Contacts of the strand formed by residues 655 - 659 (chain A) in PDB entry 2OK5
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 PHE 655 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A TYR* 3.4 24.9 - - + -
549A ASP* 4.1 11.0 - - - -
628A LYS* 4.8 9.5 + - - -
632A GLU* 4.7 8.6 - - - +
650A VAL 3.9 15.3 - - - -
651A VAL* 4.3 15.9 - - + -
652A THR* 3.2 47.8 + - + +
653A PRO 3.2 3.9 - - - +
654A ARG* 1.3 79.3 - - - +
656A LEU* 1.3 68.5 + - - +
693A SER* 3.8 8.5 - - - -
694A TRP* 3.2 31.0 - + - -
716A PHE* 3.8 18.8 - + + -
717A HIS 3.3 13.2 - - - -
718A ILE* 3.6 17.0 - - + -
719A ASN* 4.6 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 656 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A LEU* 4.4 12.8 - - + -
622A ILE* 4.1 27.8 - - + -
624A ASN* 4.4 14.6 - - - +
628A LYS* 6.3 1.1 - - - +
655A PHE* 1.3 76.7 - - - +
657A CYS* 1.3 60.1 + - - +
678A LEU* 4.1 21.3 - - + -
689A VAL* 3.9 25.6 - - + +
690A GLY* 4.7 1.8 - - - -
716A PHE* 3.3 9.4 - - - +
717A HIS* 2.7 42.0 + - + +
719A ASN* 3.6 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 657 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A ILE* 3.3 7.4 - - - +
623A LYS* 2.8 41.0 + - - +
628A LYS* 5.2 1.8 - - + +
631A CYS* 2.0 53.6 - - + -
632A GLU* 4.9 8.3 - - + +
656A LEU* 1.3 76.3 - - - +
658A THR* 1.3 60.3 + - - +
714A ARG* 4.0 6.3 - - - -
715A ASP 3.5 2.0 - - - -
716A PHE* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 658 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A PHE* 6.0 0.5 - - - -
620A VAL* 3.8 26.5 - - + +
621A TYR 3.4 17.9 - - - +
622A ILE* 3.8 21.5 - - + -
623A LYS* 3.8 2.2 - - - +
631A CYS* 4.5 1.1 - - - -
657A CYS* 1.3 78.0 - - - +
659A GLY* 1.3 64.1 + - - +
666A ASP* 4.0 3.8 - - - -
678A LEU* 4.4 2.0 - - + -
714A ARG* 3.3 9.9 - - - +
715A ASP* 2.9 34.2 + - - +
717A HIS* 2.7 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 659 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A LYS* 2.6 28.1 + - - +
658A THR* 1.3 75.6 - - - +
660A GLY* 1.3 66.0 + - - +
666A ASP* 2.9 27.3 + - - +
667A PRO 4.9 2.2 + - - -
668A ASN* 4.2 7.9 - - - -
713A ALA 3.4 11.4 - - - -
714A ARG* 2.9 9.4 + - - -
715A ASP* 5.2 0.4 - - - -
----------------------------------------------------------
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