Contacts of the helix formed by residues 371 - 382 (chain N) in PDB entry 1OCR
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 TYR 371 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38N ARG* 4.3 3.8 - - - -
41N LEU* 3.4 22.9 - - + +
370N THR* 1.3 72.6 - - - +
372N TYR* 1.3 64.5 + - - +
373N VAL 3.1 0.4 - - - -
374N VAL* 3.0 24.3 + - + +
375N ALA* 2.9 24.3 + - - +
428N GLN* 3.7 55.3 - - + +
431N LEU* 4.0 18.8 - - + -
432N GLY* 3.9 1.5 - - - +
436N MET* 3.1 34.3 + - + +
437N PRO 3.3 27.4 - - - -
438N ARG* 4.0 11.9 - - - -
439N ARG 4.7 0.7 - - - -
440N TYR 5.0 1.0 + - - -
451N ASN* 5.4 0.4 - - - -
515N HEA 3.3 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 372 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354N THR* 3.5 35.2 + - + +
357N VAL* 3.7 29.1 - - + +
358N LEU* 3.6 27.6 - - + -
367N LEU* 4.0 15.0 - - + -
370N THR* 3.0 14.2 + - - +
371N TYR* 1.3 78.1 - - - +
373N VAL* 1.3 61.1 + - - +
375N ALA* 3.3 4.7 + - - +
376N HIS* 3.1 18.2 + - - +
428N GLN 4.4 3.4 - - - -
429N HIS* 3.7 35.0 - + - -
432N GLY* 3.5 11.8 - - - -
433N LEU* 3.9 29.8 - - + -
24O HIS* 4.7 5.6 + - - -
28O LEU* 5.5 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 373 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358N LEU* 4.2 17.9 - - + -
367N LEU 3.5 20.2 - - - +
369N ASP* 3.9 13.2 - - - +
370N THR 3.3 12.8 - - - +
371N TYR 3.1 0.2 - - - -
372N TYR* 1.3 75.2 - - - +
374N VAL* 1.3 63.0 + - - +
376N HIS* 3.2 6.8 + - - +
377N PHE* 2.9 39.3 + - + -
438N ARG* 3.5 27.4 - - - +
516N HEA 4.2 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 374 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371N TYR* 3.0 32.3 + - + +
373N VAL* 1.3 79.3 - - - +
375N ALA* 1.3 59.8 + - - +
377N PHE* 3.5 11.3 + - + -
378N HIS* 2.7 52.6 + - + +
428N GLN* 3.5 15.7 - - - +
438N ARG* 3.7 40.2 - - + +
515N HEA 3.9 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 375 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371N TYR 2.9 12.7 + - - +
372N TYR 3.5 9.2 - - - +
374N VAL* 1.3 75.6 - - - +
376N HIS* 1.3 65.8 + - - +
378N HIS* 3.3 3.7 + - - +
379N TYR* 3.0 30.7 + - - -
425N PHE* 4.1 11.7 - - - +
428N GLN* 4.2 13.4 + - + -
429N HIS* 3.8 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 376 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351N GLY* 2.8 25.0 + - - -
354N THR* 3.1 24.6 - - + +
355N GLY* 3.3 17.2 - - - -
358N LEU* 3.9 12.3 - - + -
372N TYR 3.1 9.2 + - - +
373N VAL 3.5 7.0 - - - +
375N ALA* 1.3 77.2 - - - +
377N PHE* 1.3 74.4 + - + +
379N TYR* 3.0 16.9 + - - +
380N VAL* 3.2 14.2 + - + +
429N HIS* 5.4 0.2 - - - -
516N HEA 1.9 89.7 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 377 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373N VAL* 2.9 34.6 + - + -
374N VAL* 3.5 14.6 - - + -
376N HIS* 1.3 81.1 - - - +
378N HIS* 1.3 77.4 + + - +
379N TYR 3.3 0.2 - - - -
380N VAL* 3.7 7.4 - - - -
381N LEU* 3.0 37.8 + - + +
438N ARG* 3.8 16.2 - - - -
515N HEA 3.2 55.4 - + + -
516N HEA 3.3 56.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 378 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374N VAL* 2.7 35.3 + - + +
375N ALA 3.9 1.1 - - - +
376N HIS 3.1 1.2 - - - -
377N PHE* 1.3 91.2 - + - +
379N TYR* 1.3 61.7 + - - +
382N SER* 2.8 35.3 + - - +
383N MET* 3.3 6.6 + - - +
425N PHE* 3.3 35.9 - + + -
515N HEA 1.9 94.5 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 379 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347N LEU* 3.7 23.5 - - + +
350N VAL* 3.5 29.6 - - + -
351N GLY* 3.5 14.8 - - - -
375N ALA 3.0 20.6 + - - +
376N HIS* 3.0 9.0 + - - +
378N HIS* 1.3 77.4 - - - +
380N VAL* 1.3 62.0 + - - +
383N MET* 3.2 61.3 + - + +
384N GLY* 3.4 2.6 + - - -
422N ASN* 3.1 21.8 + - - -
425N PHE* 3.8 16.4 - - + -
426N PHE* 3.4 28.1 + + - +
429N HIS* 3.8 24.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 380 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247N ILE* 3.7 3.3 - - - +
348N PHE* 4.2 24.9 - - + +
351N GLY* 3.5 32.3 - - - +
352N GLY* 3.8 6.5 - - - +
376N HIS* 3.2 12.1 + - + +
377N PHE* 3.7 9.6 - - - +
379N TYR* 1.3 77.7 - - - +
381N LEU* 1.3 58.5 + - - +
384N GLY* 3.2 20.3 - - - +
385N ALA 3.3 3.8 + - - -
516N HEA 3.4 56.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 381 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66N ILE* 5.2 2.5 - - + -
246N LEU* 3.7 32.5 - - + -
377N PHE* 3.0 29.5 + - + +
378N HIS* 4.8 0.4 - - - -
380N VAL* 1.3 75.4 - - - +
382N SER* 1.3 60.0 + - - +
383N MET 3.2 1.1 - - - -
385N ALA* 3.3 14.1 + - + +
386N VAL* 3.1 29.6 + - - +
515N HEA 3.9 39.8 - - + +
516N HEA 3.6 53.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 382 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378N HIS* 2.8 38.1 + - - -
381N LEU* 1.3 75.7 - - - +
383N MET* 1.3 62.2 + - - +
386N VAL* 3.4 19.8 - - - +
387N PHE* 3.9 5.7 - - - -
417N MET* 5.4 0.2 - - - +
421N VAL* 4.3 5.4 - - - +
425N PHE* 4.0 10.5 - - - -
515N HEA 3.1 46.8 + - - +
----------------------------------------------------------
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