Contacts of the helix formed by residues 302 - 312 (chain G) 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 THR 302 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293G GLN* 5.4 3.4 - - - +
296G ALA* 3.9 2.5 - - - -
301G CYS* 1.3 82.0 - - - +
303G LEU* 1.3 64.8 + - - +
304G PRO* 3.2 6.9 - - - +
305G GLN* 2.9 27.2 + - - +
306G LEU* 3.2 16.6 + - - +
332G GLU* 2.8 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 303 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G MET* 5.7 1.3 - - - -
251G VAL* 3.2 27.8 - - + +
252G SER 4.4 10.5 - - - +
253G GLY* 5.1 1.1 - - - -
289G LEU* 3.9 35.4 - - + +
292G LEU* 3.8 37.9 - - + +
293G GLN* 3.6 23.3 + - + +
296G ALA* 4.0 5.1 - - + +
302G THR* 1.3 69.4 - - - +
304G PRO* 1.3 74.8 - - + +
306G LEU* 3.2 14.8 + - + +
307G ALA* 2.9 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 304 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246G LEU* 3.8 21.3 - - + -
251G VAL 5.1 0.9 - - - +
252G SER* 4.0 22.9 - - - +
302G THR* 3.2 11.0 - - - +
303G LEU* 1.3 93.6 - - + +
305G GLN* 1.3 54.9 + - - +
307G ALA* 3.2 2.3 + - + +
308G ILE* 2.9 37.6 + - - +
332G GLU* 3.3 15.7 - - - +
333G ASN* 4.0 8.7 - - - +
1001G NAP 3.6 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 305 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301G CYS* 3.4 10.6 - - + +
302G THR* 2.9 43.8 + - - +
303G LEU 3.2 0.6 - - - -
304G PRO* 1.3 75.3 - - - +
306G LEU* 1.3 57.6 + - - +
308G ILE* 5.1 0.7 - - - -
309G ALA* 3.0 28.6 + - - +
331G MET 5.1 0.2 + - - -
332G GLU* 3.0 40.9 + - + +
335G GLY* 3.7 18.6 + - - -
336G ALA* 3.2 21.2 - - - +
339G VAL* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G MET* 4.5 16.4 - - + -
292G LEU* 3.9 24.9 - - + +
295G ILE* 4.4 8.3 - - + -
296G ALA* 4.3 9.0 - - + +
299G LEU* 3.7 29.8 - - + -
301G CYS* 3.9 10.0 - - - -
302G THR 3.2 10.0 + - - +
303G LEU* 3.2 19.9 + - + +
305G GLN* 1.3 75.5 - - - +
307G ALA* 1.3 59.5 + - - +
309G ALA* 3.8 1.2 - - - +
310G TRP* 2.8 31.7 + - - +
339G VAL* 4.4 8.1 - - + -
343G LEU* 4.0 19.0 - - + +
351G ILE* 4.4 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 307 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G MET* 4.2 17.5 - - + -
245G PRO 4.2 4.9 - - - +
246G LEU* 3.9 8.5 - - + -
251G VAL* 3.5 28.0 - - + -
303G LEU* 2.9 17.5 + - + +
304G PRO 3.2 4.5 + - - +
306G LEU* 1.3 78.4 - - - +
308G ILE* 1.3 62.4 + - - +
310G TRP* 3.4 9.4 - - - +
311G CYS* 3.2 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 308 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G LEU* 3.8 27.8 - - + -
245G PRO* 4.4 9.0 - - + -
246G LEU* 4.1 17.9 - - + -
304G PRO 2.9 20.7 + - - +
307G ALA* 1.3 74.8 - - - +
309G ALA* 1.3 64.9 + - - +
311G CYS* 3.1 17.3 + - - +
312G LEU* 3.3 14.7 + - + +
320G VAL* 4.7 5.6 - - + -
322G LEU* 3.4 27.4 - - + -
333G ASN* 3.5 34.5 - - + +
336G ALA* 3.5 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 309 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305G GLN 3.0 18.2 + - - +
306G LEU 3.8 3.4 - - - +
308G ILE* 1.3 76.2 - - - +
310G TRP* 1.3 64.5 + - - +
312G LEU* 3.0 15.3 + - - +
313G ARG 3.2 2.4 + - - -
336G ALA* 3.4 22.6 - - - +
339G VAL* 4.0 9.9 - - + -
340G LEU* 3.2 40.6 - - + +
343G LEU* 3.7 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 310 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217G TYR* 3.7 14.4 - + - -
218G HIS* 3.6 23.3 - - - -
219G MET* 3.6 36.1 - - + -
222G ARG* 3.5 42.0 - - + -
226G GLU* 3.6 8.1 - - - -
306G LEU* 2.8 20.5 + - + +
307G ALA 3.4 5.8 - - - +
309G ALA* 1.3 76.7 - - - +
311G CYS* 1.3 72.4 + - - +
313G ARG* 2.8 75.3 + - - +
343G LEU* 3.8 13.6 - - + +
348G VAL* 4.8 7.6 + - + +
351G ILE* 4.0 27.8 - - + +
352G ASP* 5.1 2.5 + - - -
355G LEU* 4.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 311 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217G TYR* 3.6 47.4 - - + -
218G HIS* 4.1 6.3 - - - -
219G MET 5.3 0.2 - - - -
242G THR* 5.2 0.7 - - - -
245G PRO* 3.9 17.5 - - - -
307G ALA 3.2 15.4 + - - -
308G ILE* 3.1 10.8 + - - +
310G TRP* 1.3 87.9 - - - +
312G LEU* 1.3 58.1 + - - +
314G ASN* 3.0 18.4 - - - +
317G VAL* 3.8 12.5 - - - +
320G VAL* 3.9 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 312 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G ARG* 4.2 18.3 + - - +
51G CYS* 3.7 48.7 - - + +
52G LEU* 4.1 17.5 - - + -
308G ILE* 3.3 12.7 + - + +
309G ALA* 3.0 14.1 + - - +
311G CYS* 1.3 76.7 - - - +
313G ARG* 1.3 62.8 + - - +
314G ASN 3.1 11.4 - - - +
315G GLU* 4.7 2.4 - - - +
317G VAL* 4.4 8.7 - - + +
319G SER* 4.9 1.1 - - - -
320G VAL* 3.7 17.9 - - + +
336G ALA* 6.0 0.2 - - + -
337G ILE* 4.8 7.9 - - + +
340G LEU* 4.1 26.0 - - + +
----------------------------------------------------------
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