Contacts of the helix formed by residues 375 - 386 (chain B) in PDB entry 1OJ7
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 375 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A LYS* 4.4 24.5 - - + -
365B MET 5.5 0.4 - - - -
366B THR* 3.3 16.8 - - - +
367B GLN* 5.6 1.3 - - + -
372B HIS 5.8 0.4 - - - +
373B ASP* 3.3 13.8 + - - +
374B ILE* 1.3 75.5 - - - +
376B LEU* 1.3 60.0 + - - +
377B ASP* 3.5 8.3 + - - +
378B VAL* 3.1 23.4 + - + +
379B SER* 2.9 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LEU* 3.6 40.5 - - + +
360B LEU* 3.8 24.2 - - + -
361B GLU* 3.9 35.2 - - + +
365B MET 4.1 10.5 - - - -
366B THR* 4.0 20.4 + - + +
375B THR* 1.3 75.3 - - - +
377B ASP* 1.3 56.7 + - - +
379B SER* 3.5 3.0 + - - -
380B ARG* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B THR* 3.2 8.3 + - - +
376B LEU* 1.3 75.2 - - - +
378B VAL* 1.3 65.3 + - - +
380B ARG* 3.4 23.4 + - - +
381B ARG* 3.0 51.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLU* 3.8 27.4 - - + +
296B LYS* 4.6 5.8 - - + +
373B ASP 3.9 13.0 - - - +
374B ILE* 3.9 21.1 - - + -
375B THR* 3.1 25.6 + - + +
377B ASP* 1.3 75.4 - - - +
379B SER* 1.3 65.6 + - - +
381B ARG* 3.1 31.1 + - - +
382B ILE* 3.0 25.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B LEU* 3.5 19.1 - - - +
357B LEU* 4.0 4.5 - - - -
360B LEU* 3.8 24.2 - - - +
365B MET 5.1 1.0 - - - -
368B LEU* 4.3 3.8 - - - +
374B ILE* 3.4 17.0 + - - +
375B THR 2.9 18.5 + - - -
376B LEU* 3.7 7.1 - - - -
378B VAL* 1.3 75.7 - - - +
380B ARG* 1.3 61.8 + - - +
382B ILE* 3.2 9.2 + - - +
383B TYR* 3.0 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ILE* 4.1 10.2 - - + +
354B PRO* 4.8 15.2 - - - +
357B LEU* 3.5 37.4 - - + +
376B LEU* 3.0 15.3 + - - +
377B ASP* 3.5 25.9 + - - +
378B VAL 3.2 0.2 - - - -
379B SER* 1.3 77.0 - - - +
381B ARG* 1.3 57.9 + - - +
383B TYR* 3.4 1.7 + - - +
384B GLU* 2.9 59.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLU* 2.7 47.6 + - - +
377B ASP* 3.0 34.1 + - - +
378B VAL* 3.1 36.5 + - - +
380B ARG* 1.3 80.1 - - + +
382B ILE* 1.3 58.1 + - - +
384B GLU* 3.5 10.9 + - - +
385B ALA* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B LEU* 3.8 21.3 - - + -
288B VAL* 4.2 9.0 - - + -
291B ALA* 3.5 9.4 - - + +
292B LEU* 3.9 48.5 - - + +
295B GLU* 3.8 25.4 - - + -
296B LYS* 5.1 0.9 - - + -
374B ILE* 4.2 13.9 - - + -
378B VAL* 3.0 32.2 + - + +
379B SER 3.6 6.5 - - - +
380B ARG 3.2 0.2 - - - -
381B ARG* 1.3 74.9 - - - +
383B TYR* 1.3 67.1 + - + +
385B ALA* 3.3 4.9 + - - +
386B ALA* 3.0 21.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B LEU* 2.6 55.2 + - + +
272B GLU* 3.8 14.4 - - - +
273B LEU* 4.0 25.4 - - + -
288B VAL* 4.4 7.9 - - + -
343B LEU* 3.8 13.5 - - + +
353B ILE* 3.7 34.8 - - + +
356B LEU* 3.9 25.8 - - + -
357B LEU* 4.3 4.3 - - + -
360B LEU* 4.2 18.3 - - + +
379B SER 3.0 24.1 + - - +
380B ARG 3.8 2.2 - - - +
382B ILE* 1.3 76.4 - - + +
384B GLU* 1.3 64.2 + - - +
386B ALA* 3.0 20.9 + - + +
387B ARG* 3.4 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ILE* 3.9 20.9 - - + +
380B ARG* 2.9 52.6 + - + +
381B ARG* 3.8 10.3 - - - +
383B TYR* 1.3 75.2 - - - +
385B ALA* 1.3 60.3 + - - +
387B ARG* 3.3 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ALA* 4.2 17.4 - - + +
294B ASN* 5.6 7.0 - - - +
331B ARG* 5.5 4.5 + - - -
342B HIS* 5.3 3.1 + - - -
381B ARG 3.0 18.8 + - - +
382B ILE* 3.7 6.1 - - - +
384B GLU* 1.3 76.1 - - - +
386B ALA* 1.3 59.1 + - - +
387B ARG 3.2 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ILE* 3.6 34.7 - - + +
288B VAL* 4.9 2.9 - - + -
291B ALA* 3.9 7.4 - - + -
331B ARG* 6.2 1.8 - - - +
341B THR 5.2 1.8 - - - -
342B HIS* 3.5 9.2 - - - -
343B LEU* 2.9 27.0 + - + +
382B ILE* 3.0 13.3 + - + +
383B TYR* 3.0 18.0 + - + +
385B ALA* 1.3 75.6 - - - +
387B ARG* 1.3 60.4 + - - +
----------------------------------------------------------
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