Contacts of the helix formed by residues 253 - 262 (chain H) 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 ASN 253 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154H GLU* 5.6 4.2 + - - -
249H GLY 4.0 7.3 + - - +
250H PHE 3.0 2.3 + - - +
252H THR* 1.3 78.7 - - - +
254H ILE* 1.3 67.5 + - - +
255H MET* 2.8 45.3 + - - +
256H ASN* 3.1 34.9 + - - +
257H ILE* 3.2 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 254 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252H THR 3.4 6.1 + - - +
253H ASN* 1.3 76.2 + - - +
255H MET* 1.3 77.2 + - + +
257H ILE* 3.2 14.1 + - + +
258H ILE* 3.0 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 255 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253H ASN* 2.8 22.8 + - - +
254H ILE* 1.3 87.8 - - + +
256H ASN* 1.3 55.4 - - - +
258H ILE* 3.4 10.3 + - - +
259H ASP* 2.8 31.2 + - - +
304H SER* 3.4 41.7 - - - +
305H ARG* 3.2 45.9 + - + +
311H GLN* 4.1 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 256 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150H TRP* 6.0 2.2 - - - -
240H ARG* 4.4 8.3 - - - -
249H GLY 4.7 0.2 + - - -
250H PHE* 2.9 76.8 + - + +
251H PHE* 5.1 1.8 - - - -
253H ASN* 3.1 20.5 + - - +
255H MET* 1.3 74.3 - - - +
257H ILE* 1.3 66.4 + - - +
259H ASP* 3.1 10.8 + - - +
260H ILE* 3.0 30.2 + - + +
305H ARG* 3.9 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251H PHE* 3.5 36.8 - - + +
252H THR 5.1 1.3 - - - +
253H ASN 3.3 14.6 - - - +
254H ILE* 3.2 16.4 + - + +
256H ASN* 1.3 78.1 - - - +
258H ILE* 1.3 59.5 + - + +
260H ILE* 3.2 14.9 + - + +
261H VAL* 2.9 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 258 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254H ILE* 3.0 35.9 + - + +
255H MET* 3.4 16.6 - - - +
257H ILE* 1.3 77.6 - - + +
259H ASP* 1.3 62.6 + - - +
261H VAL* 3.3 8.3 + - - +
262H ALA* 2.9 24.2 + - + +
298H LEU 4.7 4.9 - - - +
301H PHE* 3.5 39.0 - - + +
302H LYS* 3.8 15.3 - - + +
304H SER* 3.5 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 259 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233H PHE 4.9 0.3 - - - +
236H GLU* 4.5 1.0 - - - +
237H PHE* 4.6 22.2 - - + +
240H ARG* 4.3 16.9 + - - -
255H MET 2.8 22.2 + - - +
256H ASN* 3.1 14.6 + - - +
258H ILE* 1.3 76.7 - - - +
260H ILE* 1.3 60.2 + - - +
262H ALA* 3.5 11.8 - - - +
263H ILE* 3.9 14.2 - - - +
302H LYS* 3.1 37.0 + - - +
305H ARG* 2.9 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 260 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237H PHE* 3.5 26.7 - - + -
250H PHE* 4.9 0.4 - - + -
251H PHE* 3.5 39.7 - - + -
256H ASN 3.0 19.2 + - - +
257H ILE* 3.5 12.1 - - + +
259H ASP* 1.3 73.4 - - - +
261H VAL* 1.3 65.2 + - + +
262H ALA 2.9 4.7 - - - -
263H ILE* 2.9 27.0 + - + +
264H ILE* 3.0 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 261 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257H ILE* 2.9 35.2 + - + +
258H ILE* 3.3 8.3 + - + +
260H ILE* 1.3 75.2 - - + +
262H ALA* 1.3 56.2 + - - +
264H ILE* 4.0 15.3 - - + -
265H PRO* 3.1 25.6 - - - +
295H MET* 4.3 15.4 - - + +
298H LEU* 3.6 39.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 262 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230H ILE* 4.6 6.8 - - - +
233H PHE* 4.0 17.6 - - + -
258H ILE* 2.9 16.5 + - + +
259H ASP 3.5 9.6 - - - +
260H ILE 2.9 0.8 - - - -
261H VAL* 1.3 77.6 - - - +
263H ILE* 1.3 59.9 + - + +
265H PRO* 4.3 4.1 - - - +
296H ARG* 6.1 1.5 - - - +
298H LEU 5.7 0.7 - - - -
299H ARG* 4.6 27.1 + - - +
302H LYS* 3.7 28.3 - - + -
----------------------------------------------------------
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