Contacts of the strand formed by residues 293 - 297 (chain D) in PDB entry 6F0X
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 VAL 293 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D THR* 6.1 0.2 - - - +
171D TRP* 4.8 1.7 - - - -
173D ARG* 3.1 33.5 - - + +
236D ILE* 5.9 0.2 - - + -
240D ILE* 3.8 25.1 - - + -
247D VAL* 3.4 31.0 - - + -
249D VAL* 4.8 3.6 - - + -
287D ILE* 4.6 18.8 - - + +
290D HIS* 3.8 6.6 + - + +
291D SER 3.8 0.4 - - - -
292D ASN* 1.3 94.4 - - - +
294D VAL* 1.3 80.1 + - - +
295D ILE* 4.4 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D TYR* 4.8 12.1 - - + +
153D VAL* 4.0 35.0 - - + -
156D THR* 5.6 3.1 - - + +
171D TRP* 5.7 1.6 - - + -
173D ARG* 3.7 8.7 - - + +
175D VAL* 5.1 3.6 - - + -
192D LEU* 6.0 0.2 - - + -
196D LEU* 5.8 0.4 - - + -
246D LEU* 6.1 2.2 - - + -
247D VAL 2.9 7.4 + - - +
248D PHE* 3.3 26.9 - - + -
249D VAL 2.9 22.7 + - - -
292D ASN 5.6 0.4 - - - -
293D VAL* 1.3 82.2 - - - +
295D ILE* 1.3 66.5 + - - +
296D LEU* 3.5 30.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D ASN 5.1 1.1 - - - +
173D ARG* 2.7 17.6 + - + +
174D VAL* 3.7 28.2 - - + -
175D VAL* 2.9 29.5 + - - +
233D PHE* 5.7 1.8 - - + -
249D VAL* 3.4 31.4 - - + +
251D ILE* 4.4 3.4 - - + -
284D ILE* 3.9 18.8 - - + -
287D ILE* 3.5 31.6 - - + -
293D VAL* 4.4 7.0 - - + -
294D VAL* 1.3 71.8 - - - +
296D LEU* 1.3 59.7 + - - +
297D THR* 3.5 21.7 - - + +
309D PHE* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D LEU* 5.3 2.2 - - + -
175D VAL* 3.8 17.3 - - + -
177D LEU* 5.6 1.1 - - + -
189D CYS* 3.4 54.7 - - + +
192D LEU* 4.4 19.5 - - + -
193D ALA* 4.5 2.2 - - + -
248D PHE* 4.2 19.5 - - + -
249D VAL 2.8 8.4 + - - +
250D LEU* 3.5 14.1 - - + -
251D ILE 2.9 29.6 + - - +
294D VAL* 3.5 26.0 + - + +
295D ILE* 1.3 72.6 - - - +
297D THR* 1.3 60.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D VAL* 4.6 6.9 - - + +
175D VAL 2.2 29.4 + - - +
176D LEU* 3.0 21.1 - - - +
177D LEU* 2.9 29.3 + - - +
189D CYS* 4.7 1.5 - - - -
251D ILE* 3.5 12.8 - - + -
254D VAL* 3.4 27.4 - - + -
295D ILE* 3.5 24.2 - - + +
296D LEU* 1.3 81.4 - - - +
298D THR* 1.3 67.5 + - - +
309D PHE* 5.4 5.2 - - + -
----------------------------------------------------------
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