Contacts of the strand formed by residues 259 - 265 (chain A) in PDB entry 4JF7
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 GLN 259 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A TYR* 2.7 33.4 + - + +
240A CYS 3.8 1.6 - - - -
241A PHE* 3.9 10.5 - - - +
256A PRO* 5.3 0.6 - - - +
257A PRO* 2.9 27.9 + - - +
258A GLU* 1.3 72.0 - - - +
260A ARG* 1.3 64.5 - - - +
274A ILE* 3.3 10.3 - - - +
275A ILE* 3.1 52.7 + - + +
277A PRO* 5.1 6.3 - - + -
280A VAL* 5.9 3.1 - - + -
287A LEU* 3.0 50.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ASP* 5.0 0.8 + - - -
222A VAL* 4.0 16.4 - - - +
224A ARG* 3.4 16.5 - - - +
238A MET 3.8 0.3 - - - +
239A TYR* 3.4 8.9 - - - -
240A CYS* 2.8 43.5 + - + +
242A VAL* 3.7 14.8 - - + +
258A GLU* 2.7 30.2 + - - +
259A GLN* 1.3 80.0 - - - +
261A ILE* 1.3 63.7 + - - +
262A ILE* 4.2 5.5 - - + +
272A GLU* 2.9 43.9 + - + +
273A ARG 3.3 9.9 - - - +
274A ILE* 4.2 6.7 - - + +
275A ILE* 4.7 0.4 - - - -
372D THR* 3.1 29.7 + - - -
373D ASN* 3.4 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A MET* 3.7 22.0 - - + -
238A MET 3.4 2.0 - - - +
239A TYR* 3.6 37.5 - - + -
260A ARG* 1.3 71.8 - - - +
262A ILE* 1.3 62.9 + - - +
263A ILE* 4.2 8.5 - - + +
271A VAL 3.7 2.3 - - - +
272A GLU* 3.4 1.4 - - - -
273A ARG* 2.8 38.0 + - + +
275A ILE* 3.8 30.3 - - + +
303A PHE* 4.2 8.3 - - + -
363A LEU* 4.5 0.7 - - + -
365A CYS* 4.0 22.0 - - - -
371A LEU* 3.7 24.9 - - + -
375A CYS* 4.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LEU* 4.2 10.8 - - + -
224A ARG* 3.9 18.2 - - - -
237A MET* 3.3 2.6 - - - -
238A MET* 2.6 65.4 + - + +
240A CYS* 4.2 13.5 - - + -
260A ARG* 4.6 4.0 - - + +
261A ILE* 1.3 76.6 - - - +
263A ILE* 1.3 63.3 + - - +
264A MET* 3.7 29.5 - - + +
270A ILE* 4.2 11.0 - - + -
271A VAL 3.6 1.8 - - - -
272A GLU* 3.3 44.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A VAL* 4.8 2.0 - - + -
236A CYS 3.4 9.6 - - - +
237A MET* 3.8 29.8 - - + -
261A ILE* 4.2 5.6 - - + -
262A ILE* 1.3 76.1 - - - +
264A MET* 1.3 64.3 + - - +
265A TYR* 3.5 39.1 - - + +
269A THR 3.8 1.2 - - - +
270A ILE* 3.2 6.1 - - - +
271A VAL* 2.9 43.3 + - + +
367A LEU* 4.4 10.3 - - + -
368A ARG 3.3 31.2 - - - +
369A GLN* 4.5 9.9 - - + -
371A LEU* 4.6 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A VAL* 3.7 39.3 - - + -
197A MET* 3.7 14.7 - - + +
216A LEU* 3.8 28.9 - - + -
218A LEU* 5.1 4.7 - - - -
229A ILE* 4.6 0.4 - - + -
235A GLY* 3.3 2.4 - - - -
236A CYS* 2.9 49.4 + - + +
238A MET* 3.9 22.0 - - + -
262A ILE* 3.7 37.0 - - + +
263A ILE* 1.3 77.0 - - - +
265A TYR* 1.3 65.2 + - - +
269A THR 3.7 4.3 - - - +
270A ILE* 4.1 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A MET* 4.4 3.7 - - - +
214A LYS* 3.7 9.7 - - - +
232A VAL* 4.3 6.5 - - + -
233A PRO 3.6 17.5 - - - -
234A GLY* 3.5 20.4 - - - +
235A GLY 4.1 1.1 - - - -
263A ILE* 3.5 31.8 - - + +
264A MET* 1.3 77.0 - - - +
266A TYR* 1.3 64.2 + - - +
267A ASN* 3.2 26.2 - - - +
268A ASP* 3.1 14.4 + - - -
269A THR* 2.9 29.6 + - + +
270A ILE* 5.9 0.2 - - - +
271A VAL* 5.3 0.9 - - + -
367A LEU* 3.9 18.5 - - + +
368A ARG* 6.0 0.2 - - - -
369A GLN* 4.0 35.5 + - + +
----------------------------------------------------------
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