Contacts of the helix formed by residues 346 - 356 (chain B) in PDB entry 1OX6
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 ALA 346 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ILE* 4.5 2.0 - - - +
334B LYS* 3.8 26.5 - - - +
335B ASP* 2.6 18.6 + - - +
345B PRO* 1.3 69.4 - - - +
347B LEU* 1.3 64.2 + - - +
349B VAL* 3.1 3.2 + - - +
350B ALA* 2.9 25.4 + - - +
386B PRO* 3.7 37.7 - - + -
389B THR* 4.8 0.9 - - - +
390B ILE* 4.4 5.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B PRO* 3.1 5.5 + - + +
346B ALA* 1.3 79.3 - - - +
348B GLU* 1.3 69.3 + - + +
350B ALA* 3.2 2.3 + - - +
351B SER* 2.9 26.9 + - - +
389B THR* 3.8 41.6 + - + +
390B ILE* 4.0 15.5 - - + -
393B ALA* 4.2 10.1 - - + -
394B TYR* 4.0 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B LEU* 5.5 0.7 - - - +
344B ILE* 3.9 14.4 - - + +
345B PRO* 3.0 35.0 + - - +
347B LEU* 1.3 86.1 - - + +
349B VAL* 1.3 67.4 + - - +
351B SER* 3.5 10.4 - - - +
352B LEU* 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B LEU* 4.3 13.0 - - + -
332B GLY 3.7 21.8 - - - +
333B ILE* 4.3 5.8 - - - -
334B LYS 3.4 21.3 - - - +
336B ILE* 3.8 18.2 - - + -
344B ILE* 3.7 18.4 - - + +
345B PRO 3.1 12.3 + - - +
346B ALA* 3.1 6.9 + - - +
348B GLU* 1.3 75.8 - - - +
350B ALA* 1.3 62.1 + - - +
352B LEU* 3.2 7.6 + - - +
353B TYR* 3.2 40.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ILE* 4.0 13.9 - - + +
346B ALA 2.9 11.9 + - - +
347B LEU* 3.4 9.6 - - + +
349B VAL* 1.3 76.4 - - - +
351B SER* 1.3 65.2 + - - +
353B TYR* 3.2 4.9 + - - +
354B PHE* 2.9 43.3 + - + -
361B VAL* 4.3 8.1 - - + -
390B ILE* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 2.9 21.3 + - - +
348B GLU* 3.2 15.4 + - - +
350B ALA* 1.3 76.5 - - - +
352B LEU* 1.3 58.1 + - - +
354B PHE* 3.4 4.7 + - - +
355B ARG* 2.9 41.5 + - - +
394B TYR* 2.7 32.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B LEU* 3.6 41.7 - - + +
308B LYS* 4.5 8.1 - - + +
313B LEU* 3.6 26.0 - - + -
348B GLU 3.0 12.1 + - - +
349B VAL* 3.4 10.5 - - - +
350B ALA 3.1 0.2 - - - -
351B SER* 1.3 75.3 - - - +
353B TYR* 1.3 65.0 + - + +
355B ARG* 3.4 10.0 + - + +
356B SER* 2.7 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ASN* 3.4 16.9 + - - -
307B LEU* 5.2 8.0 - - + +
310B THR* 4.0 15.1 + - + +
312B MET* 3.7 24.2 - - + -
313B LEU* 3.6 25.4 - - + -
316B LEU* 3.6 19.8 - - + +
329B VAL* 3.9 18.2 - - + -
331B GLY 4.4 2.1 + - - -
332B GLY* 4.8 5.6 + - - -
333B ILE* 3.5 26.7 - - + -
349B VAL* 3.2 36.6 + - + -
350B ALA* 3.2 7.4 + - - +
352B LEU* 1.3 80.2 - - + +
354B PHE* 1.3 62.9 - - - +
356B SER* 3.1 9.0 + - - -
357B GLY 3.2 1.0 + - - -
358B ALA* 3.0 30.3 + - + +
361B VAL* 4.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLY* 4.2 14.4 - - - -
13B ASN* 3.1 22.1 - - - +
350B ALA* 2.9 23.0 + - + +
351B SER* 3.6 4.9 - - - +
353B TYR* 1.3 76.7 - - - +
355B ARG* 1.3 62.4 + - - +
356B SER 3.0 1.4 + - - -
357B GLY 3.0 10.2 + - - -
358B ALA* 3.4 20.8 - - + +
359B ASP 3.7 22.4 - - - -
360B LYS* 3.8 2.7 - - - -
361B VAL* 3.6 29.6 - - + -
390B ILE* 4.2 8.1 - - + -
394B TYR* 3.5 50.7 - + - -
398B ALA* 3.9 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASP* 4.6 6.7 + - - -
10B GLU* 3.5 53.8 + - - +
11B SER* 3.9 1.8 - - - +
12B GLY 3.5 27.6 + - - +
13B ASN* 4.4 0.4 - - - +
14B LEU* 5.1 4.7 + - - +
15B GLN* 3.3 27.6 + - - +
32B LYS* 4.5 9.5 - - - +
351B SER* 2.9 26.3 + - - +
352B LEU* 4.0 11.2 - - + +
354B PHE* 1.3 75.6 - - - +
356B SER* 1.3 57.3 + - - +
357B GLY 3.4 0.2 - - - -
394B TYR* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLN* 3.8 7.5 - - - +
313B LEU* 3.4 39.5 - - - +
316B LEU* 3.5 4.0 - - - -
317B LYS* 3.2 35.8 + - - +
352B LEU* 2.7 25.5 + - - +
353B TYR 3.4 6.3 - - - -
354B PHE 3.0 1.0 - - - -
355B ARG* 1.3 79.6 - - - +
357B GLY* 1.3 55.9 + - - +
358B ALA 3.8 0.4 - - - -
----------------------------------------------------------
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