Contacts of the helix formed by residues 384 - 407 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 5.1 1.1 - - + -
296B ASP* 3.2 12.3 + - - +
382B ILE* 3.5 2.9 - - - -
383B GLU* 1.3 77.8 - - + +
385B VAL* 1.3 60.0 + - - +
386B GLU* 3.6 11.1 + - - +
387B ALA* 2.8 41.5 + - + +
388B VAL* 3.0 28.8 + - - +
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Residues in contact with VAL 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ILE* 4.1 24.2 - - + +
383B GLU 3.9 3.2 + - - +
384B ASP* 1.3 68.6 + - - +
386B GLU* 1.3 76.2 + - - +
388B VAL* 3.1 5.6 + - + +
389B GLN* 2.9 25.8 + - + +
354E LYS* 4.3 26.7 - - - +
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Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ASP* 3.5 7.5 + - - +
385B VAL* 1.3 85.4 + - - +
387B ALA* 1.3 58.4 + - - +
389B GLN* 3.3 7.1 + - - +
390B LYS* 2.9 30.7 + - - +
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Residues in contact with ALA 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 3.5 25.5 - - + +
384B ASP* 2.8 34.5 + - - +
386B GLU* 1.3 72.4 - - - +
388B VAL* 1.3 61.8 + - - +
390B LYS* 3.4 8.6 + - - +
391B LEU* 3.2 20.4 + - - +
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Residues in contact with VAL 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 4.4 16.2 - - + -
296B ASP* 5.0 2.9 - - - -
300B LEU* 4.1 24.7 - - + -
375B ALA* 3.5 22.6 - - - +
382B ILE* 3.4 27.6 - - + -
384B ASP 3.0 17.5 - - - +
385B VAL* 3.1 6.3 + - - +
387B ALA* 1.3 73.9 - - - +
389B GLN* 1.3 60.4 + - - +
391B LEU* 3.3 7.2 + - + +
392B GLN* 3.1 31.9 + - - +
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Residues in contact with GLN 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B VAL* 2.9 20.4 + - + +
386B GLU* 3.6 7.6 - - - +
388B VAL* 1.3 73.2 - - - +
390B LYS* 1.3 61.6 + - - +
392B GLN* 3.0 28.9 + - - +
393B ASP* 2.7 65.8 + - - +
355E LYS* 5.6 7.8 - - - +
359E MET* 6.0 2.0 - - - +
416E LYS* 3.7 21.6 - - - +
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Residues in contact with LYS 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B GLU 2.9 17.9 + - - +
387B ALA* 3.6 9.9 - - - +
388B VAL 3.3 0.2 - - - -
389B GLN* 1.3 78.3 - - - +
391B LEU* 1.3 55.5 + - - +
393B ASP* 3.5 23.8 + - - +
394B VAL* 3.0 44.5 + - + +
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ILE* 3.9 9.4 - - + -
287B PRO 3.2 27.6 - - - +
288B GLY* 4.6 4.9 - - - -
289B PHE* 4.5 24.5 - - + +
292B LEU* 4.6 7.0 - - + -
300B LEU* 4.5 15.7 - - + -
374B LEU* 6.1 1.6 - - + -
375B ALA* 3.7 24.2 - - + -
387B ALA 3.2 13.0 + - - +
388B VAL* 3.6 9.9 - - - +
389B GLN 3.1 0.2 - - - -
390B LYS* 1.3 74.4 - - - +
392B GLN* 1.3 65.3 + - - +
394B VAL* 4.1 5.1 - - + +
395B LEU* 3.1 47.8 + - + +
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Residues in contact with GLN 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ILE* 5.4 1.8 - - - +
375B ALA* 3.2 39.7 + - + +
376B ASN* 3.5 25.0 + - - +
378B ASP* 5.6 3.2 + - - +
388B VAL* 3.1 20.1 + - - +
389B GLN* 3.0 32.8 + - - +
391B LEU* 1.3 77.5 - - - +
393B ASP* 1.3 55.0 + - - +
395B LEU* 3.3 3.1 + - - +
396B HIS* 2.8 37.6 + - - +
355E LYS* 5.8 4.8 - - - +
419E MET* 4.0 22.1 - - + +
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Residues in contact with ASP 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B GLN* 2.7 59.2 + - - +
390B LYS* 3.7 27.1 + - - +
392B GLN* 1.3 74.7 - - - +
394B VAL* 1.3 58.0 + - + +
396B HIS* 3.3 8.4 + - - +
397B GLU* 2.8 29.3 + - - +
412E ARG* 4.1 8.8 + - - +
416E LYS* 3.2 25.8 + - - +
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Residues in contact with VAL 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ILE* 3.3 28.7 - - + +
287B PRO* 5.1 10.3 - - + +
390B LYS* 3.0 36.8 + - + +
391B LEU* 4.1 7.9 - - + +
392B GLN 3.4 0.2 - - - -
393B ASP* 1.3 73.2 - - - +
395B LEU* 1.3 67.5 + - + +
397B GLU* 3.4 15.1 + - - +
398B ALA* 3.1 21.8 + - - +
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Residues in contact with LEU 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ILE* 4.3 20.6 - - + -
241B LEU* 5.0 2.5 - - + -
286B ILE* 4.1 16.4 - - + -
287B PRO* 4.5 7.0 - - + -
368B THR* 4.0 7.5 - - + +
371B ALA* 3.3 47.1 - - + +
372B ILE* 3.9 15.7 - - + +
375B ALA* 3.7 10.1 - - + -
391B LEU* 3.1 36.0 + - + +
392B GLN* 3.7 3.1 - - - +
394B VAL* 1.3 74.1 - - + +
396B HIS* 1.3 65.2 + - - +
398B ALA* 3.2 7.5 + - - +
399B LEU* 3.2 20.4 + - - +
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Residues in contact with HIS 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ILE* 4.3 8.6 - - + +
392B GLN 2.8 21.5 + - - +
393B ASP* 3.5 7.9 + - - +
395B LEU* 1.3 73.8 - - - +
397B GLU* 1.3 64.7 + - - +
399B LEU* 3.0 8.6 + - + +
400B GLN* 2.9 35.2 + - + +
414B ALA* 5.6 1.5 - - + +
418B LEU* 3.6 26.7 - - + +
412E ARG* 3.3 50.7 + - + +
415E GLY* 3.4 19.9 - - - -
416E LYS* 4.3 8.5 + - - +
419E MET* 4.5 14.9 - - - -
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Residues in contact with GLU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ASN* 5.7 1.8 - - - +
393B ASP 2.8 17.3 + - - +
394B VAL* 3.5 15.0 - - - +
396B HIS* 1.3 76.9 - - - +
398B ALA* 1.3 57.3 + - - +
400B GLN* 3.3 2.7 + - - +
401B ASP* 2.8 38.2 + - + +
412E ARG* 3.5 43.2 + - - +
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Residues in contact with ALA 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ASN* 3.4 29.2 + - - +
237B ILE* 3.9 23.8 - - + +
238B VAL* 3.8 13.3 - - + +
368B THR* 4.6 3.8 - - + -
394B VAL 3.1 13.8 + - - +
395B LEU* 3.5 9.9 - - - +
396B HIS 3.2 0.4 - - - -
397B GLU* 1.3 77.0 - - - +
399B LEU* 1.3 61.1 + - - +
401B ASP* 3.7 1.7 + - - +
402B TYR* 3.1 24.3 + - - +
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Residues in contact with LEU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 5.5 0.4 - - - -
365B GLU* 4.8 13.2 - - + +
368B THR* 4.2 22.2 - - + +
369B LEU* 4.7 7.2 - - + -
372B ILE* 3.9 19.5 - - + -
395B LEU 3.2 10.7 + - - +
396B HIS* 3.0 12.6 + - + +
398B ALA* 1.3 73.7 - - - +
400B GLN* 1.3 65.9 + - - +
402B TYR* 3.1 9.4 + - + +
403B GLU* 2.9 54.8 + - + +
414B ALA* 4.1 23.3 - - + +
417B MET* 4.4 13.2 - - + -
418B LEU* 4.5 12.3 - - + -
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Residues in contact with GLN 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B HIS* 2.9 31.3 + - - +
397B GLU* 3.8 9.2 - - - +
399B LEU* 1.3 76.4 - - - +
401B ASP* 1.3 57.9 + - - +
403B GLU* 3.1 4.7 + - - +
404B ALA* 2.8 33.8 + - - +
411B PRO 5.0 5.3 + - - +
414B ALA* 3.8 25.3 - - + +
415B GLY 5.3 1.4 - - - +
400E GLN* 5.0 12.7 + - - +
411E PRO 5.1 8.0 + - - +
412E ARG* 4.4 15.9 - - + +
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Residues in contact with ASP 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B TYR 5.4 0.2 - - - -
235B ASN* 3.7 35.6 + - - +
397B GLU* 2.8 25.9 + - + +
400B GLN* 1.3 73.9 - - - +
402B TYR* 1.3 62.1 + - - +
404B ALA* 3.4 8.0 + - - +
405B GLY* 3.1 19.4 + - - -
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Residues in contact with TYR 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B TYR* 3.8 27.4 + + - -
235B ASN* 5.0 5.4 - - + +
238B VAL* 4.4 17.0 - - + -
362B GLU* 2.5 30.4 + - - -
364B GLU* 3.3 43.9 - - + +
365B GLU* 3.7 18.6 - - + -
398B ALA 3.1 17.8 + - - +
399B LEU* 3.1 8.8 + - + +
401B ASP* 1.3 77.4 + - - +
403B GLU* 1.3 77.6 + - - +
405B GLY* 3.4 1.0 + - - -
406B GLN* 2.9 53.2 + - + +
407B HIS* 4.4 1.1 - + - -
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Residues in contact with GLU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B GLU* 3.0 31.6 - - - +
399B LEU* 2.9 29.6 + - + +
400B GLN* 3.6 8.1 - - - +
402B TYR* 1.3 78.4 - - - +
404B ALA* 1.3 60.6 + - - +
407B HIS* 2.9 48.6 + - - +
410B ASP 5.4 2.0 - - - +
413B ARG* 3.3 32.4 - - + +
414B ALA* 3.7 33.9 - - + +
417B MET* 4.4 2.4 - - - +
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Residues in contact with ALA 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B GLN* 2.8 21.1 + - - +
401B ASP* 3.5 9.4 - - - +
403B GLU* 1.3 79.6 - - - +
405B GLY* 1.3 58.6 + - - +
407B HIS 5.1 0.4 - - - -
408B MET* 3.1 30.0 - - - +
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Residues in contact with GLY 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B ASP 3.1 13.7 + - - -
402B TYR 3.9 1.6 - - - -
404B ALA* 1.3 79.2 - - - +
406B GLN* 1.3 62.9 + - - +
408B MET* 3.7 20.2 - - - +
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Residues in contact with GLN 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B PRO 5.0 1.6 - - - +
234B TYR* 3.2 37.9 + - - -
362B GLU* 4.6 1.8 - - - +
402B TYR* 2.9 41.9 + - + +
405B GLY* 1.3 79.5 + - - +
407B HIS* 1.3 82.4 + - + +
408B MET* 4.0 2.7 - - - -
409B GLU* 4.3 2.3 - - - +
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Residues in contact with HIS 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B GLU* 2.7 37.5 + - - -
402B TYR* 4.4 1.6 - + - -
403B GLU* 2.9 38.2 + - - +
404B ALA* 5.1 0.2 - - - -
406B GLN* 1.3 106.3 + - + +
408B MET* 1.3 57.5 + - - +
409B GLU* 2.8 33.7 + - - +
410B ASP 3.0 21.7 + - - +
411B PRO* 4.8 1.2 - - - +
413B ARG* 3.2 41.9 + - - -
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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
------------------------------------------------------------
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