Contacts of the helix formed by residues 225 - 236 (chain B) in PDB entry 1OVM
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 LEU 225 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B VAL* 2.9 23.5 + - + +
223B HIS* 3.6 20.9 - - + +
224B GLY* 1.3 76.9 - - - +
226B LYS* 1.3 63.3 + - - +
227B HIS 3.4 2.2 - - - -
228B ALA* 3.4 21.4 + - + +
229B LEU* 3.2 24.4 + - - +
324B MET* 3.6 38.8 - - + -
325B ASN* 3.8 31.4 - - + +
328B ILE* 3.9 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B VAL* 3.8 11.5 + - + +
221B LEU* 4.5 20.0 - - + +
224B GLY* 3.4 4.4 - - - -
225B LEU* 1.3 77.7 - - - +
227B HIS* 1.3 74.5 + - + +
229B LEU* 3.3 4.7 + - - +
230B GLN* 3.0 47.2 + - - +
248B GLY 3.4 24.3 + - - -
249B ILE* 3.8 18.4 - - + +
398B ASP* 4.3 23.4 + - - +
399B VAL 4.2 11.9 + - - +
400B ASN* 5.7 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B GLY 5.2 1.9 + - - +
225B LEU 3.4 0.2 - - - -
226B LYS* 1.3 89.2 + - + +
228B ALA* 1.3 61.0 + - - +
230B GLN* 3.6 20.9 - - - +
231B LYS* 2.8 35.1 + - - +
398B ASP* 5.5 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU* 3.4 32.1 + - + +
226B LYS 3.3 0.4 - - - -
227B HIS* 1.3 77.9 - - - +
229B LEU* 1.3 61.3 + - + +
231B LYS* 3.8 7.0 - - - +
232B TRP* 3.0 27.5 + - - +
328B ILE* 4.9 9.9 - - + -
332B VAL* 5.2 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 4.6 6.5 - - + +
216B ALA* 3.3 33.9 - - + -
220B VAL* 4.1 14.4 - - + -
225B LEU* 3.2 16.3 + - + +
226B LYS 3.8 6.7 - - - +
227B HIS 3.2 0.6 - - - -
228B ALA* 1.3 81.3 - - + +
230B GLN* 1.3 64.6 + - - +
232B TRP* 3.2 16.3 + - + +
233B VAL* 3.0 25.6 + - - +
249B ILE* 3.6 13.7 - - + -
250B PHE* 3.7 15.5 - - + -
283B VAL* 4.6 6.7 - - + -
328B ILE* 3.7 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LYS* 3.0 34.6 + - - +
227B HIS* 3.6 24.6 - - - +
229B LEU* 1.3 74.9 - - - +
231B LYS* 1.3 65.9 + - - +
233B VAL* 3.0 12.9 - - - +
234B LYS* 3.0 24.0 + - - +
249B ILE 3.1 26.6 + - - +
250B PHE* 4.5 6.2 - - + -
251B ASP* 4.5 13.5 - - - +
397B ALA* 6.0 1.8 - - - +
398B ASP* 5.4 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B HIS 2.8 16.7 + - - +
228B ALA* 3.8 7.2 - - - +
230B GLN* 1.3 76.8 - - - +
232B TRP* 1.3 63.9 + - - +
234B LYS* 3.0 11.2 + - + +
235B GLU* 2.9 54.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 4.0 22.7 - - + -
228B ALA 3.0 17.6 + - - +
229B LEU* 3.3 18.4 - - + +
231B LYS* 1.3 78.0 - - - +
233B VAL* 1.3 59.0 + - - +
235B GLU* 3.1 3.8 + - - +
236B VAL* 2.8 36.0 + - + -
238B MET* 3.2 25.5 - - + +
281B LEU* 3.4 36.8 - - + -
283B VAL* 4.3 15.5 - - + -
328B ILE* 3.8 30.5 - - + -
331B LEU* 3.8 23.1 - - + -
332B VAL* 3.5 26.8 - - + +
335B CYS* 3.8 21.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 4.9 4.9 - - + -
229B LEU 3.0 12.4 + - - +
230B GLN* 3.0 18.6 - - - +
232B TRP* 1.3 82.1 - - - +
234B LYS* 1.3 62.8 + - + +
236B VAL 3.4 20.7 - - - +
237B PRO* 3.6 6.8 - - - +
238B MET* 4.2 11.2 - - + +
240B HIS* 3.1 46.4 - - + +
250B PHE* 3.8 22.2 - - + -
254B GLN* 6.6 0.2 - - + -
255B ALA 4.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B GLN 3.0 18.4 + - - +
231B LYS* 3.0 10.5 + - + +
233B VAL* 1.3 81.8 - - + +
235B GLU* 1.3 65.7 + - + +
237B PRO* 4.0 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LYS* 2.9 56.7 + - + +
232B TRP* 3.8 3.8 - - - +
234B LYS* 1.3 80.9 - - + +
236B VAL* 1.3 66.6 + - + +
237B PRO* 3.1 10.4 - - - +
332B VAL* 5.0 2.2 - - + +
336B LYS* 3.1 33.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B TRP* 2.8 23.0 + - + +
233B VAL* 3.4 11.1 - - - +
235B GLU* 1.3 79.2 - - + +
237B PRO* 1.3 69.4 - - + +
238B MET* 3.3 34.1 + - + +
332B VAL 4.7 0.7 - - - +
335B CYS* 4.0 22.2 - - + +
336B LYS* 3.6 38.6 - - + +
338B HIS 5.6 2.2 - - - +
339B VAL* 6.1 4.9 - - + -
----------------------------------------------------------
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