698B LEU* 1.3 73.9 - - - +
700B ASN* 1.3 66.8 + - - +
710B MET 3.2 13.6 + - - -
711B VAL* 4.3 7.0 - - - +
735B PHE* 3.6 8.1 - - - -
738B ASN* 3.0 32.5 + - - +
740B LEU* 3.5 13.2 - - - +
750B ILE* 3.3 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 700 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654B LEU* 5.6 0.2 - - - +
676B VAL* 4.3 5.1 - - - +
677B LYS 2.7 27.5 + - - -
678B ASP* 4.1 11.7 + - - +
679B VAL 5.3 0.2 - - - +
681B VAL* 5.1 5.4 - - + +
682B GLN 4.2 7.0 - - - +
683B MET* 3.8 21.4 - - + +
698B LEU* 4.0 8.1 - - - +
699B SER* 1.3 76.5 + - - +
701B ALA* 1.3 62.6 + - - +
710B MET* 2.7 33.9 + - - +
712B HIS* 2.9 28.1 + - - -
735B PHE* 3.7 6.5 - - - -
738B ASN* 3.6 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 701 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677B LYS* 4.1 7.3 - - - +
679B VAL* 4.2 18.3 + - + +
681B VAL* 4.3 8.2 - - + +
700B ASN* 1.3 90.5 + - - +
702B GLY* 1.3 62.2 + - - +
703B GLY* 3.7 0.3 + - - -
705B LYS 4.0 7.6 - - - +
706B ARG* 4.3 1.1 - - - -
707B GLU 3.6 17.3 - - - +
708B ASN 4.0 0.7 - - - -
712B HIS* 5.5 0.2 - - - -
735B PHE* 3.5 35.0 - - + +
736B ALA 4.7 2.7 + - - +
----------------------------------------------------------
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