Contacts of the helix formed by residues 191 - 203 (chain B) in PDB entry 2XAR
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B CYS 5.1 4.7 - - - -
173B PHE 5.6 0.9 - - - -
174B LEU* 3.6 16.1 - - - +
189B SER 3.9 0.8 + - - -
190B VAL* 1.3 79.5 - - - +
192B ARG* 1.3 64.5 + - - +
193B PHE* 3.7 8.2 + - - +
194B LYS* 3.2 24.1 + - - +
195B MET* 3.1 19.2 + - - +
213B ASP* 3.4 23.0 + - - -
214B PRO* 4.3 3.4 - - - +
215B LEU* 4.1 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B CYS* 5.5 14.9 + - + +
173B PHE 5.6 1.8 + - - -
190B VAL 3.6 1.4 + - - -
191B SER* 1.3 72.4 - - - +
193B PHE* 1.3 55.4 + - - +
195B MET* 3.3 14.4 + - + +
196B HIS* 2.7 56.5 + - + +
315B ILE* 5.4 1.4 - - - +
360B TYR* 5.9 1.0 + - - -
419B TYR* 4.7 9.7 + - - +
422B LEU* 3.9 25.2 - - - +
423B ASP* 2.7 47.7 + - - +
426B ILE* 4.7 11.8 - - - +
500B IHP 4.9 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LYS* 4.0 26.5 - - + -
171B CYS 5.0 4.2 + - - +
191B SER* 3.2 2.1 - - - +
192B ARG* 1.3 82.4 - - - +
194B LYS* 1.3 59.1 + - - +
196B HIS* 3.4 6.1 + - + +
197B GLN* 3.1 64.7 + - + +
200B LYS* 5.8 4.9 - - - -
210B SER* 4.1 11.4 - - - -
212B TYR* 3.3 44.9 - + - -
214B PRO* 3.6 29.2 - - + -
238B ASN* 6.1 0.2 - - - -
239B ASN* 3.6 33.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B VAL* 3.8 21.3 - - + -
191B SER* 3.2 20.8 + - - +
193B PHE* 1.3 81.4 - - + +
195B MET* 1.3 65.5 + - - +
197B GLN* 3.5 19.3 - - - +
198B LEU* 3.8 6.2 + - - +
209B GLU* 3.7 24.7 + - - +
212B TYR 5.6 3.4 - - - +
213B ASP* 5.4 11.2 - - + +
430B TYR* 4.5 14.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU 4.6 5.4 - - - +
187B LYS* 3.9 30.5 - - + +
190B VAL* 3.6 36.6 - - + +
191B SER 3.1 13.2 + - - +
192B ARG* 3.8 14.1 - - + +
194B LYS* 1.3 74.4 - - - +
196B HIS* 1.3 63.8 + - - +
198B LEU* 3.2 18.9 + - - +
199B LEU* 3.8 2.9 + - - +
423B ASP* 5.6 2.2 - - - +
426B ILE* 3.5 25.6 - - + +
427B ILE* 3.7 25.8 - - + -
429B PHE* 5.6 0.9 - - - -
430B TYR* 3.8 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ARG* 2.7 37.5 + - + +
193B PHE* 3.8 7.0 - - + +
194B LYS 3.3 0.2 - - - -
195B MET* 1.3 73.4 - - - +
197B GLN* 1.3 57.2 + - - +
199B LEU* 3.1 8.0 + - + +
200B LYS* 3.0 71.0 + - + +
205B GLU* 5.2 2.7 - - - -
422B LEU* 3.9 21.4 - - + +
426B ILE* 3.1 42.5 - - + +
500B IHP 3.8 18.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PHE* 3.1 46.8 + - + +
194B LYS* 3.5 12.3 - - - +
195B MET 3.2 0.2 - - - -
196B HIS* 1.3 76.9 - - - +
198B LEU* 1.3 57.2 + - - +
200B LYS* 4.0 19.2 - - - +
201B LEU* 3.0 32.1 + - - +
206B ILE* 3.1 19.2 - - - +
209B GLU* 3.6 17.6 - - + +
210B SER* 2.7 35.5 + - - +
237B GLN* 2.7 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LYS 3.8 4.2 + - - +
195B MET 3.2 10.8 + - - +
196B HIS 3.2 1.0 - - - -
197B GLN* 1.3 79.7 - - - +
199B LEU* 1.3 58.0 + - - +
201B LEU* 4.1 15.3 - - + +
202B GLU* 3.2 18.0 + - - +
209B GLU* 4.2 20.0 - - - +
429B PHE* 3.2 26.0 - - + -
430B TYR* 3.4 39.7 - - + +
433B LYS* 3.4 36.8 - - + +
434B GLN* 5.1 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B MET 3.8 3.0 + - - +
196B HIS* 3.1 13.4 + - + +
198B LEU* 1.3 78.5 - - - +
200B LYS* 1.3 54.8 + - + +
202B GLU* 3.0 2.1 + - + +
203B TYR* 2.7 65.4 + - + -
422B LEU* 4.8 6.3 - - + -
425B LYS* 3.9 32.1 - - + +
426B ILE* 3.2 34.1 - - + -
429B PHE* 3.8 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PHE* 5.8 5.4 - - - -
196B HIS* 3.0 49.8 + - + +
197B GLN* 3.8 26.5 - - - +
199B LEU* 1.3 75.6 - - - +
201B LEU* 1.3 58.4 + - - +
203B TYR 3.0 7.3 + - - -
205B GLU* 2.8 58.3 + - + +
206B ILE* 3.6 23.0 - - + +
237B GLN* 5.1 0.7 - - - +
238B ASN* 4.4 8.2 + - - -
256B SER* 5.7 0.8 + - - -
500B IHP 2.8 37.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B GLN 3.0 16.9 + - - +
198B LEU* 4.1 17.7 - - + +
200B LYS* 1.3 76.4 - - - +
202B GLU* 1.3 61.4 + - - +
204B ILE* 3.4 14.4 + - - +
206B ILE* 3.4 29.6 - - + +
207B SER 3.5 22.9 - - - +
208B GLU* 3.7 7.9 - - - -
209B GLU* 4.1 22.0 - - + +
433B LYS* 5.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU 3.2 17.5 + - - +
199B LEU* 3.0 7.8 + - - +
201B LEU* 1.3 80.6 - - - +
203B TYR* 1.3 67.8 + - + +
204B ILE* 3.2 17.8 - - - +
429B PHE* 3.3 37.9 - - + -
433B LYS* 4.9 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LEU* 2.7 57.6 + - + +
200B LYS 3.0 0.6 + - - -
202B GLU* 1.3 83.1 - - + +
204B ILE* 1.3 73.2 + - - +
205B GLU* 3.2 27.7 + - + +
425B LYS* 3.2 32.2 + - - -
429B PHE* 6.0 0.7 - + - -
----------------------------------------------------------
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