Contacts of the strand formed by residues 258 - 263 (chain A) in PDB entry 3QKJ
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 MET 258 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 3.7 10.0 - - - -
219A ASP* 4.4 0.2 - - - +
254A ALA* 3.7 3.0 - - - +
255A MET* 2.9 39.7 + - + +
256A SER 4.1 2.7 - - - +
257A GLY* 1.4 81.9 - - - +
259A ARG* 1.3 76.7 + - - +
271A GLU* 3.7 49.1 - - + +
272A VAL 3.4 6.1 - - - +
273A SER* 3.6 28.3 - - - +
308C LYS* 4.8 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 3.6 42.1 + - - +
219A ASP* 2.7 42.4 + - - -
221A LYS* 3.1 17.4 + - - +
222A GLU 3.1 19.1 + - - +
223A PHE* 2.7 29.6 + - + -
243A VAL* 4.2 9.6 - - + -
254A ALA* 4.5 2.5 - - - -
257A GLY 4.3 1.4 - - - -
258A MET* 1.3 93.3 + - - +
260A TRP* 1.3 69.1 + - - +
261A VAL* 3.7 0.7 + - + +
270A SER 3.6 0.3 - - - +
271A GLU* 3.5 2.0 - - - -
272A VAL* 2.8 33.4 + - - +
274A ALA* 4.7 6.5 - - + -
277A LEU* 3.9 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 3.0 16.4 + - - +
243A VAL* 3.5 5.5 - - - +
244A VAL* 3.0 29.8 + - + +
246A TRP* 3.5 21.7 - - + +
249A THR* 3.7 28.7 - - + -
251A LYS* 3.8 31.0 - - + -
252A ARG* 2.8 54.0 + - + -
254A ALA* 3.4 25.5 - - + +
259A ARG* 1.3 74.2 - - - +
261A VAL* 1.3 62.1 + - - +
269A PHE* 4.2 9.6 - - + -
270A SER* 3.4 30.1 - - - -
271A GLU* 3.5 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A VAL* 4.3 4.7 - - + -
241A ALA* 3.9 12.1 - - + -
242A MET 3.3 8.1 - - - +
243A VAL* 4.2 12.6 - - + -
244A VAL* 4.3 4.0 - - - -
259A ARG* 4.3 4.9 - - + +
260A TRP* 1.3 78.9 - - - +
262A GLN* 1.3 60.0 + - - +
263A TRP* 3.9 25.3 + - + -
268A LYS 3.9 0.2 - - - +
269A PHE* 3.3 6.2 - - - +
270A SER 2.9 40.0 + - - +
272A VAL* 3.8 16.6 - - + -
277A LEU* 3.9 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ALA* 3.3 2.8 - - - -
242A MET 2.8 29.7 + - - +
244A VAL* 4.0 10.0 - - + +
261A VAL* 1.3 72.6 - - - +
263A TRP* 1.3 61.0 + - - +
267A GLY* 3.0 34.6 + - - +
268A LYS 3.3 5.4 - - - +
269A PHE* 3.5 32.9 - - + -
253D GLN* 4.1 3.4 + - - +
254D ALA 3.0 25.5 + - - +
255D MET* 3.5 35.6 - - + +
256D SER* 3.6 14.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLY* 3.6 31.9 - - - -
233A ILE* 3.4 26.7 - - + -
239A TRP* 3.4 33.4 - + + -
240A PRO 3.7 11.4 - - - +
241A ALA* 3.7 17.5 - - + -
261A VAL* 3.9 17.3 - - + -
262A GLN* 1.3 71.8 - - - +
264A PHE* 1.4 61.7 + - - +
266A ASP* 3.5 17.9 - - - +
267A GLY* 2.9 31.2 + - - -
268A LYS 2.9 33.5 + - - -
270A SER* 2.8 29.3 + - - +
272A VAL* 4.1 5.2 - - + -
356A BTB 3.4 37.2 - - - -
255D MET* 3.7 3.9 - - - +
----------------------------------------------------------
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