Contacts of the helix formed by residues 362 - 376 (chain F) in PDB entry 2GPV
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 GLU 362 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F TYR* 4.0 4.5 - - - -
360F LYS* 3.3 15.8 - - - +
361F LEU* 1.3 75.6 - - - +
363F LYS* 1.3 62.1 + - - +
364F GLU* 3.2 13.0 - - - +
365F GLU* 2.8 38.4 + - + +
366F PHE* 2.9 12.6 + - - +
402F TYR* 2.7 22.1 + - - +
406F GLN* 5.4 3.3 + - - +
407F HIS* 2.6 41.2 + - - -
413F ARG* 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 363 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242F LEU* 4.1 16.6 - - + -
245F GLU* 3.9 34.3 + - - +
315F TYR* 3.3 45.1 + - + +
362F GLU* 1.3 72.5 - - - +
364F GLU* 1.3 65.2 + - - +
365F GLU 3.1 0.2 + - - -
366F PHE* 3.2 4.3 + - + +
367F VAL* 2.9 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 364 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234F TYR* 3.7 20.6 + - + -
238F VAL* 3.9 21.5 - - + +
242F LEU* 4.0 23.0 - - + +
362F GLU* 3.8 5.5 - - - +
363F LYS* 1.3 89.2 + - - +
365F GLU* 1.3 59.0 + - - +
367F VAL* 3.7 4.0 - - - +
368F THR* 2.8 28.4 + - - -
399F LEU* 5.6 0.3 - - - +
402F TYR* 3.5 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 365 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361F LEU* 3.6 13.9 - - + -
362F GLU* 2.8 53.6 + - + +
364F GLU* 1.3 75.4 - - - +
366F PHE* 1.3 69.0 + - - +
367F VAL 3.2 0.2 - - - -
368F THR* 3.4 3.9 + - - -
369F LEU* 2.9 29.8 + - + +
399F LEU* 4.8 7.1 - - + +
402F TYR* 3.5 16.8 - - + -
403F GLU* 2.7 28.4 - - - +
413F ARG* 3.0 26.0 + - - -
417F MET* 3.1 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 366 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245F GLU* 3.2 23.3 - - - -
311F LEU* 3.4 41.3 - - + -
312F GLY* 4.0 11.2 - - - -
315F TYR* 3.5 55.9 - + + -
316F ARG* 5.8 1.3 - - + -
361F LEU* 4.1 10.8 - - + +
362F GLU 2.9 8.3 + - - +
363F LYS* 3.4 11.9 - - + +
365F GLU* 1.3 77.2 - - - +
367F VAL* 1.3 67.0 + - + +
369F LEU* 3.5 5.9 - - - +
370F LYS* 3.0 52.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 367 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238F VAL* 4.7 2.7 - - + +
241F LEU* 3.5 42.5 - - + +
242F LEU* 4.3 12.1 - - + -
245F GLU* 3.6 28.7 - - + +
282F TRP* 4.5 2.9 - - - +
363F LYS* 2.9 28.0 + - + +
364F GLU* 3.7 13.2 - - - +
366F PHE* 1.3 85.9 - - + +
368F THR* 1.3 69.6 + - - +
370F LYS* 3.5 10.8 + - - +
371F ALA* 3.3 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 368 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238F VAL* 3.4 19.1 - - - +
241F LEU* 3.7 15.3 - - + +
364F GLU 2.8 21.3 + - - -
365F GLU 3.4 4.3 + - - -
367F VAL* 1.3 79.0 - - - +
369F LEU* 1.3 57.0 + - - +
371F ALA* 3.1 4.4 - - + +
372F ILE* 3.0 29.9 + - + +
395F LEU* 3.6 26.7 - - + +
398F ALA* 4.4 6.5 - - + -
399F LEU* 3.9 29.9 + - + +
402F TYR* 5.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 369 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311F LEU* 4.1 11.6 - - + +
356F TYR* 4.0 26.5 - - + +
361F LEU* 4.5 5.2 - - + -
365F GLU 2.9 20.0 + - - +
366F PHE* 3.5 5.4 - - - +
368F THR* 1.3 74.8 - - - +
370F LYS* 1.3 59.7 + - - +
371F ALA 3.1 1.3 - - - -
372F ILE* 3.7 14.1 - - + +
373F ALA* 2.8 32.2 + - - +
399F LEU* 4.8 6.1 - - + -
417F MET* 4.1 44.6 - - + +
418F LEU* 4.7 1.8 - - + +
420F THR* 4.2 3.4 - - - +
421F LEU* 4.1 31.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 370 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245F GLU* 2.9 39.2 + - - -
246F PRO* 4.5 8.1 - - - +
282F TRP* 3.5 32.0 - - + -
308F ILE* 4.1 34.1 - - + +
311F LEU* 3.6 25.3 - - + +
312F GLY* 5.3 0.8 - - - -
366F PHE* 3.0 37.1 + - + +
367F VAL* 3.8 10.8 - - - +
368F THR 3.4 0.2 - - - -
369F LEU* 1.3 76.2 - - - +
371F ALA* 1.3 62.0 + - - +
373F ALA* 3.6 5.3 + - - +
374F LEU* 3.3 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 371 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F LEU* 4.1 15.3 - - + -
282F TRP* 3.9 9.4 - - - -
286F ILE* 4.3 8.0 - - + +
367F VAL 3.3 10.3 + - - +
368F THR 3.1 12.5 + - - +
370F LYS* 1.3 78.8 - - - +
372F ILE* 1.3 62.2 + - - +
374F LEU* 3.2 8.0 + - - +
375F ALA 3.1 17.0 + - - -
395F LEU* 3.4 35.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 372 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C MET* 4.1 22.9 - - + -
368F THR* 3.0 28.9 + - + +
369F LEU* 3.3 9.4 + - + +
371F ALA* 1.3 74.4 - - - +
373F ALA* 1.3 58.9 + - - +
375F ALA* 3.3 3.6 + - + +
376F ASN* 2.9 30.6 + - + +
392F GLN 5.2 1.1 - - - +
395F LEU* 3.7 41.5 - - + +
396F HIS* 4.2 7.4 - - - +
399F LEU* 4.0 22.9 - - + -
418F LEU* 4.4 7.0 - - + -
421F LEU* 4.1 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 373 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304F ALA* 3.8 4.2 - - - +
307F GLU* 4.2 23.6 - - + +
308F ILE* 4.9 8.5 - - + -
311F LEU* 5.3 0.7 - - + -
369F LEU 2.8 18.4 + - - +
370F LYS* 3.7 8.3 - - - +
371F ALA 3.3 0.2 - - - -
372F ILE* 1.3 74.8 - - - +
374F LEU* 1.3 65.1 + - - +
376F ASN* 3.9 3.5 - - - -
377F SER* 3.4 21.5 + - - -
421F LEU* 4.7 8.9 - - + +
424F LEU* 4.5 15.9 - - + -
425F ARG* 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282F TRP* 4.4 5.2 - - + -
283F ALA* 4.2 11.7 - - + -
286F ILE* 3.6 27.8 - - + -
289F PHE* 3.7 24.0 - - + -
300F LEU* 3.7 42.4 - - + +
301F LEU* 3.7 19.1 - - + +
304F ALA* 3.7 14.3 - - + +
308F ILE* 3.9 9.5 - - + +
370F LYS 3.3 10.2 + - - +
371F ALA 3.2 10.8 + - - +
373F ALA* 1.3 78.0 - - - +
375F ALA* 1.3 59.7 + - - +
377F SER* 2.7 25.5 + - - -
391F LEU* 6.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 375 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300F LEU* 4.2 12.5 - - - +
371F ALA 3.1 9.3 + - - +
372F ILE* 3.3 8.0 + - + +
374F LEU* 1.3 80.1 - - - +
376F ASN* 1.3 51.7 + - - +
377F SER 3.3 2.5 + - - -
378F ASP 5.0 0.5 + - - -
388F VAL* 3.6 12.2 - - - +
391F LEU* 4.2 11.7 - - + -
392F GLN* 2.7 54.0 + - + +
395F LEU* 4.0 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 376 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C LYS* 4.2 4.9 + - - +
419C MET* 2.8 54.6 + - + +
422C PRO* 4.2 11.9 - - - +
372F ILE* 2.9 19.4 + - + +
373F ALA* 3.9 4.5 - - - +
374F LEU 3.3 0.2 - - - -
375F ALA* 1.3 75.7 - - - +
377F SER* 1.3 55.4 + - - +
378F ASP* 3.2 20.5 + - - +
392F GLN* 3.5 24.6 + - + +
421F LEU* 5.1 6.5 - - + +
425F ARG* 3.0 18.7 + - - +
----------------------------------------------------------
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