Contacts of the strand formed by residues 310 - 315 (chain B) in PDB entry 2FQ6
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 310 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B SER* 6.4 0.9 - - - -
159B ILE 5.7 2.0 - - - +
161B MET* 3.5 12.5 - - + +
188B TRP* 2.8 43.5 + - + +
211B TYR* 3.6 2.0 + - - +
288B HIS* 5.2 1.3 - - - -
308B SER* 3.6 2.5 + - - +
309B GLY* 1.3 77.1 - - - +
311B PHE* 1.3 66.7 + - - +
340B TRP* 3.5 67.1 - - + +
372B ARG* 3.9 32.8 - - + +
373B LEU 3.4 15.9 - - - +
374B HIS* 4.0 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B MET* 4.0 10.5 - - + -
270B SER* 3.8 11.9 - - - -
273B VAL* 3.9 12.1 - - + -
274B ALA* 3.8 16.6 - - + -
277B LEU* 3.6 32.1 - - + -
286B VAL* 3.9 12.1 - - + -
287B ASN 3.4 11.7 - - - +
288B HIS* 3.5 27.6 - - + +
289B PRO* 4.7 0.7 - - + -
309B GLY 4.0 7.4 - - - -
310B LEU* 1.3 77.5 - - - +
312B SER* 1.3 84.3 + - - +
313B PHE* 4.8 0.2 - + - -
372B ARG* 3.4 8.1 - - - +
373B LEU* 2.8 44.8 + - + +
375B ILE* 3.6 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE 2.7 28.1 + - - -
161B MET* 3.8 0.9 - - - +
287B ASN* 2.7 57.7 + - - +
311B PHE* 1.3 86.9 - - - +
313B PHE* 1.3 58.7 + - - +
370B LEU* 3.7 14.1 - - - +
371B ILE 3.0 15.0 - - - -
372B ARG* 3.9 3.4 - - - -
373B LEU 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU* 3.6 27.8 - - + -
283B VAL* 3.9 16.6 - - + -
285B ARG 3.4 13.9 - - - +
286B VAL* 4.1 15.7 - - + +
287B ASN* 4.4 2.2 - - - +
311B PHE* 4.8 0.2 - + - -
312B SER* 1.3 77.2 - - - +
314B VAL* 1.3 68.6 + - - +
315B LEU* 3.7 27.6 - - + -
327B TYR* 3.5 23.3 - - - -
370B LEU* 3.6 3.1 - - - +
371B ILE* 2.8 63.6 + - + -
373B LEU* 3.9 21.8 - - + -
387B LEU* 5.0 2.5 - - + -
391B PHE* 4.1 11.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B VAL* 3.7 2.9 - - - +
284B ALA* 2.7 38.6 + - + +
285B ARG* 2.9 34.6 + - + +
287B ASN* 4.0 17.9 - - - +
313B PHE* 1.3 78.1 - - - +
315B LEU* 1.3 65.7 + - - +
366B PHE* 3.9 30.5 - - + -
368B GLY 3.8 28.9 - - - +
369B THR 3.5 3.1 - - - +
370B LEU* 4.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLN* 3.7 12.3 - - + +
283B VAL* 4.6 0.2 - - - +
284B ALA* 3.8 2.9 - - - +
313B PHE* 3.7 25.9 - - + -
314B VAL* 1.3 78.9 - - - +
316B LYS* 1.3 63.8 + - - +
317B LYS* 3.6 15.9 - - + +
319B LEU* 3.8 32.8 - - + -
327B TYR* 5.0 3.6 - - + +
368B GLY* 3.4 17.3 - - - -
369B THR* 2.9 19.4 + - - +
371B ILE* 4.0 18.6 - - + -
391B PHE* 3.7 20.9 - - + -
394B ILE* 3.8 19.1 - - + -
----------------------------------------------------------
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