Contacts of the helix formed by residues 360 - 376 (chain B) in PDB entry 1W1J
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 PRO 360 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A VAL* 5.7 3.4 - - + -
370A THR* 6.0 2.0 - - - +
273B PRO 4.3 7.6 - - - +
274B ARG 3.8 10.5 - - - +
359B GLY* 1.3 84.2 - - - +
361B GLU* 1.3 55.1 + - - +
362B PRO* 3.3 11.7 - - + -
363B ILE* 2.8 48.1 + - + +
364B ARG* 3.3 7.7 + - - -
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Residues in contact with GLU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B PRO* 1.3 69.2 - - - +
362B PRO* 1.3 77.0 - - + +
363B ILE 3.0 0.2 + - - -
364B ARG* 3.4 34.8 - - + +
365B ARG* 2.8 56.0 + - - +
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Residues in contact with PRO 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A VAL* 3.8 37.0 - - + +
360B PRO* 3.6 9.4 - - + +
361B GLU* 1.3 103.1 - - + +
363B ILE* 1.3 58.3 - - - +
365B ARG* 3.3 21.2 - - + +
366B VAL* 3.5 14.7 - - - +
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Residues in contact with ILE 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ILE* 4.1 25.2 - - + +
366A VAL* 4.0 27.4 - - + -
367A LEU* 3.6 33.4 - - + -
306B GLN* 5.0 3.1 - - - +
358B TYR 4.3 17.3 - - - +
360B PRO* 2.8 33.0 + - + +
362B PRO* 1.3 70.7 - - - +
364B ARG* 1.3 67.1 + - - +
365B ARG 3.2 1.1 - - - -
366B VAL* 3.2 8.1 + - - +
367B LEU* 3.2 36.4 + - + +
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Residues in contact with ARG 364 (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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274B ARG 4.7 0.8 + - - -
275B GLY* 3.7 23.4 - - - -
276B TYR 4.1 11.9 + - - +
277B GLN* 4.3 18.1 + - - +
357B LEU* 3.7 35.9 - - + +
358B TYR 4.4 2.5 - - - +
359B GLY 2.9 32.0 + - - +
360B PRO* 3.3 1.4 + - - +
361B GLU* 3.2 46.2 + - + +
363B ILE* 1.3 80.4 - - - +
365B ARG* 1.3 63.1 + - - +
367B LEU* 3.5 6.1 + - - +
368B TRP* 3.0 28.3 + - - +
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Residues in contact with ARG 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B GLU* 2.8 48.6 + - - +
362B PRO* 3.3 12.0 - - - +
364B ARG* 1.3 74.8 - - - +
366B VAL* 1.3 65.3 + - + +
368B TRP* 3.5 4.7 + - - +
369B GLU* 3.2 37.9 + - - +
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Residues in contact with VAL 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A PRO* 5.2 7.2 - - + -
362A PRO* 4.0 34.5 - - + -
363A ILE* 4.4 20.0 - - + -
366A VAL* 6.3 1.1 - - + -
362B PRO 3.5 16.2 - - - +
363B ILE* 3.2 6.1 + - - +
365B ARG* 1.3 73.1 - - + +
367B LEU* 1.3 63.7 + - + +
369B GLU* 3.3 10.1 + - - +
370B THR* 2.6 37.7 + - - +
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Residues in contact with LEU 367 (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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363A ILE* 3.9 22.7 - - + -
303B MET 4.1 6.3 - - - +
304B ALA* 3.6 34.3 - - + +
306B GLN* 3.3 36.1 - - + +
357B LEU* 3.5 16.8 - - + -
358B TYR 5.4 0.2 - - - +
363B ILE* 3.2 25.0 + - + +
364B ARG* 3.8 1.6 - - - +
366B VAL* 1.3 79.5 - - + +
368B TRP* 1.3 51.7 + - - +
370B THR* 2.9 12.0 + - - +
371B ILE* 2.8 41.8 + - + +
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Residues in contact with TRP 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR* 3.5 53.8 - + + -
280B LEU 5.3 0.4 - - - -
281B ILE* 4.6 0.4 - - + -
357B LEU* 3.9 17.0 - - + +
364B ARG 3.0 16.5 + - - +
365B ARG* 3.8 3.1 - - - +
367B LEU* 1.3 75.5 - - - +
369B GLU* 1.3 63.9 + - + +
371B ILE* 4.0 18.6 - - + -
372B LYS* 2.9 64.1 + - + +
383B PHE* 3.7 33.9 - + + -
384B TYR 5.6 0.2 - - - -
385B PHE* 3.8 34.6 - + - -
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Residues in contact with GLU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B ARG* 3.2 31.1 + - - +
366B VAL* 3.7 11.0 - - + +
367B LEU 3.3 0.2 - - - -
368B TRP* 1.3 79.8 - - + +
370B THR* 1.3 58.0 + - - +
372B LYS* 3.7 7.9 - - + +
373B ASP* 2.9 35.9 + - - +
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Residues in contact with THR 370 (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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299B LEU* 4.6 16.1 - - + +
304B ALA* 5.3 6.3 - - + -
366B VAL* 2.6 29.4 + - - +
367B LEU* 2.9 12.6 + - - +
369B GLU* 1.3 76.9 - - - +
371B ILE* 1.3 60.2 + - - +
373B ASP* 3.9 9.8 - - - +
374B ALA* 3.2 23.7 + - - +
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Residues in contact with ILE 371 (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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279B TYR* 4.0 20.6 - - - +
281B ILE* 4.0 24.9 - - + -
299B LEU* 4.7 11.4 - - + -
304B ALA* 3.9 26.7 - - + +
305B LEU* 4.8 5.6 - - + -
353B PHE* 4.9 2.2 - - + -
357B LEU* 3.8 21.3 - - + -
367B LEU 2.8 31.6 + - - +
368B TRP* 3.9 13.9 - - + +
370B THR* 1.3 70.2 - - - +
372B LYS* 1.3 68.2 + - - +
374B ALA* 3.1 14.8 + - - +
375B PHE* 3.1 24.4 + - + -
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Residues in contact with LYS 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B TRP* 2.9 54.7 + - + +
369B GLU* 3.7 8.1 - - + +
371B ILE* 1.3 72.3 - - - +
373B ASP* 1.3 59.3 + - + +
374B ALA 3.0 5.7 + - - -
375B PHE 3.1 9.5 + - - -
376B SER* 3.2 16.7 + - - -
383B PHE* 3.4 49.5 - - + +
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Residues in contact with ASP 373 (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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369B GLU* 2.9 19.6 + - + +
370B THR* 4.1 10.5 - - - +
372B LYS* 1.3 74.8 - - + +
374B ALA* 1.3 59.5 + - - +
376B SER* 4.1 16.5 - - - -
377B ALA* 5.1 1.4 + - - +
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Residues in contact with ALA 374 (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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295B ILE* 3.3 38.0 - - + +
299B LEU* 4.1 15.5 - - + -
370B THR 3.2 17.5 + - - +
371B ILE 3.1 5.3 + - - +
372B LYS 3.1 0.8 - - - -
373B ASP* 1.3 76.9 - - - +
375B PHE* 1.3 61.7 + - - +
376B SER 3.2 5.4 + - - -
377B ALA* 3.9 9.5 + - - +
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Residues in contact with PHE 375 (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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281B ILE* 3.8 24.0 - - + -
283B LEU* 3.9 25.1 - - + -
292B ALA* 4.2 14.6 - - + -
295B ILE* 3.7 24.5 - - + -
296B ILE* 3.8 21.1 - - + -
299B LEU* 4.4 7.2 - - + -
353B PHE* 3.7 39.9 - + + -
371B ILE* 3.1 25.2 + - + +
372B LYS 3.1 4.2 + - - +
374B ALA* 1.3 74.6 - - + +
376B SER* 1.3 61.0 - - - +
377B ALA 3.2 2.9 - - - -
378B ILE* 3.4 21.2 + - + +
381B VAL* 3.5 15.5 - - - +
383B PHE* 4.0 15.0 - - + -
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Residues in contact with SER 376 (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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372B LYS 3.2 17.6 + - - -
373B ASP* 4.1 14.6 - - - -
374B ALA 3.2 1.4 - - - -
375B PHE* 1.3 73.8 - - - +
377B ALA* 1.3 56.8 + - - +
378B ILE 3.0 16.5 + - - +
379B PRO* 4.5 1.4 - - - +
381B VAL* 4.3 8.9 - - - +
383B PHE* 4.5 8.7 - - - -
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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