Contacts of the helix formed by residues 289 - 297 (chain A) in PDB entry 1OV1
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 289 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLN* 5.7 0.9 - - - +
40A LEU* 3.9 28.3 - - + -
183A MET* 3.6 32.0 + - + +
186A SER* 5.1 3.0 + - - -
285A PRO 2.7 21.7 + - - -
286A ILE* 3.2 20.8 + - + -
288A MET* 1.3 79.6 - - - +
290A ILE* 1.3 67.9 + - - +
293A PHE* 3.2 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ILE* 3.1 37.4 + - + +
287A PHE* 4.7 4.7 - - - +
289A THR* 1.3 78.9 - - - +
291A PRO* 1.4 65.6 - - + +
293A PHE* 3.6 1.8 - - - +
294A PHE* 2.8 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 3.7 10.1 - - + +
267A PRO* 4.7 4.9 - - - +
270A GLY* 4.6 24.9 - - - +
271A VAL* 4.5 18.4 - - + -
274A TYR* 6.2 0.9 - - + -
287A PHE 3.2 26.9 - - - +
288A MET* 3.5 8.7 - - + -
289A THR 3.5 2.9 - - - -
290A ILE* 1.4 99.4 - - + +
292A ALA* 1.3 67.2 + - + +
294A PHE* 3.5 7.2 - - + +
295A ALA* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A SER* 4.4 11.0 - - - -
187A CYS 4.3 17.5 - - - +
267A PRO* 5.5 4.0 - - - -
271A VAL* 5.7 4.4 - - + +
288A MET* 4.0 16.8 - - + +
291A PRO* 1.3 79.7 - - + +
293A PHE* 1.3 66.3 + - - +
295A ALA* 2.9 16.8 + - - +
296A LYS* 3.0 31.6 + - - +
400A RET 4.2 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 3.5 39.9 - - + -
43A TYR* 4.3 25.1 - + + -
44A MET* 3.8 37.2 - - + -
47A LEU* 5.0 0.8 - - + +
94A THR* 4.6 6.5 - - + -
98A SER* 5.7 1.1 - - - -
185A CYS* 3.1 34.5 - - + -
186A SER* 4.3 9.4 - - - -
289A THR* 3.2 33.7 - - + +
290A ILE* 3.4 2.2 + - - +
292A ALA* 1.3 80.1 - - + +
294A PHE* 1.3 53.9 + - - +
296A LYS* 3.1 14.0 + - + +
297A THR* 2.6 37.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TYR* 5.4 4.5 - - - -
266A LEU* 3.6 40.1 - - + +
290A ILE* 2.8 25.9 + - + +
291A PRO* 3.5 9.0 - - + +
293A PHE* 1.3 77.7 - - - +
295A ALA* 1.3 61.3 + - - +
297A THR* 3.4 18.0 + - + -
298A SER* 3.5 10.9 + - - -
301A TYR* 5.5 16.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A MET* 5.2 1.7 - - - +
263A ILE* 5.4 1.5 - - - +
266A LEU* 3.7 18.6 - - + -
267A PRO* 3.8 25.8 - - + -
291A PRO 3.1 13.0 + - - +
292A ALA 2.9 9.5 + - - +
294A PHE* 1.3 76.2 - - - +
296A LYS* 1.3 59.9 + - - +
297A THR 3.2 0.2 - - - -
298A SER* 2.9 28.2 + - - -
299A ALA 4.7 0.2 + - - -
400A RET 4.3 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A MET* 4.8 16.4 - - + -
47A LEU* 5.5 0.4 - - - -
86A MET* 3.9 20.1 - - + +
91A PHE* 3.0 35.6 - - + -
94A THR* 5.3 5.2 - - + +
113A GLU* 3.0 38.8 + - - +
185A CYS 5.7 2.0 - - - -
186A SER* 5.6 3.4 - - - +
187A CYS* 4.8 8.6 - - - +
292A ALA* 3.0 22.9 + - - +
293A PHE* 3.1 15.2 + - + +
295A ALA* 1.3 74.3 - - - +
297A THR* 1.3 59.4 + - - +
298A SER 3.1 6.3 + - - -
299A ALA* 3.7 5.6 + - - +
400A RET 1.5 66.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TYR* 3.4 15.4 + - - +
47A LEU* 3.2 45.3 - - + +
293A PHE 2.6 20.0 + - - -
294A PHE* 3.6 14.6 - - + -
295A ALA 3.2 0.8 - - - -
296A LYS* 1.3 74.1 - - - +
298A SER* 1.3 53.8 + - - +
299A ALA 3.0 2.9 - - - -
300A VAL* 2.9 11.6 + - + +
301A TYR* 2.7 44.7 + - + +
----------------------------------------------------------
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