Contacts of the helix formed by residues 285 - 296 (chain B) in PDB entry 2R9R
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 285 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 3.7 33.7 - - + +
276B ASN* 3.9 22.4 - - + +
281B GLN 3.8 3.8 - - - +
282B PHE* 2.7 28.3 + - + +
284B ASN* 1.3 79.0 - - - +
286B ARG* 1.3 67.5 + - - +
287B ARG* 3.2 3.8 - - - +
288B VAL* 3.0 28.0 + - + +
289B VAL* 3.0 21.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TYR* 3.1 41.7 + - - -
208B SER* 6.0 0.8 - - - -
209B THR* 3.0 34.7 + - + +
282B PHE* 2.8 17.2 + - + +
283B GLN 4.0 10.7 + - - +
284B ASN 3.7 0.6 - - - -
285B VAL* 1.3 78.9 - - - +
287B ARG* 1.3 52.8 + - + +
289B VAL* 3.2 8.8 + - - +
290B GLN* 2.8 71.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ASN* 4.4 17.9 + - - +
285B VAL* 3.2 1.3 - - - -
286B ARG* 1.3 76.8 - - + +
288B VAL* 1.3 71.6 + - + +
290B GLN* 3.4 15.2 + - - +
291B ILE* 3.0 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 3.6 24.2 - - + -
285B VAL* 3.0 22.2 + - + +
287B ARG* 1.3 84.5 - - + +
289B VAL* 1.3 67.3 + - - +
291B ILE* 3.2 11.0 + - + +
292B PHE* 3.1 46.0 + - + -
514B PGW 4.8 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B THR* 3.8 13.7 - - + +
210B ILE* 3.7 32.3 - - + -
269B THR* 4.5 12.8 + - + +
272B LEU* 3.8 27.4 - - + -
273B THR* 5.2 2.0 - - + -
282B PHE* 4.2 17.7 - - + -
285B VAL* 3.0 22.7 + - + +
286B ARG* 3.4 9.4 - - - +
288B VAL* 1.3 75.8 - - - +
290B GLN* 1.3 63.2 + - - +
292B PHE* 3.1 8.1 + - - +
293B ARG* 3.1 18.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B THR* 3.7 20.4 - - + +
286B ARG* 2.8 61.5 + - - +
287B ARG* 3.6 16.8 - - - +
289B VAL* 1.3 73.2 - - - +
291B ILE* 1.3 62.5 + - + +
293B ARG* 3.0 17.9 + - - +
294B ILE* 3.2 22.9 + - + +
501B PGW 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ARG* 3.0 25.7 + - + +
288B VAL* 3.2 13.2 + - + +
290B GLN* 1.3 76.0 - - + +
292B PHE* 1.3 66.7 + - + +
294B ILE* 3.3 13.5 + - + +
295B MET* 3.1 25.7 + - + +
503B PGW 4.0 54.2 - - + +
514B PGW 4.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ILE* 3.9 17.3 - - + -
265B PRO* 3.5 24.6 - - + +
268B VAL* 3.8 27.6 - - + -
269B THR* 4.5 11.4 - - - +
272B LEU* 4.6 1.8 - - + -
288B VAL* 3.1 44.9 + - + -
289B VAL* 3.1 9.6 + - - +
291B ILE* 1.3 77.0 - - + +
293B ARG* 1.3 65.3 + - - +
295B MET* 3.3 41.6 + - + +
296B ARG* 3.3 16.3 + - - +
514B PGW 3.8 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B PHE* 3.4 16.9 + - + -
183B GLU* 3.7 27.1 + - - +
184B THR* 3.9 19.9 - - - +
208B SER 3.2 17.2 + - - -
209B THR 3.0 26.9 + - - +
210B ILE* 3.2 16.4 + - - +
211B GLY* 3.4 23.1 - - - -
289B VAL 3.1 9.7 + - - +
290B GLN* 3.0 13.5 + - - +
292B PHE* 1.3 77.1 - - - +
294B ILE* 1.3 65.1 + - + +
296B ARG* 3.1 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B PHE* 4.9 4.7 - - - -
290B GLN* 3.2 21.5 + - + +
291B ILE* 3.6 11.4 - - + +
292B PHE 3.2 0.2 - - - -
293B ARG* 1.3 80.3 - - + +
295B MET* 1.3 61.6 + - - +
296B ARG 3.1 0.7 + - - -
297B ILE* 3.1 32.8 + - + +
298B LEU* 5.2 0.2 - - - +
501B PGW 3.9 41.1 - - + -
503B PGW 4.6 16.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B VAL* 4.4 15.1 - - + +
264B ILE* 4.7 9.2 - - - -
265B PRO* 4.1 14.0 - - + +
291B ILE* 3.1 20.5 + - + +
292B PHE* 3.5 42.6 - - + +
293B ARG 3.2 0.2 - - - -
294B ILE* 1.3 77.0 - - - +
296B ARG* 1.3 62.9 + - - +
298B LEU* 3.0 36.7 + - + +
299B ARG 4.5 0.3 + - - -
503B PGW 3.9 27.1 - - + +
514B PGW 4.2 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B SER* 6.2 0.2 - - - -
180B PHE* 3.4 31.1 - - + +
183B GLU* 2.9 41.2 + - - -
210B ILE 3.6 15.7 + - - -
212B TYR* 3.7 13.0 - - - -
226B GLU* 3.0 41.7 + - - +
261B VAL 5.9 0.4 - - - -
262B ALA* 6.0 1.6 - - - +
265B PRO* 3.6 20.9 - - + -
266B TYR* 5.8 1.1 - - - +
292B PHE 3.3 10.6 + - - +
293B ARG* 3.2 26.2 - - - +
294B ILE 3.1 1.0 - - - -
295B MET* 1.3 77.2 - - - +
297B ILE* 1.3 60.5 + - - +
299B ARG* 2.9 46.4 + - - +
----------------------------------------------------------
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