Contacts of the strand formed by residues 508 - 514 (chain A) in PDB entry 2WCO
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 508 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A HIS* 3.4 39.3 - - + +
400A LEU* 5.5 0.2 - - + -
502A ALA 3.4 11.7 - - - +
503A THR* 3.8 3.1 - - - -
507A TYR* 1.3 80.7 - - - +
509A ALA* 1.3 60.0 + - - +
510A VAL* 4.0 9.4 - - + -
527A TRP 3.7 1.0 - - - +
528A PHE* 3.4 6.4 - - - +
529A PHE* 2.9 33.5 + - + +
530A LEU* 5.6 0.5 - - - +
673A LEU* 6.0 0.2 - - - +
675A ALA* 5.7 0.2 - - - -
696A LEU* 4.5 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A GLY* 3.0 4.7 - - - -
502A ALA* 2.9 34.5 + - + +
508A ALA* 1.3 70.9 - - - +
510A VAL* 1.3 63.2 + - - +
527A TRP 3.7 4.0 - - - -
528A PHE* 3.9 20.9 - - + -
675A ALA* 4.1 12.6 - - + -
676A ALA 4.6 0.9 - - - +
677A ASN* 3.7 9.4 - - - +
694A SER* 3.5 17.7 - - - +
695A VAL 4.4 9.6 - - - +
696A LEU* 4.9 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A HIS* 4.4 2.7 - - + -
400A LEU* 4.1 21.3 - - + -
407A ALA* 4.5 1.3 - - + -
418A LEU* 3.7 15.0 - - + -
420A MET* 3.6 28.7 - - + -
500A GLY 3.5 11.4 - - - +
501A GLY* 4.1 0.2 - - - -
508A ALA* 4.0 15.3 - - + -
509A ALA* 1.3 80.7 - - - +
511A GLY* 1.3 61.7 + - - +
526A SER* 3.2 0.3 - - - -
527A TRP* 2.7 41.4 + - + +
529A PHE* 3.8 24.5 - - + -
677A ASN* 3.1 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A MET* 3.8 6.8 - - - +
498A TRP* 3.6 18.7 - - - -
499A VAL* 3.3 4.7 - - - -
500A GLY 2.9 36.3 + - - +
510A VAL* 1.3 77.2 - - - +
512A GLN* 1.3 60.1 + - - +
525A LYS 3.3 8.7 - - - -
527A TRP* 4.5 0.2 - - - -
677A ASN* 3.6 7.7 - - - +
679A TRP* 3.8 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A MET* 3.3 22.8 - - + +
421A ALA* 3.3 23.0 + - - +
442A GLY 2.9 23.4 + - - -
443A ALA 4.4 0.4 - - - -
444A GLY* 3.1 29.3 + - - -
494A PRO* 5.5 1.0 - - - +
498A TRP 4.0 1.1 - - - -
499A VAL* 4.2 3.6 - - + -
511A GLY* 1.3 73.8 - - - +
513A HIS* 1.3 71.0 + - - +
514A LEU* 3.3 29.7 + - - +
524A ARG* 3.7 0.5 - - - -
525A LYS* 2.7 36.7 + - + +
527A TRP* 3.7 14.0 - - + -
679A TRP* 3.6 4.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ALA 4.8 1.0 - - - +
494A PRO* 5.2 0.3 - - - +
495A ASP 5.2 0.2 - - - -
496A VAL* 3.3 51.7 - - + +
497A ARG 4.8 2.4 + - - -
498A TRP* 3.0 26.6 + - + +
499A VAL* 4.1 0.4 - - - +
512A GLN* 1.3 73.9 - - - +
514A LEU* 1.3 61.3 + - - +
515A LYS* 3.8 8.1 + - - -
522A GLU* 2.7 37.7 + - + +
523A ALA 3.6 11.4 - - - -
524A ARG* 3.4 39.5 + - - +
679A TRP* 3.7 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A HIS* 4.7 6.1 - - - +
442A GLY 4.8 0.2 - - - +
443A ALA* 3.9 21.3 - - + +
475A THR* 3.4 30.3 - - - +
494A PRO* 5.7 1.1 - - + -
512A GLN* 3.3 29.8 + - + +
513A HIS* 1.3 73.5 - - - +
515A LYS* 1.3 83.4 + - - +
516A GLY* 4.3 5.2 - - - +
521A LEU* 4.2 11.2 - - + -
522A GLU* 3.2 7.3 - - - +
523A ALA* 2.8 42.9 + - + +
525A LYS* 3.9 23.6 - - + -
----------------------------------------------------------
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