Contacts of the helix formed by residues 376 - 388 (chain B) in PDB entry 4OGB
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 ILE 376 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B MET* 4.1 13.0 - - + -
276B HIS* 3.7 32.6 - - + +
277B MET* 4.0 11.4 - - + -
319B LEU* 3.7 20.9 - - + -
372B PHE* 2.9 43.0 + - + +
374B ASP 3.6 0.6 - - - -
375B TYR* 1.3 93.4 - - + +
377B VAL* 1.3 65.2 + - - +
378B HIS 3.4 1.3 - - - -
379B PRO* 3.6 2.6 - - - +
380B LEU* 3.2 25.1 + - - +
501B 2SR 4.6 15.9 - - + -
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Residues in contact with VAL 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 3.7 19.5 - - + +
322B PRO* 4.0 12.6 - - + -
323B THR* 4.6 0.7 - - + -
372B PHE* 3.0 53.5 + - + +
373B ILE* 3.8 9.9 - - + -
376B ILE* 1.3 74.3 - - + +
378B HIS* 1.3 60.4 + - - +
380B LEU* 3.4 3.2 + - - +
381B TRP* 2.9 48.6 + - + +
399B LEU* 4.0 20.6 - - + -
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Residues in contact with HIS 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ILE* 2.7 31.9 + - + +
374B ASP* 4.7 4.3 - - - +
377B VAL* 1.3 70.7 - - - +
379B PRO* 1.4 63.1 - - + +
381B TRP 3.2 0.2 + - - -
382B GLU* 2.7 70.7 + - + +
396B LEU* 3.9 5.1 - - + +
399B LEU* 3.6 23.6 - - + -
400B GLU* 2.8 44.1 + - + +
403B ARG* 6.5 0.7 - - + -
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Residues in contact with PRO 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU* 3.8 20.3 - - + +
284B LYS* 5.2 5.7 - - - +
373B ILE 3.6 1.8 - - - +
374B ASP 3.3 26.2 - - - +
375B TYR* 3.6 16.2 - - - +
376B ILE 3.6 9.2 - - - +
378B HIS* 1.4 91.3 - - + +
380B LEU* 1.3 59.0 + - - +
382B GLU* 3.8 11.6 - - + +
383B THR* 2.8 29.8 + - - -
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B HIS* 4.1 8.5 - - + -
280B LEU* 3.7 18.4 - - + +
283B LEU* 4.5 5.4 - - + -
312B ASN* 4.0 19.3 - - - +
315B HIS* 3.6 29.8 - - + +
316B CYS* 3.7 35.0 - - - -
319B LEU* 3.8 24.0 - - + -
376B ILE 3.2 15.8 + - - +
377B VAL 3.7 3.1 - - - +
378B HIS 3.2 0.6 - - - -
379B PRO* 1.3 79.8 - - - +
381B TRP* 1.3 63.6 + - + +
383B THR* 3.3 4.3 + - - -
384B TRP* 2.9 23.4 + - - +
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Residues in contact with TRP 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TRP* 3.6 36.3 - + - -
175B LEU* 4.0 16.4 - - + -
316B CYS* 3.3 33.5 + - + +
319B LEU* 3.2 18.3 + - - +
320B SER* 4.1 2.2 - - - -
323B THR* 3.8 15.6 - - + +
377B VAL* 2.9 42.1 + - + +
378B HIS 4.2 0.2 - - - +
380B LEU* 1.3 81.9 - - + +
382B GLU* 1.3 56.8 + - - +
384B TRP* 3.6 30.0 - + + +
385B ALA* 2.7 37.1 + - + +
392B ALA* 4.7 5.6 - - + -
395B ILE* 3.6 28.3 - - + -
396B LEU* 4.0 17.6 - - + +
399B LEU* 4.2 4.7 - - + -
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Residues in contact with GLU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B HIS* 2.7 51.4 + - + +
379B PRO* 3.8 9.8 - - - +
381B TRP* 1.3 71.5 - - - +
383B THR* 1.3 64.5 + - - +
385B ALA* 3.5 2.9 + - - +
386B ASP* 3.2 29.5 + - - +
396B LEU* 3.8 19.0 - - + +
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Residues in contact with THR 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU* 3.6 12.6 - - + +
283B LEU* 3.8 25.4 - - + -
284B LYS* 3.8 31.5 - - + +
287B VAL* 3.9 17.1 - - + +
379B PRO 2.8 14.3 + - - -
380B LEU 3.5 7.4 - - - -
381B TRP 3.1 0.4 - - - -
382B GLU* 1.3 78.0 + - - +
384B TRP* 1.3 65.3 + - - +
386B ASP* 3.1 22.9 - - + +
387B LEU* 3.2 5.2 + - - +
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Residues in contact with TRP 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 3.8 26.7 - - + +
178B THR* 5.4 1.0 - - + +
181B LEU* 4.0 19.1 - - + -
283B LEU* 4.2 17.8 - - + +
309B VAL* 3.9 22.9 - - + -
312B ASN* 4.3 3.8 - - + -
313B MET* 3.6 45.8 - - + -
316B CYS* 3.8 22.7 - - - -
380B LEU 2.9 16.6 + - - +
381B TRP* 3.2 28.2 + + - +
383B THR* 1.3 76.5 - - - +
385B ALA* 1.3 63.1 + - - +
387B LEU* 3.2 24.9 + - + +
388B VAL* 3.1 43.1 + - + +
392B ALA* 4.6 3.1 - - + +
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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
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381B TRP* 2.7 21.2 + - + +
382B GLU 3.6 6.7 - - - +
383B THR 3.2 0.2 - - - -
384B TRP* 1.3 72.4 - - - +
386B ASP* 1.3 52.0 + - - +
388B VAL* 3.5 1.3 + - - +
389B HIS* 2.8 40.6 + - - +
390B PRO* 5.0 0.5 - - - +
392B ALA* 3.9 29.0 + - + +
393B GLN* 5.7 2.2 - - - +
396B LEU* 4.2 23.3 - - + -
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Residues in contact with ASP 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B VAL* 3.6 25.3 - - + +
290B LYS* 4.1 7.3 + - - +
382B GLU* 3.2 17.9 + - - +
383B THR* 3.1 15.6 + - - +
385B ALA* 1.3 75.0 - - - +
387B LEU* 1.3 66.9 + - - +
389B HIS* 3.1 22.5 + - - +
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Residues in contact with LEU 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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180B ALA* 4.9 4.2 - - - +
181B LEU* 5.4 0.4 - - + -
283B LEU* 4.1 15.0 - - + -
286B MET* 3.5 25.8 - - + -
287B VAL* 3.8 26.0 - - + -
290B LYS* 3.3 31.7 + - + +
298B LEU* 4.0 33.3 - - + +
309B VAL* 4.3 11.0 - - + -
383B THR 3.2 3.7 + - - +
384B TRP* 3.2 38.3 + - + +
386B ASP* 1.3 79.8 - - - +
388B VAL* 1.3 61.1 + - + +
389B HIS 3.5 0.2 - - - -
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Residues in contact with VAL 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B THR* 4.1 11.9 - - + +
180B ALA* 3.3 14.2 - - + +
181B LEU* 3.7 32.5 - - + -
384B TRP* 3.1 45.0 + - + +
385B ALA 4.0 3.1 - - - +
387B LEU* 1.3 84.5 - - + +
389B HIS* 1.3 69.5 + - - +
391B ASP* 2.9 26.3 + - + -
392B ALA* 4.1 18.4 - - + +
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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
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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