Contacts of the helix formed by residues 362 - 376 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315D TYR* 3.9 3.8 - - - -
360D LYS* 3.2 18.3 - - - +
361D LEU* 1.3 75.0 - - - +
363D LYS* 1.3 61.9 + - - +
364D GLU* 3.2 9.7 - - - +
365D GLU* 2.8 33.1 + - - +
366D PHE* 2.9 11.6 + - - +
402D TYR* 2.6 30.7 + - - +
406D GLN* 4.1 6.0 + - - +
407D HIS* 2.7 38.0 + - - -
413D ARG* 4.2 0.3 + - - -
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Residues in contact with LYS 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D LEU* 4.3 19.7 - - + -
245D GLU* 4.2 27.7 - - - +
315D TYR* 3.2 36.9 + - + +
362D GLU* 1.3 73.0 - - - +
364D GLU* 1.3 69.3 + - - +
366D PHE* 3.5 5.3 - - + +
367D VAL* 3.0 36.6 + - + +
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Residues in contact with GLU 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D VAL* 3.8 23.7 - - + +
242D LEU* 4.1 21.4 - - + +
362D GLU* 3.2 5.9 - - - +
363D LYS* 1.3 87.7 + - - +
365D GLU* 1.3 54.1 + - + +
367D VAL* 3.4 7.4 - - - +
368D THR* 2.7 28.6 + - - -
402D TYR* 3.4 45.2 + - + +
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Residues in contact with GLU 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361D LEU* 3.7 15.0 - - + +
362D GLU* 2.8 37.1 + - + +
364D GLU* 1.3 78.4 - - - +
366D PHE* 1.3 60.2 + - - +
367D VAL 3.4 0.2 - - - -
368D THR* 4.0 3.7 - - - -
369D LEU* 2.8 35.0 + - - +
399D LEU* 4.9 7.1 - - + +
402D TYR* 3.4 22.8 - - + -
403D GLU* 2.3 34.6 - - - +
407D HIS* 4.1 0.9 - - - -
413D ARG* 3.0 35.9 + - - -
417D MET* 3.8 10.1 - - - +
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Residues in contact with PHE 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D GLU* 3.6 11.9 - - - -
311D LEU* 3.3 37.0 - - + -
312D GLY* 3.9 11.7 - - - -
315D TYR* 3.4 59.9 - + + -
316D ARG* 5.7 1.1 - - + -
361D LEU* 4.2 11.5 - - + +
362D GLU 2.9 5.5 + - - -
363D LYS* 3.5 10.3 - - + +
365D GLU* 1.3 77.1 - - - +
367D VAL* 1.3 71.9 + - + +
369D LEU* 3.5 4.7 - - - +
370D LYS* 2.9 68.7 + - + +
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Residues in contact with VAL 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D VAL* 4.5 4.0 - - + -
241D LEU* 3.8 34.5 - - + +
242D LEU* 4.4 13.7 - - + -
245D GLU* 3.4 27.1 - - + +
282D TRP* 4.5 5.7 - - - +
363D LYS* 3.0 22.6 + - + +
364D GLU* 3.4 19.7 - - - +
366D PHE* 1.3 83.1 - - + +
368D THR* 1.3 70.1 + - - +
370D LYS* 3.4 10.2 + - - +
371D ALA* 3.2 21.3 + - - +
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Residues in contact with THR 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D VAL* 3.4 19.6 - - - +
241D LEU* 3.9 13.1 - - + +
364D GLU 2.7 23.0 + - - -
365D GLU* 3.5 5.5 + - - -
366D PHE 3.3 0.4 - - - -
367D VAL* 1.3 82.8 - - - +
369D LEU* 1.3 58.9 + - - +
371D ALA* 3.2 5.0 + - - +
372D ILE* 3.0 29.0 + - + +
395D LEU* 3.9 24.9 - - + +
398D ALA* 4.5 5.8 - - + -
399D LEU* 4.0 28.5 - - + +
402D TYR* 6.0 0.3 - - - +
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Residues in contact with LEU 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D LEU* 4.1 11.3 - - + +
356D TYR* 3.6 34.8 - - + +
361D LEU* 4.8 4.3 - - + -
365D GLU 2.8 20.5 + - - +
366D PHE* 3.5 4.0 - - - +
368D THR* 1.3 75.1 - - - +
370D LYS* 1.3 65.3 + - - +
372D ILE* 3.3 21.6 + - + +
373D ALA* 3.0 24.1 + - - +
399D LEU* 4.4 11.2 - - + -
417D MET* 3.8 42.4 - - + +
418D LEU* 4.7 1.1 - - + -
420D THR* 4.1 0.4 - - - +
421D LEU* 4.2 20.5 - - + +
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Residues in contact with LYS 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D GLU* 3.0 37.5 + - - -
246D PRO* 4.6 8.7 - - - +
282D TRP* 3.8 25.6 - - + +
308D ILE* 3.9 36.5 - - + +
311D LEU* 3.6 25.7 - - + +
312D GLY* 5.2 1.4 - - - -
366D PHE* 2.9 47.3 + - + +
367D VAL* 3.7 10.1 - - - +
369D LEU* 1.3 70.6 - - - +
371D ALA* 1.3 64.6 + - - +
373D ALA* 3.3 6.0 + - - +
374D LEU* 3.2 19.1 + - - +
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Residues in contact with ALA 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D LEU* 4.2 15.5 - - + -
282D TRP* 4.0 10.0 - - + -
286D ILE* 4.3 10.3 - - + +
367D VAL 3.2 9.6 + - - +
368D THR 3.2 10.5 + - - +
369D LEU 3.1 0.4 - - - -
370D LYS* 1.3 79.9 - - - +
372D ILE* 1.3 62.4 + - - +
374D LEU* 3.2 8.1 + - - +
375D ALA* 3.1 17.0 + - - +
395D LEU* 3.4 35.4 - - + +
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Residues in contact with ILE 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A MET* 4.9 9.0 - - + -
368D THR* 3.0 18.7 + - + +
369D LEU* 3.6 13.9 - - + +
371D ALA* 1.3 73.4 - - - +
373D ALA* 1.3 60.8 + - - +
375D ALA* 3.1 2.8 + - - +
376D ASN* 2.7 36.0 + - + +
392D GLN* 5.3 2.0 - - - +
395D LEU* 3.8 27.6 - - + +
396D HIS* 4.2 17.9 - - + +
399D LEU* 4.0 18.4 - - + -
418D LEU* 3.8 25.1 - - + -
421D LEU* 3.8 25.8 - - + -
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Residues in contact with ALA 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D ALA* 4.5 2.0 - - - -
307D GLU* 4.1 29.9 - - + +
308D ILE* 5.4 3.4 - - + -
311D LEU* 5.3 0.2 - - + -
369D LEU 3.0 13.1 + - - +
370D LYS* 3.7 10.3 - - - +
371D ALA 3.3 0.4 - - - -
372D ILE* 1.3 77.9 - - - +
374D LEU* 1.3 65.0 + - - +
376D ASN* 3.2 4.3 + - - -
377D SER* 3.1 25.8 + - - -
421D LEU* 4.5 14.6 - - + -
424D LEU* 4.6 9.2 - - + -
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Residues in contact with LEU 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282D TRP* 4.2 6.5 - - + -
283D ALA* 4.0 11.9 - - + -
286D ILE* 3.5 28.9 - - + -
289D PHE* 3.5 26.2 - - + -
300D LEU* 3.1 40.9 - - + +
301D LEU* 3.8 16.4 - - + +
304D ALA* 3.5 16.7 - - + +
308D ILE* 4.2 7.8 - - + +
370D LYS 3.2 9.3 + - - +
371D ALA* 3.2 9.8 + - - +
373D ALA* 1.3 79.6 - - - +
375D ALA* 1.3 58.0 - - - +
377D SER* 2.8 22.2 + - - -
391D LEU* 6.3 0.4 - - + -
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Residues in contact with ALA 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D LEU* 3.8 8.7 - - - +
371D ALA 3.1 12.7 + - - +
372D ILE* 3.1 6.5 + - - +
374D LEU* 1.3 77.8 - - - +
376D ASN* 1.3 58.2 + - - +
377D SER 3.3 3.1 + - - -
378D ASP 5.1 0.5 + - - -
388D VAL* 3.8 12.7 - - - +
391D LEU* 3.9 29.4 - - + -
392D GLN* 3.0 34.1 + - + +
395D LEU* 3.9 12.8 - - + -
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Residues in contact with ASN 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A LYS* 4.3 9.9 + - - -
419A MET* 2.8 56.2 + - + +
422A PRO* 4.2 14.3 - - - +
372D ILE* 2.7 24.8 + - + +
373D ALA* 3.4 5.8 - - - +
375D ALA* 1.3 72.8 - - - +
377D SER* 1.3 54.4 + - - -
378D ASP* 3.2 12.8 + - - +
392D GLN* 3.6 22.6 + - + +
421D LEU* 4.8 6.4 - - + +
425D ARG* 3.0 17.9 + - - +
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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