Contacts of the helix formed by residues 362 - 376 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A TYR* 4.2 3.1 - - - -
360A LYS* 3.4 16.2 - - - +
361A LEU* 1.3 75.2 - - - +
363A LYS* 1.3 67.9 + - - +
364A GLU* 3.2 9.6 - - - +
365A GLU* 2.7 28.9 + - + +
366A PHE 3.0 9.2 + - - -
402A TYR* 2.5 31.9 + - - +
406A GLN* 4.3 2.6 + - - +
407A HIS* 2.8 40.0 + - - -
413A ARG* 4.3 0.4 + - - -
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Residues in contact with LYS 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A LEU* 3.7 23.6 - - + -
245A GLU* 4.0 28.9 + - - +
315A TYR* 3.4 40.2 + - + +
362A GLU* 1.3 70.6 - - - +
364A GLU* 1.3 72.7 + - - +
366A PHE* 2.9 17.7 + - + +
367A VAL* 3.0 19.9 + - + +
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Residues in contact with GLU 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A TYR* 2.6 46.3 + - + -
238A VAL* 4.0 11.3 - - + +
242A LEU* 4.0 18.6 - - + +
362A GLU* 3.9 3.6 - - - +
363A LYS* 1.3 86.6 + - - +
365A GLU* 1.3 56.0 + - - +
367A VAL* 3.3 14.5 - - - +
368A THR* 2.6 28.6 + - - -
402A TYR* 3.4 34.0 + - + +
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Residues in contact with GLU 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A LEU* 3.3 12.1 - - + -
362A GLU* 2.7 53.6 + - + +
364A GLU* 1.3 70.3 - - - +
366A PHE* 1.3 52.4 + - - +
368A THR* 3.4 4.9 + - - -
369A LEU* 2.7 38.9 + - + +
399A LEU* 4.8 6.4 - - + +
402A TYR* 3.6 15.7 - - + -
403A GLU* 2.5 32.7 - - - +
407A HIS* 3.9 0.3 + - - -
413A ARG* 2.9 34.0 + - - -
417A MET* 3.1 15.2 - - + +
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Residues in contact with PHE 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A GLU* 4.1 18.2 - - - -
311A LEU* 3.1 39.7 - - + +
312A GLY* 3.9 13.2 - - - -
315A TYR* 3.5 51.4 - + + -
316A ARG* 6.3 0.4 - - + -
361A LEU* 3.9 11.9 - - + +
362A GLU 3.0 5.0 + - - +
363A LYS* 2.9 10.8 + - + +
365A GLU* 1.3 76.5 - - - +
367A VAL* 1.4 62.9 + - + +
369A LEU* 3.2 6.3 + - - +
370A LYS* 2.8 68.7 + - + +
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Residues in contact with VAL 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A VAL* 4.8 2.0 - - + +
241A LEU* 3.7 35.4 - - + +
242A LEU* 4.3 11.9 - - + -
245A GLU* 3.8 33.7 - - + +
282A TRP* 4.2 7.1 - - - +
363A LYS* 3.0 21.4 + - + +
364A GLU* 3.3 20.0 - - - +
366A PHE* 1.4 86.6 - - + +
368A THR* 1.3 69.1 + - - +
370A LYS* 3.6 11.4 + - - +
371A ALA* 3.2 16.5 + - - +
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Residues in contact with THR 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A VAL* 3.8 17.0 - - - +
241A LEU* 3.8 14.8 - - + +
364A GLU 2.6 22.9 + - - -
365A GLU* 3.8 4.9 - - - -
366A PHE 3.3 0.2 - - - -
367A VAL* 1.3 82.3 - - - +
369A LEU* 1.3 57.0 + - - +
371A ALA* 3.2 4.7 + - - +
372A ILE* 3.0 34.8 + - + +
395A LEU* 3.8 25.8 - - + +
398A ALA* 4.6 6.3 - - + -
399A LEU* 3.9 28.4 - - + +
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Residues in contact with LEU 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LEU* 4.2 12.5 - - + +
356A TYR* 4.2 17.3 - - + +
361A LEU* 4.1 11.7 - - + -
365A GLU* 2.7 24.7 + - + +
366A PHE* 3.2 6.0 + - - +
368A THR* 1.3 70.3 - - - +
370A LYS* 1.3 53.6 + - - +
372A ILE* 3.2 16.6 + - + +
373A ALA* 2.7 35.7 + - - +
399A LEU* 4.9 7.2 - - + -
417A MET* 3.8 53.2 - - + +
418A LEU* 4.7 3.4 - - + +
420A THR* 4.8 0.7 - - - +
421A LEU* 4.0 25.5 - - + +
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Residues in contact with LYS 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A GLU* 3.0 25.9 + - - -
246A PRO* 4.6 4.4 - - - +
279A ILE* 6.1 1.8 - - - +
282A TRP* 3.8 36.1 - - + +
308A ILE* 3.7 36.6 - - + +
311A LEU* 3.7 20.6 - - + +
312A GLY* 5.4 0.2 - - - -
366A PHE* 2.8 51.3 + - + +
367A VAL* 3.6 13.2 - - - +
369A LEU* 1.3 71.6 - - - +
371A ALA* 1.3 63.3 + - - +
373A ALA* 3.3 5.3 + - - +
374A LEU* 3.1 22.0 + - - +
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Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A LEU* 4.0 10.5 - - + -
282A TRP* 3.7 11.8 - - + -
286A ILE* 4.3 14.5 - - + +
367A VAL 3.2 9.6 + - - +
368A THR 3.2 10.8 + - - +
370A LYS* 1.3 78.1 - - - +
372A ILE* 1.3 58.4 + - - +
374A LEU* 3.2 7.3 + - - +
375A ALA 2.9 23.4 + - - -
395A LEU* 3.5 35.4 - - + +
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Residues in contact with ILE 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A THR* 3.0 30.0 + - + +
369A LEU* 3.7 11.0 - - + +
371A ALA* 1.3 73.7 - - - +
373A ALA* 1.3 57.4 + - - +
375A ALA* 4.3 2.2 - - + +
376A ASN* 2.7 41.1 + - + +
392A GLN* 5.4 1.8 - - - +
395A LEU* 3.8 32.8 - - + +
396A HIS* 4.4 4.5 - - - +
399A LEU* 4.0 27.6 - - + -
418A LEU* 4.6 7.0 - - + -
421A LEU* 4.3 14.4 - - + -
419D MET* 3.6 31.9 - - + -
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Residues in contact with ALA 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ALA* 3.8 4.8 - - - +
307A GLU* 3.9 26.9 - - + +
308A ILE* 4.9 5.6 - - + -
311A LEU* 5.0 1.3 - - + -
369A LEU 2.7 20.0 + - - +
370A LYS* 3.3 9.6 + - - +
372A ILE* 1.3 73.6 - - - +
374A LEU* 1.3 65.5 + - - +
376A ASN* 3.6 4.1 - - - -
377A SER* 3.3 19.8 + - - -
421A LEU* 4.8 10.2 - - + +
424A LEU* 4.3 16.8 - - + -
425A ARG* 5.3 0.3 + - - -
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Residues in contact with LEU 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A TRP* 4.1 9.0 - - + -
283A ALA* 4.2 6.1 - - + -
286A ILE* 3.3 31.4 - - + -
289A PHE* 3.8 24.5 - - + -
300A LEU* 3.7 41.0 - - + +
301A LEU* 3.8 15.5 - - + +
304A ALA* 3.8 7.8 - - + +
308A ILE* 4.2 16.6 - - + +
370A LYS 3.1 12.7 + - - +
371A ALA 3.3 7.4 - - - +
372A ILE 3.1 0.2 - - - -
373A ALA* 1.3 79.3 - - - +
375A ALA* 1.3 65.4 + - - +
377A SER* 3.1 18.9 + - - -
391A LEU* 5.8 1.8 - - + -
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Residues in contact with ALA 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A LEU* 4.6 5.9 - - - +
371A ALA 2.9 10.7 + - - +
372A ILE* 3.8 3.8 - - - +
374A LEU* 1.3 73.3 - - - +
376A ASN* 1.3 56.3 + - - +
377A SER* 3.1 6.9 + - - -
378A ASP 4.9 0.5 + - - -
388A VAL* 3.6 12.0 - - - +
391A LEU* 3.8 24.4 - - + +
392A GLN* 3.3 35.3 + - + -
395A LEU* 3.7 27.4 - - + -
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Residues in contact with ASN 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A ILE* 2.7 23.2 + - + +
373A ALA* 3.6 5.2 - - - +
375A ALA* 1.3 71.5 - - - +
377A SER* 1.3 54.3 + - - +
378A ASP* 3.3 19.0 + - - +
392A GLN* 3.7 19.3 + - - +
421A LEU* 3.7 23.8 - - + +
425A ARG* 3.1 17.7 + - - +
355D LYS* 5.1 1.7 + - - -
419D MET* 3.1 50.8 + - + +
422D PRO* 4.3 8.1 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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