Contacts of the strand formed by residues 555 - 560 (chain A) in PDB entry 2WP9
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 CYS 555 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ILE* 3.7 7.6 - - - +
533A ARG* 2.8 27.4 + - - -
552A ASN 4.2 0.7 - - - -
553A TRP* 2.8 32.8 + - - +
554A LEU* 1.3 76.7 - - - +
556A HIS* 1.3 59.6 + - - +
568A ARG* 3.2 37.9 - - + -
569A ARG 3.4 13.9 - - - +
570A SER* 4.9 2.2 - - - -
571A VAL* 3.3 17.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ILE* 3.0 27.3 + - - +
81A ASP* 2.9 35.0 + - - -
234A GLN* 3.3 34.2 + - + +
235A ASP* 2.6 32.5 + - - +
393A SER* 3.8 7.9 - - - -
533A ARG* 3.8 0.4 - - - -
555A CYS* 1.3 76.4 - - - +
557A SER* 1.3 60.5 + - - +
568A ARG* 3.3 9.2 - - - +
569A ARG* 2.9 36.7 + - + +
570A SER 3.1 27.6 - - - -
571A VAL* 3.8 4.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A GLN* 3.3 6.9 - - - +
235A ASP* 2.7 35.4 + - - -
237A GLU* 2.9 31.3 + - - -
529A SER* 4.2 0.7 + - - -
532A PHE* 4.1 17.3 - - - -
533A ARG* 3.5 15.2 - - - +
553A TRP* 4.9 1.3 - - - -
555A CYS* 5.6 0.7 - - - -
556A HIS* 1.3 75.0 - - - +
558A LEU* 1.3 60.0 + - - +
566A MET* 3.8 18.2 - - - +
567A THR 3.6 3.6 - - - -
568A ARG* 4.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A PRO* 3.7 25.8 - - + -
233A VAL 3.6 16.4 - - - +
234A GLN* 3.9 20.6 - - + +
361A PRO* 4.2 10.3 - - + -
370A THR 5.7 0.2 - - - -
371A VAL* 3.8 41.1 - - + -
557A SER* 1.3 73.4 - - - +
559A TYR* 1.3 59.7 + - - +
560A LEU* 3.8 8.4 + - + -
566A MET* 3.4 9.3 - - - +
567A THR* 2.8 53.1 + - + +
568A ARG 4.8 5.2 - - - +
569A ARG* 4.1 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ILE* 4.0 25.7 - - + +
232A PRO* 3.2 24.9 - - - +
233A VAL* 2.9 31.1 + - + +
236A MET* 5.5 0.2 - - + -
491A ARG* 4.4 2.9 + - - -
521A GLU* 5.4 1.1 + - - -
524A TYR* 3.4 27.2 - + - -
525A ALA* 3.9 18.2 - - + -
528A VAL* 4.0 24.7 - - + -
529A SER* 4.2 8.3 - - - +
557A SER 4.3 0.2 - - - -
558A LEU* 1.3 68.8 - - - +
560A LEU* 1.3 61.5 + - - +
561A PRO* 3.3 19.6 - - + +
564A GLU* 3.6 35.4 - - - +
565A SER 4.1 2.0 - - - -
566A MET* 3.8 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A PRO* 4.3 7.9 - - + -
371A VAL* 3.9 28.0 - - + -
558A LEU* 4.1 16.4 - - + -
559A TYR* 1.3 73.8 - - - +
561A PRO* 1.3 58.9 - - + +
562A GLU* 3.3 3.0 + - + +
563A SER* 3.8 11.4 - - - +
564A GLU* 2.7 36.1 + - - -
565A SER* 2.8 30.3 + - - +
566A MET 4.8 0.9 - - - +
567A THR* 3.7 25.6 - - + -
----------------------------------------------------------
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