Contacts of the helix formed by residues 376 - 390 (chain B) in PDB entry 5WWZ
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 MET 376 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B PRO 4.5 4.0 - - - +
325B GLY* 3.4 36.6 - - - +
326B GLN* 3.7 15.3 - - + +
357B HIS 5.2 0.8 + - - -
375B GLY* 1.3 72.9 - - - +
377B PRO* 1.3 68.6 - - + +
378B GLU* 3.3 3.8 - - + +
379B ASN* 3.0 31.3 + - + +
380B VAL* 2.7 33.1 + - - +
323C LEU* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLY 3.5 18.4 - - - +
327B THR* 4.2 24.9 - - + +
375B GLY 3.6 1.8 - - - +
376B MET* 1.3 93.0 - - + +
378B GLU* 1.3 61.5 + - - +
380B VAL* 3.4 4.5 + - + +
381B ASP* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B MET* 3.3 2.8 - - + +
377B PRO* 1.3 80.1 - - - +
379B ASN* 1.3 62.6 + - - +
381B ASP* 3.5 8.6 + - - +
382B ARG* 3.2 19.8 + - - +
323C LEU* 3.6 24.8 - - + +
324C PRO* 4.3 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B THR* 3.2 27.0 + - - +
357B HIS* 4.2 20.4 + - - +
358B THR* 3.4 15.0 - - + +
376B MET* 3.0 33.2 + - + +
378B GLU* 1.3 74.8 - - - +
380B VAL* 1.3 65.5 + - - +
382B ARG* 3.3 9.0 + - - +
383B ALA* 3.0 17.8 + - - +
323C LEU* 3.5 34.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B THR* 3.7 9.9 - - - +
329B VAL* 3.5 41.3 - - + -
358B THR* 4.5 0.4 - - + -
373B VAL* 3.9 18.8 - - + +
374B THR 3.7 6.7 - - - -
375B GLY* 3.4 34.8 - - - +
376B MET 2.7 19.5 + - - +
377B PRO* 3.8 7.6 - - + +
378B GLU 3.3 0.2 - - - -
379B ASN* 1.3 71.0 - - - +
381B ASP* 1.3 65.3 + - - +
383B ALA* 3.2 3.3 + - - +
384B ARG* 3.0 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B VAL* 6.0 0.5 - - - +
377B PRO* 2.9 22.0 + - - +
378B GLU* 3.8 8.2 - - - +
379B ASN 3.3 0.2 - - - -
380B VAL* 1.3 82.0 - - - +
382B ARG* 1.3 61.3 + - - +
384B ARG* 3.3 17.8 + - - +
385B GLU* 3.3 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B THR* 4.0 8.5 - - + -
378B GLU 3.2 14.1 + - - +
379B ASN* 3.5 12.6 - - - +
380B VAL 3.3 0.2 - - - -
381B ASP* 1.3 78.3 - - - +
383B ALA* 1.3 61.2 + - - +
385B GLU* 3.4 7.2 + - - +
386B GLU* 3.4 24.9 + - - +
401C SO4 3.5 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ILE* 4.2 9.5 - - + +
356B THR* 3.6 27.3 - - - +
358B THR* 3.7 5.4 - - - +
360B ILE* 4.3 3.1 - - + -
373B VAL* 3.6 28.5 - - + -
379B ASN 3.0 9.6 + - - +
380B VAL 3.2 2.0 + - - +
382B ARG* 1.3 73.6 - - - +
384B ARG* 1.3 65.3 + - - +
386B GLU* 3.4 3.2 + - - +
387B ILE* 3.1 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B VAL* 3.4 25.5 - - - +
330B GLN 2.9 28.4 + - - -
331B VAL* 3.9 31.3 - - + +
332B ARG 5.1 1.0 - - - +
373B VAL* 5.2 0.2 - - - +
380B VAL* 3.0 14.2 + - - +
381B ASP* 3.6 21.3 + - - +
382B ARG 3.3 0.2 - - - -
383B ALA* 1.3 77.6 - - - +
385B GLU* 1.3 58.3 + - + +
387B ILE* 3.3 2.6 + - - +
388B GLU* 2.9 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A GLN* 4.6 7.2 - - - +
357A HIS* 5.7 2.1 - - - -
358A THR 3.3 27.7 + - - +
359A TYR* 4.0 22.0 - - + +
381B ASP 3.3 11.2 + - - +
382B ARG* 3.9 9.0 - - - +
383B ALA 3.3 0.4 - - - -
384B ARG* 1.3 81.5 - - + +
386B GLU* 1.3 58.9 + - + +
388B GLU* 3.2 21.8 + - - +
389B MET* 2.8 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 3.7 26.7 - - + +
326A GLN* 5.3 0.7 - - - +
352B ILE* 3.3 40.0 - - + +
355B GLN* 3.8 21.7 + - - +
356B THR* 3.4 24.2 - - - +
382B ARG 3.4 9.0 + - - +
383B ALA 3.8 5.8 - - - +
384B ARG 3.4 0.6 - - - -
385B GLU* 1.3 77.8 - - + +
387B ILE* 1.3 53.9 + - - +
389B MET* 3.6 15.7 + - - +
390B HIS* 2.6 34.7 + - - -
318C HIS* 5.8 1.2 - - - -
401C SO4 4.3 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B VAL* 3.7 15.5 - - + -
333B VAL* 3.6 25.8 - - + -
341B VAL* 3.9 26.2 - - + +
349B ILE* 4.9 0.2 - - + -
352B ILE* 4.1 14.4 - - + -
360B ILE* 4.2 12.1 - - + -
371B PHE* 4.1 23.6 - - + -
373B VAL* 3.9 26.5 - - + -
383B ALA 3.1 15.2 + - - +
384B ARG 3.6 6.7 - - - +
385B GLU 3.2 0.2 - - - -
386B GLU* 1.3 76.8 - - - +
388B GLU* 1.3 61.5 + - - +
390B HIS* 3.1 22.8 + - - +
391B ILE* 4.1 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A GLN* 6.0 3.5 - - - +
357A HIS* 3.2 29.2 - - + +
331B VAL* 4.3 10.4 - - + +
332B ARG 5.1 5.4 - - - +
384B ARG* 2.9 55.7 + - + +
385B GLU* 3.4 19.8 - - - +
387B ILE* 1.3 76.8 - - + +
389B MET* 1.3 61.2 + - - +
390B HIS 3.2 0.2 - - - -
391B ILE* 3.3 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLN* 3.3 44.6 - - - +
357A HIS 3.4 23.8 - - - +
358A THR* 4.4 4.5 - - - -
359A TYR* 4.0 17.9 - - + -
374A THR* 3.4 31.6 - - + +
375A GLY* 3.6 8.1 - - - -
376A MET* 4.4 11.3 + - - +
379A ASN* 3.9 15.2 + - - -
385B GLU* 2.8 37.7 + - - +
386B GLU* 3.8 8.5 - - - +
387B ILE 3.2 0.4 - - - -
388B GLU* 1.3 72.8 - - - +
390B HIS* 1.3 57.6 + - - +
391B ILE 3.0 11.1 + - - -
318C HIS* 6.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 3.5 30.9 - - + +
324A PRO 4.9 7.9 + - - -
326A GLN* 3.9 9.5 + - + +
337B VAL* 3.7 19.1 - - - +
340B LEU* 3.5 31.0 - - + +
341B VAL* 3.7 17.0 - - + +
348B THR* 3.4 21.6 - - + +
352B ILE* 4.3 4.0 - - + +
386B GLU 2.6 26.9 + - - -
387B ILE* 3.1 11.9 + - - +
389B MET* 1.3 75.3 - - - +
391B ILE* 1.3 61.6 + - - +
392B ALA 4.2 0.8 + - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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