Contacts of the helix formed by residues 362 - 376 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315E TYR* 4.5 3.8 - - - -
360E LYS* 3.4 14.0 - - - +
361E LEU* 1.3 73.7 - - - +
363E LYS* 1.3 60.4 + - - +
364E GLU* 3.2 10.7 - - - +
365E GLU* 2.8 37.2 + - + +
366E PHE* 3.0 11.6 + - - +
402E TYR* 2.6 30.5 + - - -
406E GLN* 4.5 3.9 + - - +
407E HIS* 2.6 38.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 363 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242E LEU* 4.2 17.3 - - + +
245E GLU* 4.3 28.1 - - - +
315E TYR* 3.4 41.6 + - + +
362E GLU* 1.3 72.6 - - - +
364E GLU* 1.3 62.3 + - - +
366E PHE* 3.2 5.1 + - + +
367E VAL* 3.0 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 364 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234E TYR* 3.4 30.9 + - + +
238E VAL* 3.6 22.1 - - + +
242E LEU* 4.0 12.5 - - + +
362E GLU* 3.5 11.4 - - - +
363E LYS* 1.3 84.6 + - - +
365E GLU* 1.3 57.8 + - - +
367E VAL* 3.5 9.0 - - - +
368E THR* 2.7 32.2 + - - -
402E TYR* 3.5 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 365 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361E LEU* 3.6 14.8 - - + -
362E GLU* 2.8 44.1 + - + +
364E GLU* 1.3 75.1 - - - +
366E PHE* 1.3 57.0 + - - +
368E THR* 3.4 3.3 + - - -
369E LEU* 2.8 39.7 + - + +
399E LEU* 4.9 6.8 - - + +
402E TYR* 3.7 16.4 - - + -
403E GLU* 2.5 31.3 - - - +
407E HIS* 4.2 0.3 - - - -
413E ARG* 2.8 39.0 + - - -
417E MET* 3.6 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 366 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245E GLU* 3.3 21.3 - - - -
311E LEU* 3.8 33.3 - - + +
312E GLY* 4.2 8.1 - - - -
315E TYR* 3.4 63.7 - + + -
361E LEU* 4.0 13.8 - - + +
362E GLU 3.0 9.7 + - - +
363E LYS* 3.5 10.1 - - + +
365E GLU* 1.3 76.7 - - - +
367E VAL* 1.3 77.6 + - + +
369E LEU* 3.7 4.9 - - - +
370E LYS* 2.8 56.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 367 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238E VAL* 4.6 3.1 - - + +
241E LEU* 3.8 36.8 - - + +
242E LEU* 4.4 8.1 - - + +
245E GLU* 3.7 23.3 - - + +
282E TRP* 4.4 5.8 - - - +
363E LYS* 3.0 29.4 + - + +
364E GLU* 3.5 13.5 - - - +
366E PHE* 1.3 90.3 - - + +
368E THR* 1.3 65.5 + - - +
370E LYS* 3.5 9.5 + - - +
371E ALA* 3.1 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 368 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238E VAL* 3.5 18.9 - - - +
241E LEU* 3.7 18.0 - - + +
364E GLU 2.7 22.8 + - - -
365E GLU 3.9 3.4 - - - -
367E VAL* 1.3 79.9 - - - +
369E LEU* 1.3 57.3 + - - +
371E ALA* 3.1 6.0 + - + +
372E ILE* 2.9 30.1 + - + +
395E LEU* 3.7 23.8 - - + +
398E ALA* 4.6 5.2 - - + -
399E LEU* 4.0 30.7 - - + +
402E TYR* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 369 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311E LEU* 4.2 10.1 - - + -
356E TYR* 3.4 35.0 - - + +
361E LEU* 4.8 5.6 - - + -
365E GLU 2.8 19.8 + - - +
366E PHE* 3.7 4.9 - - - +
368E THR* 1.3 72.9 - - - +
370E LYS* 1.3 58.6 + - - +
372E ILE* 3.1 17.8 + - + +
373E ALA* 2.8 30.1 + - - +
399E LEU* 4.7 7.2 - - + +
417E MET* 3.9 36.6 - - + +
418E LEU* 4.5 2.2 - - + +
420E THR* 3.9 7.4 - - - +
421E LEU* 3.9 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 370 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245E GLU* 3.0 38.0 + - - -
246E PRO* 4.7 6.7 - - - +
279E ILE* 6.3 0.6 - - - +
282E TRP* 3.8 26.0 - - + -
308E ILE* 3.8 37.3 - - + +
311E LEU* 3.3 32.2 - - + +
312E GLY* 5.3 2.0 - - - +
366E PHE* 2.8 38.4 + - + +
367E VAL* 3.6 8.3 - - - +
369E LEU* 1.3 71.9 - - - +
371E ALA* 1.3 64.7 + - - +
373E ALA* 3.3 4.5 + - - +
374E LEU* 3.2 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 371 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241E LEU* 4.0 15.9 - - + -
282E TRP* 3.9 11.4 - - + -
286E ILE* 4.2 8.0 - - + +
367E VAL 3.1 10.7 + - - +
368E THR 3.1 11.4 + - - +
370E LYS* 1.3 78.3 - - - +
372E ILE* 1.3 62.5 - - - +
374E LEU* 3.0 17.0 + - - +
375E ALA* 3.1 9.2 + - - +
395E LEU* 3.8 33.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 372 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B MET* 4.3 22.2 - - + -
368E THR* 2.9 23.0 + - + +
369E LEU* 3.5 12.3 - - + +
371E ALA* 1.3 76.7 - - - +
373E ALA* 1.3 53.0 + - - +
375E ALA* 3.0 3.4 + - + +
376E ASN* 2.6 35.3 + - + +
392E GLN* 5.5 2.9 - - + +
395E LEU* 4.0 39.2 - - + +
396E HIS* 4.4 5.4 - - + +
399E LEU* 4.0 27.6 - - + -
418E LEU* 4.1 10.1 - - + -
421E LEU* 4.2 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 373 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304E ALA* 3.7 7.1 - - - +
307E GLU* 4.0 25.7 - - + +
308E ILE* 4.9 5.4 - - + -
311E LEU* 5.1 0.9 - - + -
369E LEU 2.8 19.8 + - - +
370E LYS* 3.6 8.7 - - - +
372E ILE* 1.3 70.0 - - - +
374E LEU* 1.3 67.8 + - - +
376E ASN* 4.1 3.0 - - - +
377E SER* 3.6 18.7 + - - -
421E LEU* 4.7 9.6 - - + +
424E LEU* 4.4 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282E TRP* 4.0 7.6 - - + -
283E ALA* 3.6 31.4 - - + -
286E ILE* 3.7 17.9 - - + -
289E PHE* 3.7 17.5 - - + -
300E LEU* 3.3 40.2 - - + +
301E LEU* 3.7 17.3 - - + +
304E ALA* 3.6 12.3 - - + +
308E ILE* 4.0 7.3 - - + +
370E LYS 3.2 9.9 + - - +
371E ALA 3.0 11.7 + - - +
373E ALA* 1.3 75.8 - - - +
375E ALA* 1.3 57.7 + - + +
377E SER* 2.8 27.7 + - - -
391E LEU* 6.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 375 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300E LEU* 4.6 10.1 - - - +
371E ALA 3.1 8.6 + - - +
372E ILE* 3.0 7.4 + - + +
374E LEU* 1.3 77.1 - - + +
376E ASN* 1.3 56.7 + - - +
377E SER* 3.3 7.5 + - - -
378E ASP 5.3 0.3 + - - -
388E VAL* 4.0 10.7 - - + +
391E LEU* 4.1 20.6 - - + -
392E GLN* 3.2 34.8 + - + +
395E LEU* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 376 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B LYS* 3.8 9.5 + - - -
419B MET* 2.8 56.7 + - + +
422B PRO* 4.0 17.4 - - - +
372E ILE* 2.6 23.3 + - + +
373E ALA* 4.1 4.5 - - - +
375E ALA* 1.3 72.3 - - - +
377E SER* 1.3 50.7 + - - +
378E ASP* 3.2 12.3 + - - +
392E GLN* 3.1 20.8 + - - +
421E LEU* 4.7 6.6 - - + +
425E ARG* 2.6 30.0 + - - +
----------------------------------------------------------
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