Contacts of the strand formed by residues 300 - 309 (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 TRP 300 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A VAL 3.6 0.5 - - - +
296A TYR* 3.4 3.9 - - - -
297A TYR* 2.7 41.5 + - - +
298A LEU 3.2 16.6 - - - -
299A GLY* 1.3 82.4 - - - +
301A VAL* 1.3 63.9 + - - +
302A LEU* 4.0 14.8 + - + -
364A ALA* 3.8 16.4 - - + -
365A CYS 3.5 12.8 - - - -
366A PRO* 3.4 46.7 - - + -
374A GLU* 4.2 8.1 - - + -
376A LEU* 4.4 6.5 - - + -
422A PHE* 4.2 13.2 - + + -
425A GLY 3.6 27.6 + - - -
426A GLN* 4.0 18.2 - - + -
427A PRO* 3.8 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A SER* 3.6 24.2 - - - +
232A VAL* 3.9 18.4 - - + -
237A MET* 3.8 34.1 - - + -
295A VAL 3.3 4.0 - - - +
296A TYR* 4.1 9.6 - - + -
300A TRP* 1.3 76.7 - - - +
302A LEU* 1.3 62.6 + - - +
303A PHE* 3.6 31.8 + - + -
363A LEU 3.5 2.8 - - - +
364A ALA* 3.5 0.2 - - - -
365A CYS* 2.8 42.3 + - - +
367A LEU* 4.7 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLY* 2.9 5.5 - - - -
295A VAL* 2.8 48.1 + - + +
297A TYR* 4.1 24.7 - - + -
300A TRP* 4.2 13.2 - - + -
301A VAL* 1.3 77.9 - - - +
303A PHE* 1.3 60.7 + - - +
362A ILE* 3.9 13.5 - - + -
363A LEU 3.2 2.9 - - - -
364A ALA* 3.7 27.4 - - + -
378A LEU* 6.2 0.7 - - + -
393A LEU* 3.5 15.2 - - + +
400A VAL* 4.5 6.7 - - + -
420A ILE* 3.5 32.3 - - + -
422A PHE* 6.3 0.9 - - + -
427A PRO* 5.2 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A SER* 3.7 32.3 - - - -
229A ILE 3.9 11.7 - - - -
230A SER* 4.0 5.2 - - - -
237A MET* 3.4 40.6 - - + -
239A TYR* 3.7 43.1 - + + -
261A ILE* 4.2 4.0 - - + -
294A GLY* 3.7 11.7 - - - -
301A VAL* 3.6 29.6 - - + -
302A LEU* 1.3 73.0 - - - +
304A PRO* 1.3 68.5 - - + +
362A ILE* 3.3 5.7 - - - -
363A LEU* 2.8 43.2 + - + +
365A CYS* 5.1 1.8 - - - -
393A LEU* 3.4 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A SER* 4.0 5.4 - - - +
289A PRO* 3.4 6.4 - - - +
290A GLY* 2.7 28.0 + - - +
292A GLY 3.6 14.4 - - - +
293A SER 3.5 19.3 - - - +
294A GLY* 4.1 0.2 - - - -
303A PHE* 1.3 89.8 - - + +
305A ILE* 1.3 56.3 - - - +
361A GLY 3.8 5.8 - - - +
362A ILE* 5.1 0.2 - - + -
391A GLY* 3.3 38.8 - - - +
392A ARG* 3.8 7.2 - - - +
393A LEU* 3.5 10.3 - - + -
402A TYR* 3.9 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A TYR* 3.6 32.1 - - + +
284A TRP* 4.5 5.8 - - + -
287A LEU* 3.6 21.8 - - + -
288A ASN 3.2 10.1 - - - +
290A GLY* 4.1 0.7 - - - +
304A PRO* 1.3 78.4 - - - +
306A TYR* 1.3 69.6 + - - +
360A SER* 3.7 2.3 + - - -
361A GLY* 3.0 48.6 + - - +
362A ILE 3.6 14.6 - - - +
363A LEU* 3.7 14.4 - - + +
377A VAL* 3.7 29.6 - - + -
389A ALA 4.2 5.0 - - - +
402A TYR* 4.3 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A SER* 4.6 3.6 + - - -
247A GLU* 4.1 12.8 + - - -
251A TYR* 3.8 19.7 - - - -
284A TRP* 4.0 5.8 - - - -
287A LEU* 3.5 2.5 - - - +
288A ASN* 2.8 53.4 + - + +
289A PRO 3.6 23.1 - - - -
290A GLY* 4.1 1.1 - - - -
305A ILE* 1.3 79.1 - - - +
307A GLY* 1.3 60.2 + - - +
358A ILE* 4.9 3.6 - - + -
359A GLN 3.0 15.0 - - - +
360A SER* 4.4 0.2 - - - -
388A GLY 4.2 4.5 - - - -
389A ALA* 3.3 38.4 - - - +
390A GLU* 3.8 35.0 + - + +
407A ASN* 6.2 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A TYR* 3.7 18.4 - - - -
284A TRP* 3.5 8.1 - - - -
286A THR* 3.4 15.3 - - - -
288A ASN* 6.1 0.7 - - - -
306A TYR* 1.3 78.2 - - - +
308A GLY* 1.3 58.4 + - - -
358A ILE* 3.2 7.3 - - - +
359A GLN 2.8 34.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A TYR* 3.5 20.8 - - - -
284A TRP* 3.6 3.7 - - - -
285A ALA* 2.9 27.5 + - - -
286A THR* 3.3 11.2 + - - +
307A GLY* 1.3 73.0 - - - -
309A VAL* 1.3 65.1 + - - -
356A ARG* 3.8 14.4 - - - -
357A MET 3.2 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A VAL* 3.5 12.8 - - + +
284A TRP* 3.9 20.4 - - + -
308A GLY* 1.3 75.7 - - - -
310A ILE* 1.3 67.7 + - - +
313A THR* 3.6 19.5 - - - +
315A LEU* 3.8 26.9 - - + -
316A TRP* 3.7 9.0 - - + +
356A ARG* 3.5 8.4 - - - -
357A MET* 2.7 55.4 + - + +
359A GLN* 3.9 17.9 - - + -
----------------------------------------------------------
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