Contacts of the strand formed by residues 262 - 266 (chain D) in PDB entry 3CLS
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 LEU 262 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C ILE* 4.2 3.6 - - + +
258C ILE* 3.9 23.1 - - + +
261C PHE* 3.8 37.0 - - + -
203D ASP 3.2 4.3 + - - +
204D PHE* 3.5 32.9 - - + -
205D ILE 2.9 26.9 + - - +
260D CYS* 3.2 6.1 - - - -
261D LYS* 1.3 79.0 - - - +
263D TYR* 1.3 60.1 + - - +
264D VAL* 4.5 3.6 - - + -
283D THR* 3.3 34.8 - - + +
285D ILE* 4.1 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D ILE* 3.3 32.1 - - + -
207D SER* 2.8 28.1 + - - -
250D VAL* 3.6 17.1 - - + +
257D VAL* 4.2 5.8 - - + -
260D CYS* 3.9 7.9 - - - -
262D LEU* 1.3 72.9 - - - +
264D VAL* 1.3 63.3 + - - +
265D ALA* 3.9 20.2 - - + -
274D HIS* 2.7 29.6 + - - -
278D MET* 3.8 42.8 - - + -
281D VAL* 3.8 18.8 - - + +
283D THR 3.1 5.9 + - - -
284D ILE* 3.3 7.7 - - + +
285D ILE* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C ILE* 5.3 9.9 - - + -
258C ILE* 5.5 1.1 - - + -
204D PHE* 4.1 20.0 - - + -
205D ILE 2.8 16.8 + - - +
206D MET* 3.4 17.3 - - + -
207D SER 2.7 34.2 + - - +
262D LEU* 4.5 4.3 - - + -
263D TYR* 1.3 75.9 - - - +
265D ALA* 1.3 55.7 + - - +
266D MET* 3.6 24.8 + - + +
285D ILE* 3.5 39.3 - - + +
287D VAL* 4.5 6.3 - - + -
314D LEU* 6.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D SER 3.7 3.6 - - - -
263D TYR* 3.8 22.3 + - + -
264D VAL* 1.3 69.9 - - - +
266D MET* 1.3 61.3 + - - +
267D GLY 4.0 0.7 + - - -
268D ILE* 4.2 18.2 + - + +
284D ILE* 5.0 1.6 - - + -
285D ILE 2.9 13.6 + - - +
286D ALA* 3.6 1.2 - - - +
287D VAL 3.0 27.2 + - - +
288D ASN* 5.5 0.3 - - - +
295D ILE* 4.2 28.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D MET* 3.7 36.3 - - + +
207D SER 2.8 20.3 + - - +
208D ILE* 3.4 12.5 - - + +
209D GLY 3.1 19.2 + - - -
221D PHE* 3.9 32.1 - - + +
224D LEU* 4.3 12.3 - - + -
232D LEU* 5.4 0.9 - - + -
264D VAL* 4.0 20.2 - - + +
265D ALA* 1.3 75.3 - - - +
267D GLY* 1.3 64.2 + - - +
268D ILE* 3.3 1.2 + - - +
287D VAL* 3.6 18.4 - - + -
307D ILE* 3.9 19.9 - - + +
310D ILE* 5.8 4.5 - - - -
311D GLU* 5.6 1.1 - - - -
314D LEU* 5.5 4.7 - - - -
----------------------------------------------------------
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