Contacts of the helix formed by residues 381 - 392 (chain B) in PDB entry 1GWX
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 381 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B TYR* 3.8 18.2 - - + +
222B TYR* 2.7 39.2 + - + -
223B LEU* 4.8 4.1 - - + +
229B THR* 3.1 28.4 + - - -
230B LYS* 3.1 19.4 + - - +
231B LYS* 3.4 24.3 + - + +
380B ASP* 1.3 74.5 + - - +
382B SER* 1.3 51.6 + - - +
384B LEU* 3.1 6.5 + - - +
385B ALA* 2.7 36.0 + - - +
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Residues in contact with SER 382 (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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215B SER 5.0 2.6 - - - +
219B TYR* 3.4 27.5 - - - -
380B ASP* 2.5 35.3 + - - -
381B ASP* 1.3 73.6 - - - +
383B ASP* 1.3 76.0 + - - +
385B ALA* 3.5 13.2 + - - +
386B LEU* 3.6 13.3 + - - +
420B HIS* 3.1 22.6 + - - -
424B ASN* 4.2 2.8 + - - -
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Residues in contact with ASP 383 (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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379B LEU* 3.5 23.7 - - + +
380B ASP* 2.8 21.6 + - - +
382B SER* 1.3 81.3 + - - +
384B LEU* 1.3 55.8 + - - +
386B LEU* 3.0 8.1 + - - +
387B PHE* 2.7 36.3 + - - +
417B LEU* 4.4 4.3 - - + +
420B HIS* 2.9 37.0 + - - -
421B LEU* 4.0 11.8 - - + +
424B ASN* 4.1 0.7 + - - -
425B HIS* 2.8 37.2 + - - -
435B LEU* 5.6 0.4 - - + -
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Residues in contact with LEU 384 (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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222B TYR* 3.2 24.5 - - + +
230B LYS* 4.2 17.3 - - + -
328B ALA 5.1 4.3 - - - +
329B MET* 5.2 5.6 - - + -
332B SER* 3.1 27.8 - - - +
374B PHE* 4.0 19.5 - - + -
379B LEU* 4.0 28.9 - - + -
380B ASP 3.0 10.1 + - - +
381B ASP* 3.4 10.1 - - - +
383B ASP* 1.3 77.6 - - - +
385B ALA* 1.3 63.3 + - - +
387B PHE* 3.7 8.9 - - + -
388B ILE* 2.9 38.9 + - + +
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Residues in contact with ALA 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ILE* 3.4 18.0 - - + +
219B TYR* 3.8 20.9 - - + -
222B TYR* 3.4 39.6 - - + -
299B PHE* 3.5 5.5 - - - -
381B ASP 2.7 18.3 + - - +
382B SER 3.6 7.4 - - - +
383B ASP 3.2 0.2 - - - -
384B LEU* 1.3 72.5 - - - +
386B LEU* 1.3 57.4 + - + +
388B ILE 3.7 0.2 + - - -
389B ALA 3.3 20.3 + - - -
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Residues in contact with LEU 386 (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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214B PHE* 4.6 0.4 - - + -
215B SER* 3.6 36.3 - - - +
218B ILE* 4.3 21.8 - - + -
382B SER 3.6 8.7 + - - +
383B ASP 3.0 6.3 + - - +
385B ALA* 1.3 76.7 - - + +
387B PHE* 1.3 64.5 + - - +
388B ILE 3.1 2.2 - - - -
389B ALA* 3.5 1.5 + - - +
390B ALA* 3.0 24.9 + - - +
413B ILE* 3.7 8.4 - - + +
416B ALA* 4.2 13.9 - - + -
417B LEU* 3.8 26.0 - - + +
420B HIS* 3.5 44.4 - - + +
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Residues in contact with PHE 387 (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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328B ALA* 4.2 10.1 - - + -
374B PHE* 3.6 36.1 - + - -
379B LEU* 5.1 1.8 - - + -
383B ASP 2.7 20.2 + - - +
384B LEU* 3.9 11.2 - - + +
386B LEU* 1.3 73.3 - - - +
388B ILE* 1.3 53.8 + - + +
390B ALA* 4.4 3.1 - - - -
391B ILE* 2.7 35.3 + - + +
417B LEU* 4.6 6.9 - - + +
435B LEU* 3.1 60.8 - - + -
438B LYS* 4.4 0.9 - - + -
439B MET* 3.4 32.1 - - + +
442B LEU* 3.9 23.8 - - + -
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Residues in contact with ILE 388 (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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222B TYR* 4.4 9.6 - - + -
226B PHE* 5.2 1.3 - - + -
296B LEU* 4.0 14.6 - - + -
299B PHE* 3.6 16.4 - - + -
325B ALA* 3.9 16.4 - - + +
328B ALA* 4.2 13.0 - - + -
329B MET* 3.7 30.5 - - + -
384B LEU* 2.9 31.6 + - + +
385B ALA 3.8 4.5 - - - +
387B PHE* 1.3 81.0 - - + +
389B ALA* 1.3 66.5 + - - +
390B ALA 3.0 1.3 - - - -
391B ILE* 2.9 18.8 + - + +
392B ILE* 2.9 34.9 + - + +
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Residues in contact with ALA 389 (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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218B ILE* 4.1 13.7 - - + -
299B PHE* 4.0 19.1 - - + -
303B ILE* 4.1 9.4 - - + -
385B ALA 3.3 14.7 + - - +
386B LEU 4.1 2.7 - - - +
388B ILE* 1.3 79.0 - - - +
390B ALA* 1.3 57.1 + - - +
392B ILE* 4.0 4.9 - - - +
393B LEU* 2.9 35.6 + - - +
413B ILE* 3.9 21.1 - - + -
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Residues in contact with ALA 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 LEU 3.0 17.3 + - - +
387B PHE* 3.9 1.1 - - - +
388B ILE 3.0 1.0 - - - -
389B ALA* 1.3 78.9 - - - +
391B ILE* 1.3 62.2 + - - +
393B LEU* 3.3 22.8 + - - +
394B CYS* 3.9 0.7 + - - +
410B GLN* 3.9 13.0 + - - +
413B ILE* 3.4 22.2 - - + +
414B LEU* 4.5 12.8 - - + -
417B LEU* 5.2 1.6 - - + -
439B MET* 3.3 26.7 - - + -
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Residues in contact with ILE 391 (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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321B GLY* 3.4 18.1 - - - +
324B GLU* 2.9 44.9 - - + +
325B ALA* 3.7 18.8 - - + +
387B PHE* 2.7 38.4 - - + +
388B ILE* 3.0 16.2 - - + +
390B ALA* 1.3 74.5 - - - +
392B ILE* 1.3 62.2 + - - +
394B CYS* 3.4 9.2 - - - +
397B ARG* 3.0 32.5 + - - +
410B GLN* 5.8 0.2 - - - +
439B MET* 4.3 12.8 - - + +
442B LEU* 5.7 3.4 - - + -
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Residues in contact with ILE 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B LEU* 4.2 10.8 - - + -
299B PHE* 4.7 4.5 - - + -
300B ALA* 3.9 15.3 - - + -
303B ILE* 6.6 0.2 - - + -
306B PHE* 3.6 31.6 - - + -
317B LEU* 3.1 29.2 - - + +
318B LEU* 4.4 17.3 - - + -
321B GLY* 4.7 10.5 - - - +
322B VAL* 5.1 1.6 - - - +
325B ALA* 3.7 18.6 - - + -
388B ILE* 2.9 49.6 + - + +
389B ALA* 4.0 6.3 - - - +
391B ILE* 1.3 78.5 - - - +
393B LEU* 1.3 60.1 + - + +
394B CYS* 2.9 7.4 + - - +
397B ARG* 5.2 0.3 + - - -
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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