Contacts of the strand formed by residues 317 - 322 (chain B) in PDB entry 5WWT
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 PHE 317 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LYS* 3.5 39.7 - - + +
238B ILE 4.0 7.0 - - - -
239B LEU* 3.5 42.4 - - + -
263B ILE* 3.8 16.4 - - + -
312B PHE* 3.6 43.7 - + + -
316B SER* 1.3 87.8 - - - +
318B ASP* 1.3 63.0 + - - +
319B ARG 4.3 0.4 - - - +
320B ILE* 4.0 14.8 - - + -
361B LEU* 3.3 24.9 + - + +
362B LEU* 3.7 2.8 - - - +
363B LYS* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B GLY 4.7 0.5 - - - +
236B GLU* 3.3 30.0 - - + +
237B LYS* 2.7 40.9 + - - +
317B PHE* 1.3 72.2 - - - +
319B ARG* 1.3 64.3 + - - +
362B LEU* 3.7 1.3 - - - +
363B LYS* 3.4 32.1 + - - +
366B GLY* 3.4 26.7 - - - -
367B VAL 3.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A HIS* 6.0 1.8 + - - -
230B LEU* 2.9 34.9 + - + -
231B ASN* 2.9 30.7 + - - +
232B PRO* 3.9 8.5 - - - -
233B GLN* 3.7 8.9 - - - +
236B GLU* 2.5 53.7 + - - +
237B LYS 3.0 5.8 + - - +
238B ILE* 3.2 17.3 - - + -
239B LEU 2.9 23.9 + - - -
317B PHE* 4.3 0.9 - - - +
318B ASP* 1.3 83.5 - - - +
320B ILE* 1.3 67.3 + - - +
362B LEU* 4.2 0.4 - - - -
367B VAL* 3.4 37.8 - - + +
462B LYS* 6.1 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LEU* 4.2 3.8 - - - +
239B LEU* 3.2 26.5 - - + +
241B LEU* 5.0 4.0 - - + -
317B PHE* 4.0 12.3 - - + -
319B ARG* 1.3 81.6 - - - +
321B LEU* 1.3 67.8 + - - +
322B LEU 4.5 0.2 - - - +
358B ALA* 3.2 37.5 - - + +
361B LEU* 3.7 32.5 - - + +
362B LEU* 3.9 11.2 - - + +
367B VAL 2.9 9.8 + - - +
368B LEU* 3.3 25.4 - - + +
369B VAL 2.9 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B VAL* 3.5 27.6 - - + -
227B SER* 5.4 1.1 - - - +
230B LEU* 3.9 17.6 - - + +
239B LEU 2.9 9.4 + - - -
240B ASP* 3.1 37.6 - - + +
241B LEU 3.4 5.2 + - - -
248B LYS* 3.9 35.7 - - + -
252B ILE* 3.9 17.3 - - + -
320B ILE* 1.3 73.7 - - - +
322B LEU* 1.3 59.0 + - - +
323B ASP* 3.4 10.4 + - + +
369B VAL* 3.4 24.5 - - + +
371B SER* 4.1 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 4.0 23.8 - - + +
242B CYS* 4.4 5.2 - - - +
320B ILE* 3.9 3.0 + - - -
321B LEU* 1.3 69.6 - - - +
323B ASP* 1.3 59.0 + - - +
324B ALA* 3.0 21.2 + - + -
351B GLN 4.1 3.8 - - - +
354B LEU* 3.8 21.5 - - + +
355B PHE* 3.6 37.2 - - + +
358B ALA* 4.9 4.3 - - + -
368B LEU* 4.4 10.7 - - + +
369B VAL 2.9 13.7 + - - +
370B TYR* 3.5 28.6 - - + -
371B SER 2.9 24.3 + - - +
----------------------------------------------------------
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