Contacts of the helix formed by residues 191 - 206 (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 SER 191 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G ARG 4.1 0.4 + - - -
190G TRP* 1.3 77.4 - - - +
192G SER* 1.3 64.4 + - - +
193G MET* 3.5 9.9 + - - +
194G GLU* 3.0 40.3 + - - +
195G ILE* 3.0 20.6 + - - +
224G LYS* 5.1 2.7 - - - +
228G GLN* 4.9 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 192 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G TRP 3.9 0.2 + - - -
191G SER* 1.3 73.5 - - - +
193G MET* 1.3 60.1 + - - +
195G ILE* 3.3 3.0 + - - +
196G MET* 2.9 32.1 + - - +
224G LYS* 5.9 1.2 - - - +
228G GLN* 3.8 36.0 + - - +
229G LEU* 5.3 3.0 - - - +
232G LEU* 3.9 33.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 193 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191G SER* 3.1 9.6 - - - +
192G SER* 1.3 83.8 + - - +
194G GLU* 1.3 59.3 + - + +
196G MET* 3.4 6.0 + - - +
197G GLU* 2.9 30.7 + - + +
33H GLU* 4.6 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 194 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160G PRO* 3.6 29.9 - - - +
162G PRO* 6.0 1.6 - - - +
166G MET* 3.8 6.0 - - + +
189G ARG 4.8 0.2 - - - +
190G TRP* 3.5 26.2 - - + -
191G SER* 3.0 35.8 + - - +
193G MET* 1.3 78.1 - - + +
195G ILE* 1.3 64.8 + - - +
197G GLU* 3.3 16.9 + - - +
198G ALA 3.0 19.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 195 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187G THR* 3.6 17.5 - - - +
190G TRP* 3.7 17.7 - - + +
191G SER 3.0 15.6 + - - +
192G SER* 3.8 6.3 - - - +
194G GLU* 1.3 75.2 - - - +
196G MET* 1.3 62.4 + - - +
198G ALA* 3.3 6.3 + - - +
199G TYR* 3.1 21.1 + - - +
210G PRO* 4.6 10.3 - - + +
213G GLU* 3.5 37.9 - - + +
229G LEU* 4.3 4.5 - - + -
232G LEU* 3.8 27.4 - - + -
236G ILE* 4.5 3.4 - - + -
238G VAL* 4.1 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 196 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G SER 2.9 18.4 + - - +
193G MET* 3.7 5.6 - - - +
195G ILE* 1.3 76.2 - - - +
197G GLU* 1.3 59.2 + - - +
199G TYR* 3.2 33.4 + - + +
200G SER* 2.8 33.4 + - - -
232G LEU* 4.6 12.3 - - + +
235G LYS* 3.6 31.6 - - - +
236G ILE* 4.2 17.5 - - + -
33H GLU* 3.9 27.6 - - - +
69H PHE* 4.5 0.9 - - + -
74H ASN* 3.7 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 197 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166G MET* 3.3 37.8 + - + +
193G MET* 2.9 18.4 + - + +
194G GLU* 3.5 14.3 - - - +
195G ILE 3.3 0.2 - - - -
196G MET* 1.3 76.4 - - - +
198G ALA* 1.3 63.5 + - - +
200G SER* 3.3 6.9 + - - -
201G VAL* 2.9 35.8 + - + +
33H GLU* 6.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 198 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166G MET* 3.7 26.8 - - - +
170G VAL* 3.9 6.3 - - + +
185G TRP* 4.0 18.8 - - + -
190G TRP* 3.8 11.4 - - + -
194G GLU 3.0 13.3 + - - +
195G ILE 3.3 8.7 + - - +
197G GLU* 1.3 76.1 - - - +
199G TYR* 1.3 63.1 + - - +
201G VAL* 3.4 2.6 + - - +
202G ALA* 3.1 23.6 + - - +
210G PRO* 4.2 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 199 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G ILE 3.1 13.0 + - - +
196G MET* 3.2 24.0 + - + +
198G ALA* 1.3 76.2 - - - +
200G SER* 1.3 63.9 + - - +
202G ALA* 3.4 2.9 + - - +
203G ARG* 3.1 41.2 + - + +
209G PRO* 4.0 27.6 - - + -
210G PRO* 4.3 3.8 - - + +
236G ILE* 3.6 47.3 - - + -
69H PHE* 3.8 1.6 - + - -
71H PRO* 2.5 38.2 + - + +
74H ASN* 3.3 41.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 200 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G MET* 2.8 21.3 + - - -
197G GLU* 3.5 9.4 - - - -
199G TYR* 1.3 85.3 - - - +
201G VAL* 1.3 62.4 + - - +
203G ARG* 3.4 3.0 + - - +
204G GLN* 3.1 24.1 + - - +
33H GLU* 6.5 1.1 - - - -
74H ASN* 3.8 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 201 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166G MET* 4.0 19.7 - - + -
167G GLU* 3.7 29.4 - - + +
170G VAL* 4.1 14.8 - - + -
197G GLU* 2.9 25.7 + - + +
198G ALA 3.7 3.8 - - - +
200G SER* 1.3 74.2 - - - +
202G ALA* 1.3 65.9 + - - +
204G GLN* 3.4 6.1 + - - +
205G PHE* 3.1 42.2 + - + +
207G LEU* 4.3 1.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 202 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170G VAL* 4.0 4.9 - - + +
198G ALA 3.1 18.6 + - - +
199G TYR 3.5 6.3 - - - +
201G VAL* 1.3 78.4 - - - +
203G ARG* 1.3 53.5 + - - +
206G ASN* 2.7 31.0 + - - -
207G LEU* 2.7 36.2 + - - +
208G ILE 3.8 7.0 - - - +
209G PRO* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 203 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G TYR* 3.1 40.0 + - + +
200G SER 3.9 5.6 - - - +
202G ALA* 1.3 76.0 - - - +
204G GLN* 1.3 64.9 + - - +
206G ASN* 3.4 11.9 + - - +
207G LEU 4.7 4.2 + - - -
209G PRO* 3.7 28.7 - - - +
71H PRO* 3.1 26.4 + - - +
72H LEU* 3.5 36.1 + - - +
73H ARG* 4.8 5.2 - - - +
74H ASN* 4.0 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 204 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200G SER 3.1 18.8 + - - +
201G VAL* 3.5 8.5 - - - +
203G ARG* 1.3 80.3 - - - +
205G PHE* 1.3 83.8 + - + +
206G ASN 3.8 0.2 + - - -
43H ARG* 5.8 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 205 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167G GLU* 3.7 36.1 - - + -
171G ARG* 3.2 27.0 + - - +
201G VAL* 3.1 38.3 + - + -
204G GLN* 1.3 96.9 - - + +
206G ASN* 1.3 73.4 + - - +
207G LEU* 3.4 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 206 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174G THR* 5.5 0.5 - - - +
202G ALA 2.7 9.7 + - - -
203G ARG* 3.4 10.4 + - - +
204G GLN 3.8 0.2 + - - -
205G PHE* 1.3 83.4 - - - +
207G LEU* 1.3 62.8 + - - +
208G ILE* 5.8 0.2 - - - +
----------------------------------------------------------
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