Contacts of the strand formed by residues 302 - 307 (chain D) in PDB entry 6FF7
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 302 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D LEU* 4.2 3.3 - - - +
297D HIS* 3.5 29.0 + - + +
300D ILE* 3.2 8.9 + - + +
301D ASP* 1.3 78.5 - - - +
303D LEU* 1.3 63.7 + - - +
314D ILE* 5.9 4.9 - - + -
315D TRP 3.7 9.9 - - - +
316D ASP* 5.1 2.9 - - + -
317D VAL* 5.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295D ASP 3.6 11.0 - - - +
296D LEU* 4.7 3.1 - - + +
297D HIS 5.1 0.4 - - - +
302D VAL* 1.3 77.8 - - - +
304D VAL* 1.3 61.9 + - - +
314D ILE* 3.3 7.4 - - - +
315D TRP* 2.9 45.6 + - + +
317D VAL* 6.0 1.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D LEU* 3.3 3.5 - - - +
295D ASP* 2.9 39.7 + - + +
296D LEU 5.7 0.2 - - - -
303D LEU* 1.3 75.7 - - - +
305D THR* 1.3 61.9 + - - +
312D ALA* 6.2 2.7 - - + -
313D ARG 3.5 7.0 - - - +
314D ILE* 5.3 1.8 - - + -
336D VAL* 5.3 10.8 - - + -
337D ARG 6.1 0.7 - - - +
338D CYS* 4.9 17.5 - - + -
345D ILE* 5.8 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 305 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D GLY 3.5 9.6 - - - -
294D LEU* 4.2 6.1 - - - +
303D LEU 5.8 0.2 - - - -
304D VAL* 1.3 75.9 - - - +
306D CYS* 1.3 62.0 + - - +
307D SER* 4.1 2.3 + - - -
312D ALA* 3.1 6.8 - - - +
313D ARG* 2.9 40.3 + - - +
315D TRP* 6.1 4.0 - - - -
336D VAL* 5.2 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 306 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D VAL* 4.1 2.0 - - - +
292D TYR* 3.0 7.1 + - - -
293D GLY 2.9 38.0 + - - +
305D THR* 1.3 75.2 - - - +
307D SER* 1.3 59.6 + - - +
311D THR 4.1 3.4 - - - -
312D ALA* 4.3 5.8 - - + +
333D VAL* 3.8 31.0 - - + +
335D THR 4.5 6.7 - - - +
336D VAL* 4.0 22.2 - - + +
347D THR* 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 307 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D HIS* 5.0 13.9 - - - -
289D SER* 5.3 2.0 - - - -
290D ALA 3.3 15.5 - - - -
291D VAL* 4.2 3.6 - - - +
292D TYR* 4.1 8.1 - - - +
305D THR* 5.3 2.7 - - - -
306D CYS* 1.3 73.1 - - - +
308D ARG* 1.3 61.1 + - - +
309D ASP* 3.8 4.3 - - - -
311D THR* 3.2 24.3 + - - +
332D ALA* 4.2 0.3 - - - +
333D VAL* 3.3 28.3 + - - +
----------------------------------------------------------
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