Contacts of the strand formed by residues 534 - 540 (chain A) in PDB entry 2CKH
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 TRP 534 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A LEU* 2.8 30.6 + - + -
467A ASN 4.1 0.4 - - - -
468A ASP* 3.9 21.3 - - - -
471A ILE* 4.3 16.2 - - + -
495A THR* 3.9 15.5 - - + -
527A PRO* 5.4 1.3 - - + -
528A ILE 3.4 23.6 - - - -
529A HIS* 4.0 15.7 - + + -
533A HIS* 1.3 86.8 + - - +
535A CYS* 1.3 73.7 + - - +
550A ASP* 4.5 0.9 - - - +
551A SER* 5.1 1.7 + - - -
602A CYS* 3.8 10.4 - - - +
603A GLY* 3.4 37.6 - - - +
606A ALA* 4.7 5.1 - - + +
89B GLN* 3.3 43.5 - - + -
90B THR 4.5 0.4 - - - -
91B GLY* 3.2 38.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 535 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A PRO* 3.8 2.8 - - - +
528A ILE* 2.8 40.1 + - + +
530A LEU* 4.8 3.1 - - + -
533A HIS* 3.4 24.0 - - - -
534A TRP* 1.3 85.5 - - - +
536A LEU* 1.3 61.2 + - - +
548A TYR* 3.0 38.6 - - + +
549A TYR 3.7 3.6 - - - +
550A ASP* 3.6 19.3 - - - -
606A ALA* 4.5 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 536 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A MET* 4.7 9.6 - - + -
525A LEU* 4.5 8.5 - - + -
526A VAL 2.9 38.4 - - - +
527A PRO* 3.7 9.2 - - + -
528A ILE* 3.7 3.6 - - - -
535A CYS* 1.3 77.4 - - - +
537A ALA* 1.3 65.2 + - - +
538A VAL* 4.0 16.8 - - + -
548A TYR* 3.4 2.6 - - - -
549A TYR* 2.6 49.4 + - + +
606A ALA* 3.8 21.7 - - + +
609A TYR* 4.5 2.9 - - + -
610A ALA* 3.6 34.1 - - + +
613A ILE* 4.5 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 537 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A VAL* 2.7 45.1 + - + +
528A ILE* 3.4 18.1 - - + +
536A LEU* 1.3 74.5 - - - +
538A VAL* 1.3 64.0 + - - +
546A ILE* 5.2 2.0 - - + -
547A THR 3.6 7.0 - - - +
548A TYR* 4.2 11.9 - - + +
559A ALA* 5.4 2.7 - - + -
560A CYS* 5.8 0.4 - - - -
563A LEU* 3.7 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A ILE* 3.5 26.7 - - + -
524A LEU 3.5 2.7 - - - -
525A LEU* 4.1 8.3 - - + -
536A LEU* 4.0 11.7 - - + -
537A ALA* 1.3 78.2 - - - +
539A VAL* 1.3 67.7 + - - +
540A ASP* 4.3 7.4 - - + +
545A ASN 3.5 4.0 - - - +
546A ILE* 3.4 4.0 - - - +
547A THR* 2.9 40.9 + - + +
549A TYR* 3.5 26.9 - - + +
613A ILE* 3.8 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A ILE* 3.2 5.7 - - - +
524A LEU* 2.7 70.0 + - + +
526A VAL* 5.0 5.1 - - + +
537A ALA 4.3 0.2 + - - -
538A VAL* 1.3 72.3 - - - +
540A ASP* 1.3 58.5 + - - +
541A PHE* 3.6 17.6 + - + -
546A ILE* 3.7 29.4 - - + -
563A LEU* 4.8 13.7 - - + -
567A LEU* 4.3 15.0 - - + -
584A TRP* 4.2 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 540 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A ASP 3.9 4.7 - - - +
523A ILE* 4.1 11.8 - - - +
538A VAL* 3.5 14.3 + - + +
539A VAL* 1.3 72.4 - - - +
541A PHE* 1.3 52.8 + - - +
542A ARG* 3.0 27.3 + - - +
543A LYS* 2.8 58.7 + - + +
544A LYS* 2.7 36.2 + - - -
545A ASN* 3.5 16.2 + - - +
547A THR* 5.7 1.8 - - + -
584A TRP* 4.0 2.9 - - - -
613A ILE* 5.6 2.4 - - - +
616A ASP* 5.4 0.2 - - - +
----------------------------------------------------------
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