Contacts of the helix formed by residues 286 - 303 (chain A) in PDB entry 2FV7
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 SER 286 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ASN 3.8 1.6 + - - -
285A LEU* 1.3 78.0 - - - +
287A LEU* 1.3 65.2 + - - +
288A GLU* 3.5 17.5 + - - +
289A ASP* 3.1 24.3 + - - +
290A MET* 3.1 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A VAL* 5.4 4.3 - - + -
231A VAL* 3.4 42.2 - - + -
233A ILE* 5.0 2.5 - - + -
243A VAL* 3.8 18.4 - - + -
244A LEU 5.2 0.7 - - - +
245A SER* 5.2 4.7 - - - -
275A LEU* 4.8 5.6 - - + -
279A LEU* 4.8 8.1 - - + -
285A LEU 3.8 1.4 + - - -
286A SER* 1.3 71.5 - - - +
288A GLU* 1.3 73.3 + - - +
290A MET* 3.2 24.0 + - - +
291A LEU* 3.0 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A VAL* 4.4 9.0 - - + +
248A GLU* 4.2 12.3 - - - +
252A LYS* 3.0 45.4 - - - +
254A ILE* 4.2 19.0 - - + +
286A SER* 3.5 20.0 - - - +
287A LEU* 1.3 87.4 + - - +
289A ASP* 1.3 62.6 + - - +
291A LEU* 3.4 4.6 + - - +
292A ASN* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU* 3.4 14.8 - - + +
286A SER* 3.1 25.6 + - - +
288A GLU* 1.3 79.5 - - - +
290A MET* 1.3 62.8 + - - +
292A ASN* 3.4 7.2 + - - +
293A ARG* 2.9 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU* 4.3 10.5 - - + -
278A TYR* 3.5 36.7 - - + +
279A LEU* 3.7 30.7 - - + -
282A TYR 3.0 28.3 - - - +
283A PRO* 4.1 9.4 - - + +
285A LEU* 3.7 24.0 - - + +
286A SER 3.1 14.3 + - - +
287A LEU* 3.5 19.1 - - + +
289A ASP* 1.3 76.1 - - - +
291A LEU* 1.3 57.1 + - - +
293A ARG* 3.3 8.7 + - - +
294A SER* 2.9 33.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ILE* 3.5 28.7 - - + -
241A CYS* 3.9 22.2 - - - -
243A VAL* 3.5 44.2 - - + -
254A ILE* 4.2 9.4 - - + -
271A PHE* 3.8 16.0 - - + -
275A LEU* 3.8 20.0 - - + -
287A LEU* 3.0 24.0 + - + +
288A GLU 3.9 3.1 - - - +
290A MET* 1.3 74.0 - - - +
292A ASN* 1.3 60.1 + - - +
294A SER* 3.8 3.7 - - - +
295A ASN* 2.8 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ILE* 3.7 20.2 - - + +
255A PRO* 3.7 12.5 - - - +
288A GLU 3.0 18.1 + - - +
289A ASP* 3.7 9.1 + - - +
291A LEU* 1.3 76.0 - - - +
293A ARG* 1.3 58.4 + - + +
295A ASN* 3.6 4.3 - - - +
296A PHE* 3.2 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TYR* 3.5 39.9 - - + +
282A TYR* 4.2 8.7 - - - -
285A LEU* 3.4 29.3 - - - +
289A ASP* 2.9 44.7 + - - +
290A MET 3.6 3.4 - - - +
292A ASN* 1.3 75.5 - - + +
294A SER* 1.3 58.3 + - - +
296A PHE* 3.2 4.9 + - - +
297A ILE* 3.0 33.9 + - - +
320A THR 4.4 11.8 + - - -
321A LEU* 3.3 42.6 + - + +
322A PHE 4.0 10.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PHE* 3.8 37.1 - - - -
274A ALA* 3.7 13.5 - - - +
275A LEU* 3.3 26.6 + - - +
278A TYR* 3.9 3.2 - - - -
290A MET 2.9 23.3 + - - -
291A LEU* 3.8 3.6 - - - -
293A ARG* 1.3 73.0 - - - +
295A ASN* 1.3 59.3 + - - +
297A ILE* 3.3 1.8 + - - +
298A ALA* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A GLY* 3.9 1.5 - - - -
241A CYS* 3.8 4.7 - - - -
254A ILE* 2.9 32.7 + - - +
255A PRO 2.9 26.4 + - - +
256A THR* 3.6 17.9 + - - +
271A PHE* 3.4 16.1 - - - -
291A LEU 2.8 21.5 + - - +
292A ASN* 3.6 7.0 - - - +
294A SER* 1.3 71.1 - - - +
296A PHE* 1.3 57.5 + - - +
298A ALA 3.3 1.0 + - - -
299A ALA* 2.8 32.6 + - - +
401A ADP 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A THR* 5.2 0.2 - - - -
257A GLU* 5.1 15.7 - - + +
292A ASN 3.2 12.5 + - - +
293A ARG 3.2 9.6 + - - +
295A ASN* 1.3 79.4 - - - +
297A ILE* 1.3 57.1 + - - +
299A ALA* 3.3 6.8 + - + +
300A VAL* 3.0 47.0 + - + +
317A LEU* 4.3 1.1 - - + -
318A PRO* 3.8 33.9 - - + -
321A LEU* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLN* 3.7 34.5 - - - +
65A LEU* 4.0 9.6 - - + -
270A SER* 3.8 4.8 + - - +
274A ALA* 4.0 19.7 - - + -
278A TYR* 4.7 7.2 - - + +
293A ARG 3.0 22.1 + - - +
294A SER 3.7 5.4 - - - +
296A PHE* 1.3 74.8 - - - +
298A ALA* 1.3 65.9 + - - +
300A VAL* 3.2 8.4 + - - +
301A SER* 3.2 16.3 + - - -
312A PRO* 4.1 8.3 - - + +
317A LEU* 3.2 33.9 - - + -
321A LEU* 3.3 20.4 - - + -
322A PHE* 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ALA* 3.7 16.3 - - - +
270A SER* 3.6 11.2 + - - -
271A PHE* 3.9 10.1 - - + +
294A SER 2.9 18.0 + - - +
295A ASN 3.8 0.9 - - - +
297A ILE* 1.3 75.8 - - - +
299A ALA* 1.3 55.6 + - - +
301A SER* 2.6 22.6 + - - -
302A VAL* 3.1 15.8 + - - +
401A ADP 3.3 34.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A THR* 3.7 15.7 - - - +
257A GLU* 4.1 17.5 - - + -
259A VAL* 3.9 5.0 - - + +
295A ASN 2.8 19.0 + - - +
296A PHE* 3.3 7.9 - - + +
298A ALA* 1.3 74.3 - - - +
300A VAL* 1.3 65.0 + - - +
302A VAL* 3.5 9.9 + - - +
303A GLN* 3.3 21.6 - - - +
401A ADP 3.7 21.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A PHE* 3.0 46.2 + - + +
297A ILE 3.2 7.8 + - - +
299A ALA* 1.3 73.8 - - + +
301A SER* 1.3 63.0 + - - +
303A GLN* 3.0 34.0 + - - +
304A ALA* 4.1 1.6 + - - +
310A SER 4.6 3.1 - - - +
312A PRO* 3.7 27.8 - - + -
316A ASP 6.0 0.7 - - - +
317A LEU* 4.0 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A THR 5.7 0.5 + - - -
266A GLY 5.1 0.2 - - - -
267A ALA* 3.9 12.1 - - - +
270A SER* 3.8 25.6 - - - -
297A ILE 3.2 3.3 + - - -
298A ALA* 2.6 22.1 + - - -
300A VAL* 1.3 78.5 - - - +
302A VAL* 1.3 57.4 + - - +
303A GLN 3.1 0.7 + - - -
304A ALA 3.1 7.3 + - - +
310A SER* 3.2 31.0 - - - -
311A TYR* 3.8 12.6 - - - -
312A PRO* 4.5 2.2 - - - +
403A NA 2.5 24.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A VAL* 3.9 9.4 - - + -
261A ALA* 3.3 30.3 - - + -
262A VAL 2.9 23.0 + - - -
263A ASP 3.2 17.2 + - - -
264A THR* 3.8 12.3 - - + +
267A ALA* 3.7 15.0 - - + -
298A ALA 3.1 11.1 + - - +
299A ALA 3.6 8.3 - - - +
300A VAL 3.2 0.4 - - - -
301A SER* 1.3 80.9 + - - +
303A GLN* 1.3 53.7 + - - +
304A ALA 3.3 1.8 + - - -
401A ADP 3.6 46.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A VAL* 3.0 37.9 - - + +
260A LYS 4.2 13.5 + - - +
262A VAL* 3.6 16.9 - - - +
299A ALA* 3.3 19.3 - - - +
300A VAL* 3.0 25.6 + - - +
302A VAL* 1.3 74.6 - - - +
304A ALA* 1.3 60.0 + - - +
----------------------------------------------------------
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