Contacts of the strand formed by residues 509 - 513 (chain A) in PDB entry 2WSK
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 THR 509 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TRP* 3.4 17.0 + - + -
151A THR* 3.9 33.4 - - + +
153A ILE* 3.9 10.8 - - + -
433A SER* 2.9 26.7 + - - +
435A ALA 2.8 9.9 + - - -
436A ILE* 3.3 31.0 - - + +
437A ASN* 2.8 27.8 + - - -
508A GLY* 1.3 71.6 - - - -
510A PRO* 1.3 65.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A THR 3.4 21.1 - - - +
152A ILE* 3.6 7.8 - - + +
153A ILE* 2.9 26.2 + - - +
437A ASN* 3.8 6.3 - - + +
503A LEU* 3.8 23.1 - - + +
504A LEU* 4.1 19.7 - - + +
506A SER 4.7 0.7 - - - +
508A GLY 3.3 7.9 - - - +
509A THR* 1.3 84.6 - - - +
511A MET* 1.3 60.4 + - - +
512A LEU 4.1 0.2 - - - -
558A ARG* 3.1 37.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ILE* 3.4 26.0 - - + +
155A GLU* 4.1 21.3 - - + +
197A GLU* 4.3 8.1 - - - +
392A TRP* 3.5 47.6 - - + -
436A ILE* 4.1 16.4 - - + -
437A ASN 3.0 16.0 + - - +
438A LEU* 4.1 17.9 - - + +
439A VAL 4.8 1.0 + - - -
440A THR 4.0 11.6 - - - +
441A ALA* 4.0 15.7 - - + -
503A LEU* 3.7 18.1 - - - +
510A PRO* 1.3 73.4 - - - +
512A LEU* 1.3 69.3 + - - +
513A LEU 4.1 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ILE* 5.4 3.8 - - + +
153A ILE 2.8 10.5 + - - +
154A TYR* 3.3 19.7 - - + -
155A GLU 3.0 22.6 + - - -
191A LEU* 4.3 2.9 - - + -
193A ILE* 5.2 1.8 - - + -
500A LEU* 4.1 26.2 - - + -
503A LEU* 4.1 15.5 - - + -
504A LEU* 4.6 8.1 - - + -
510A PRO 4.1 0.8 - - - -
511A MET* 1.3 75.2 - - - +
513A LEU* 1.3 67.4 + - - +
514A ALA 3.6 0.3 + - - -
516A ASP* 4.1 15.0 - - + +
517A GLU* 3.7 27.4 - - + +
551A THR* 3.9 17.7 - - + -
555A ILE* 4.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLU* 3.4 36.3 - - + +
440A THR* 3.5 27.2 + - - +
441A ALA* 3.4 25.4 - - - +
442A HIS* 3.9 5.6 - - + +
446A THR* 4.4 17.0 - - + -
511A MET* 4.1 2.5 + - + -
512A LEU* 1.3 76.5 - - - +
514A ALA* 1.3 80.1 + - + +
515A GLY 3.2 0.2 + - - -
516A ASP* 2.9 42.8 + - - +
517A GLU* 3.6 1.9 - - - +
520A HIS* 6.1 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