Contacts of the strand formed by residues 264 - 267 (chain D) in PDB entry 1D1T
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 TYR 264 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D GLY* 3.5 26.5 - - - -
188D LYS 3.5 2.4 + - - -
189D VAL* 3.6 16.4 - - + -
190D LYS* 3.1 39.8 + - - +
193D SER* 3.4 32.3 - - - -
194D THR 3.0 8.1 + - - +
195D CYS* 3.1 12.1 - - - -
196D VAL 2.8 24.4 + - - -
262D VAL* 3.5 1.9 - - - +
263D GLY* 1.3 86.0 - - - +
265D THR* 1.3 66.3 + - - +
266D PHE* 3.9 20.2 - + + -
282D CYS* 4.9 0.2 - - - -
288D THR* 3.2 31.0 - - + +
290D VAL* 6.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D VAL* 3.2 19.3 - - + -
198D PHE* 4.2 8.7 - - + -
262D VAL* 3.5 28.5 - - + -
264D TYR* 1.3 72.8 - - - +
266D PHE* 1.3 70.0 + - - +
278D ALA* 2.8 31.0 + - - +
281D SER* 4.0 8.7 - - - -
282D CYS* 4.0 7.6 - - + +
288D THR 2.9 8.0 + - - +
289D SER* 2.8 22.3 + - - -
290D VAL* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D ALA* 3.5 32.5 - - + -
183D ALA* 3.8 7.0 - - + -
187D GLY* 4.9 1.1 - - - -
189D VAL* 3.8 23.1 - - + -
195D CYS* 4.4 2.9 - - + -
196D VAL 2.8 18.1 + - - +
197D VAL* 4.3 6.3 - - + -
198D PHE* 2.8 33.7 + - - +
207D VAL* 3.6 19.5 - - + -
211D CYS* 3.7 18.8 - - - -
264D TYR* 3.9 24.2 - + + -
265D THR* 1.3 76.6 - - - +
267D GLU* 1.3 62.2 + - - +
268D VAL* 3.3 17.3 + - + +
278D ALA* 4.7 0.7 - - - -
290D VAL* 3.5 32.5 - - + +
292D VAL* 4.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D PHE* 4.0 5.6 - - + -
265D THR 4.3 0.4 - - - -
266D PHE* 1.3 70.5 - - - +
268D VAL* 1.3 58.5 + - - +
269D ILE* 2.9 15.3 + - - +
270D GLY 3.0 10.5 + - - -
271D HIS 2.9 20.1 + - - +
274D THR* 2.7 31.1 + - - +
275D MET* 3.6 42.5 - - + +
278D ALA* 4.2 11.8 - - + +
289D SER* 5.8 0.2 - - - +
290D VAL 3.0 12.9 + - - +
291D VAL* 4.4 6.3 - - + -
292D VAL* 2.9 8.7 + - - +
293D GLY* 2.8 30.8 + - - -
----------------------------------------------------------
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