Contacts of the strand formed by residues 426 - 432 (chain B) in PDB entry 2WNW
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 LYS 426 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.7 33.7 - - + +
23B PHE* 4.1 10.3 - - + -
24B SER* 3.3 16.4 - - - +
25B HIS* 4.3 5.8 + - - +
26B ARG 4.5 0.4 - - - -
422B LEU* 3.0 6.1 - - - +
423B ASP 2.8 36.1 + - - +
424B GLY 3.3 0.2 - - - -
425B ASP* 1.3 112.4 + - - +
427B GLU* 1.3 62.2 + - - +
445B GLU* 3.5 34.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 3.3 7.4 - - - -
24B SER* 2.8 39.6 + - - +
25B HIS 4.2 2.7 - - - +
26B ARG* 3.2 13.8 - - - +
27B GLN* 2.9 37.6 + - - -
33B LEU* 5.4 0.6 - - + +
420B ARG* 2.8 53.8 + - + +
421B VAL 3.1 13.7 - - - +
422B LEU* 4.2 10.2 - - + +
426B LYS* 1.3 76.2 - - - +
428B ILE* 1.3 63.3 + - - +
429B ALA* 5.1 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 3.1 48.5 - - + -
22B SER 4.1 11.9 - - - +
23B PHE* 3.5 28.9 - - + +
420B ARG* 3.5 2.4 - - - -
421B VAL* 3.0 37.3 + - + +
427B GLU* 1.3 78.2 - - - +
429B ALA* 1.3 72.8 + - - +
430B LEU* 3.7 16.1 + - + +
440B LEU* 3.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ARG* 5.6 2.8 + - - -
27B GLN* 6.2 0.9 - - - +
418B ARG* 6.6 0.2 - - + -
419B CYS 3.4 8.3 - - - +
420B ARG* 4.2 16.5 - - + +
427B GLU* 5.1 3.0 + - - +
428B ILE* 1.3 76.0 - - - +
430B LEU* 1.3 67.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 3.9 42.2 - - + -
19B ARG* 5.5 2.2 - - - +
409B VAL* 4.9 11.4 - - + -
417B ARG 4.0 0.3 - - - +
418B ARG* 3.3 5.0 - - - +
419B CYS* 2.8 46.7 + - - -
421B VAL* 3.7 23.8 - - + -
428B ILE* 4.0 27.1 - - + +
429B ALA* 1.3 84.7 - - - +
431B THR* 1.3 64.4 + - - +
432B LEU* 4.1 8.5 - - + -
438B SER* 5.0 7.9 - - - +
440B LEU* 4.7 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B GLU* 3.4 40.2 - - + +
417B ARG 3.4 6.1 - - - +
418B ARG* 3.9 16.4 - - + +
430B LEU* 1.3 77.6 + - - +
432B LEU* 1.3 68.3 + - - +
433B PRO* 4.2 4.5 - - - +
438B SER* 5.3 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B LEU* 5.0 3.4 - - + -
409B VAL* 3.7 34.5 - - + +
411B ASN* 3.3 20.7 + - + +
416B GLU* 3.3 4.8 - - - +
417B ARG 2.8 40.8 + - - +
419B CYS* 4.3 13.7 - - - -
430B LEU* 4.1 23.1 - - + -
431B THR* 1.3 81.3 - - - +
433B PRO* 1.3 70.9 - - + +
436B GLY 3.6 22.4 - - - +
438B SER* 3.8 21.8 - - - +
----------------------------------------------------------
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