Contacts of the helix formed by residues 384 - 407 (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 ASP 384 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A LEU* 5.1 2.8 - - + +
293A SER* 5.8 0.4 - - - +
296A ASP* 2.9 13.2 + - - +
382A ILE* 3.7 2.0 - - - -
383A GLU* 1.3 75.8 - - + +
385A VAL* 1.3 62.2 + - - +
386A GLU* 3.7 10.2 + - - +
387A ALA* 3.3 38.8 + - + +
388A VAL* 3.3 16.6 + - - +
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Residues in contact with VAL 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ILE* 3.9 28.5 - - + +
383A GLU 3.3 5.4 + - - +
384A ASP* 1.3 72.2 + - - +
386A GLU* 1.3 73.3 + - + +
388A VAL* 3.3 4.3 + - - +
389A GLN* 3.1 24.6 + - + +
354D LYS* 4.3 29.8 - - - +
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Residues in contact with GLU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ASP* 3.3 8.1 - - - +
385A VAL* 1.3 87.7 + - + +
387A ALA* 1.3 56.2 + - - +
389A GLN* 3.5 7.8 + - - +
390A LYS* 3.0 32.0 + - - +
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Residues in contact with ALA 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 3.6 24.3 - - + +
384A ASP* 3.3 31.0 + - - +
385A VAL 3.3 0.4 - - - -
386A GLU* 1.3 75.6 - - - +
388A VAL* 1.3 60.6 + - - +
390A LYS* 3.3 10.2 + - - +
391A LEU* 3.0 25.5 + - - +
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Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 4.5 14.6 - - + -
296A ASP* 4.6 3.1 - - - +
300A LEU* 4.4 19.1 - - + -
375A ALA* 3.6 14.1 - - - +
382A ILE* 3.6 31.4 - - + -
384A ASP 3.3 13.7 + - - +
385A VAL* 3.7 7.2 - - - +
387A ALA* 1.3 73.1 - - - +
389A GLN* 1.3 60.6 + - - +
391A LEU* 3.1 10.3 + - + +
392A GLN* 3.0 46.7 + - - +
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Residues in contact with GLN 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A VAL* 3.1 16.6 + - + +
386A GLU* 3.5 12.8 - - - +
388A VAL* 1.3 77.6 - - - +
390A LYS* 1.3 56.5 + - - +
392A GLN* 3.1 24.4 + - - +
393A ASP* 2.8 69.2 + - - +
355D LYS* 5.6 6.1 - - - +
359D MET* 6.0 2.7 - - - +
416D LYS* 4.3 14.3 - - - +
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Residues in contact with LYS 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A GLU* 3.0 15.9 + - - +
387A ALA* 3.4 13.0 - - - +
388A VAL 3.2 0.2 - - - -
389A GLN* 1.3 76.9 - - - +
391A LEU* 1.3 57.6 + - - +
393A ASP* 3.8 9.7 - - + +
394A VAL* 3.1 40.2 + - + +
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Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ILE* 4.5 9.2 - - + -
287A PRO 3.2 27.1 - - - +
288A GLY* 3.6 17.9 - - - -
289A PHE* 3.6 16.2 - - + +
292A LEU* 4.3 12.1 - - + -
300A LEU* 4.2 17.7 - - + -
374A LEU* 5.8 1.1 - - + -
375A ALA* 3.8 26.0 - - + +
387A ALA 3.0 11.9 + - - +
388A VAL* 3.2 10.8 - - - +
390A LYS* 1.3 74.5 - - - +
392A GLN* 1.3 63.4 + - - +
394A VAL* 3.5 4.9 + - + +
395A LEU* 3.3 35.5 + - + +
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Residues in contact with GLN 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A ILE* 5.4 1.2 - - - +
375A ALA* 3.3 38.4 + - + -
376A ASN* 3.7 24.6 + - - +
378A ASP* 5.8 2.0 + - - +
388A VAL* 3.0 31.3 + - - +
389A GLN* 3.1 28.5 + - - +
391A LEU* 1.3 75.7 - - - +
393A ASP* 1.3 58.7 + - - +
395A LEU* 4.0 2.7 - - - +
396A HIS* 2.9 32.7 + - - +
419D MET* 3.9 19.3 - - + +
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Residues in contact with ASP 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A GLN* 2.8 48.7 + - - +
390A LYS* 3.8 10.7 - - + +
391A LEU 3.3 0.2 - - - -
392A GLN* 1.3 76.1 - - - +
394A VAL* 1.3 63.4 + - + +
396A HIS* 3.8 6.3 + - - +
397A GLU* 3.1 25.5 + - - +
412D ARG* 4.0 9.9 + - - +
416D LYS* 2.9 39.3 + - - +
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Residues in contact with VAL 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE* 3.1 33.7 - - + +
287A PRO* 5.0 12.8 - - + +
390A LYS* 3.1 25.1 + - + +
391A LEU* 3.9 6.7 - - - +
392A GLN 3.3 0.2 - - - -
393A ASP* 1.3 75.2 - - + +
395A LEU* 1.3 68.9 + - + +
397A GLU* 3.1 15.3 + - - +
398A ALA* 3.1 19.4 + - - +
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Residues in contact with LEU 395 (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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237A ILE* 4.5 18.8 - - + -
241A LEU* 4.7 4.3 - - + -
286A ILE* 4.1 19.1 - - + -
287A PRO* 4.8 6.5 - - + +
368A THR* 3.8 10.3 - - + +
371A ALA* 3.5 48.7 - - + +
372A ILE* 3.8 14.6 - - + +
375A ALA* 3.7 14.6 - - + -
391A LEU* 3.3 26.4 + - + +
392A GLN 4.0 1.6 - - - +
394A VAL* 1.3 79.7 - - + +
396A HIS* 1.3 66.1 + - - +
398A ALA* 3.1 8.5 + - - +
399A LEU* 3.1 17.8 + - - +
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Residues in contact with HIS 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A ILE* 4.4 10.6 - - + +
392A GLN 2.9 21.6 + - - +
393A ASP* 3.8 6.2 + - - +
395A LEU* 1.3 74.9 - - - +
397A GLU* 1.3 58.8 + - - +
399A LEU* 3.2 7.2 + - + +
400A GLN* 2.9 38.6 + - + +
414A ALA* 5.7 1.1 - - + +
418A LEU* 3.8 19.1 - - + +
412D ARG* 3.4 48.5 + - + +
415D GLY* 3.5 25.3 - - - -
416D LYS* 3.7 12.8 + - - +
419D MET* 4.3 15.3 - - + -
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Residues in contact with GLU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ASN* 6.0 0.9 - - - +
393A ASP 3.1 17.8 + - - +
394A VAL* 3.1 13.2 + - - +
396A HIS* 1.3 76.5 - - - +
398A ALA* 1.3 59.8 + - - +
400A GLN* 3.9 2.8 - - - +
401A ASP* 3.0 29.2 + - + +
412D ARG* 3.5 43.3 + - - +
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Residues in contact with ALA 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ASN* 3.6 30.7 + - - +
237A ILE* 4.1 19.5 - - + -
238A VAL* 3.9 14.6 - - + +
368A THR* 4.6 3.4 - - + -
394A VAL 3.1 10.8 + - - +
395A LEU 3.1 9.2 + - - +
397A GLU* 1.3 73.8 - - - +
399A LEU* 1.3 60.7 + - - +
401A ASP* 3.3 1.4 + - - +
402A TYR* 2.9 31.7 + - - +
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Residues in contact with LEU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLU* 4.8 12.8 - - - +
368A THR* 3.9 27.2 - - + +
369A LEU* 4.9 5.6 - - + -
372A ILE* 4.0 18.8 - - + -
395A LEU 3.1 8.3 + - - +
396A HIS* 3.5 9.4 - - + +
398A ALA* 1.3 78.2 - - - +
400A GLN* 1.3 58.0 + - - +
401A ASP 3.1 0.2 + - - -
402A TYR* 3.7 5.9 - - + +
403A GLU* 2.8 63.3 + - + +
414A ALA* 4.1 24.2 - - + +
417A MET* 4.3 13.2 - - + -
418A LEU* 4.1 17.3 - - + -
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Residues in contact with GLN 400 (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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396A HIS* 2.9 28.4 + - + +
397A GLU* 4.1 7.9 - - - +
398A ALA 3.4 0.2 - - - -
399A LEU* 1.3 76.4 - - - +
401A ASP* 1.3 56.4 + - - +
403A GLU* 4.4 4.4 - - - +
404A ALA* 3.1 31.2 + - + +
411A PRO 4.8 11.0 + - - +
414A ALA* 3.1 29.1 - - - +
415A GLY 4.8 1.2 + - - -
400D GLN* 5.7 3.5 + - - -
411D PRO 5.4 4.9 - - - +
412D ARG* 4.8 14.4 - - + +
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Residues in contact with ASP 401 (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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235A ASN* 2.9 39.6 + - - +
397A GLU* 3.0 21.2 + - + +
400A GLN* 1.3 75.6 - - - +
402A TYR* 1.3 66.2 + - - +
403A GLU 3.2 0.9 - - - -
404A ALA* 3.2 7.5 + - - +
405A GLY* 3.0 19.6 + - - -
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Residues in contact with TYR 402 (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* 3.7 27.2 + + - -
235A ASN* 5.2 4.0 - - + +
238A VAL* 4.3 17.3 - - + -
362A GLU* 2.5 30.4 + - - -
364A GLU* 3.4 45.3 + - + +
365A GLU* 3.6 24.0 - - + -
398A ALA 2.9 19.7 + - - +
399A LEU* 3.7 5.8 - - + +
401A ASP* 1.3 76.8 + - - +
403A GLU* 1.3 69.7 + - + +
405A GLY* 3.2 1.3 + - - -
406A GLN* 2.8 61.7 + - + +
407A HIS* 4.4 0.9 - + - -
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Residues in contact with GLU 403 (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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365A GLU* 2.5 36.3 - - - +
399A LEU* 2.8 42.2 + - + +
400A GLN* 4.1 7.2 - - - +
402A TYR* 1.3 82.5 - - + +
404A ALA* 1.3 56.6 + - - +
407A HIS* 3.2 37.2 + - - +
410A ASP 4.5 2.8 - - - +
413A ARG* 3.0 36.6 - - + +
414A ALA* 4.1 22.2 - - + +
417A MET* 4.1 3.5 - - - +
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Residues in contact with ALA 404 (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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400A GLN* 3.1 25.9 + - + +
401A ASP* 3.5 9.6 - - - +
402A TYR 3.2 0.4 - - - -
403A GLU* 1.3 78.6 - - - +
405A GLY* 1.3 59.5 + - - +
407A HIS 5.1 0.4 - - - -
408A MET* 3.5 21.5 + - - +
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Residues in contact with GLY 405 (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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401A ASP 3.0 13.4 + - - -
402A TYR* 3.8 1.1 - - - -
404A ALA* 1.3 79.6 - - - +
406A GLN* 1.3 61.0 + - - +
407A HIS 3.5 0.2 - - - -
408A MET* 4.0 15.0 - - - +
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Residues in contact with GLN 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A TYR* 4.1 20.2 - - + -
362A GLU* 4.3 1.8 + - - +
402A TYR* 2.8 51.4 + - + +
405A GLY* 1.3 74.7 - - - +
407A HIS* 1.3 79.1 + - + +
408A MET 3.9 1.3 - - - -
409A GLU* 4.1 2.8 - - - +
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Residues in contact with HIS 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLU* 2.8 43.1 + - - -
365A GLU* 4.0 1.1 - - - -
402A TYR* 4.4 1.6 - + - -
403A GLU* 3.2 36.5 + - - +
404A ALA* 5.1 0.2 - - - -
406A GLN* 1.3 103.9 + - + +
408A MET* 1.3 60.6 + - - +
409A GLU* 2.8 31.9 + - - +
410A ASP 3.0 24.0 + - - +
411A PRO* 4.8 0.7 - - - +
413A ARG* 3.4 35.4 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
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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