Contacts of the helix formed by residues 275 - 289 (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 LYS 275 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B SER* 3.5 21.6 + - - -
269B LEU* 3.9 24.9 + - - +
270B ALA* 4.7 11.0 - - - +
272B ASP* 2.8 14.3 + - + +
274B SER* 1.3 91.7 - - - +
276B HIS* 1.3 65.4 + - - +
277B MET 3.4 2.4 + - - -
278B ASN* 3.5 13.4 + - + +
279B LEU* 3.1 28.6 + - + +
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Residues in contact with HIS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ASP 3.9 0.8 + - - -
273B MET* 3.0 31.2 + - + +
274B SER 3.3 0.4 - - - -
275B LYS* 1.3 77.9 - - - +
277B MET* 1.3 85.7 + - + +
279B LEU* 3.3 6.1 + - - +
280B LEU* 3.0 40.9 + - + +
315B HIS* 2.8 37.3 + + + +
375B TYR 4.8 0.6 + - - -
376B ILE* 3.7 52.3 + - + +
380B LEU* 4.1 15.3 - - + -
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Residues in contact with MET 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B MET 4.7 0.4 + - - -
274B SER 4.9 3.5 + - - +
275B LYS 3.4 0.4 - - - -
276B HIS* 1.3 101.5 - - + +
278B ASN* 1.3 68.3 + - - +
280B LEU* 3.2 12.6 + - + +
281B ALA* 3.0 21.9 + - - +
375B TYR* 4.5 7.4 - - + +
376B ILE* 4.0 16.4 - - + -
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Residues in contact with ASN 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B SER 5.5 4.4 + - - -
275B LYS* 3.5 12.6 + - + +
276B HIS 3.4 0.4 - - - -
277B MET* 1.3 77.6 - - - +
279B LEU* 1.3 66.2 + - - +
281B ALA* 3.3 8.7 + - - +
282B ASP* 3.0 31.7 + - - +
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ALA* 3.4 37.5 - - + +
275B LYS* 3.1 24.4 + - + +
276B HIS* 3.5 5.2 - - - +
278B ASN* 1.3 76.1 - - - +
280B LEU* 1.3 57.8 + - - +
282B ASP* 3.5 5.7 + - + +
283B LEU* 3.0 21.8 + - - +
308B GLN* 4.9 3.8 - - + +
311B GLN* 3.8 31.6 - - + +
312B ASN* 3.3 37.5 + - - +
315B HIS* 4.1 24.9 - - + +
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B HIS* 3.0 32.8 + - + +
277B MET* 3.6 16.2 - - + +
278B ASN 3.2 0.2 - - - -
279B LEU* 1.3 74.6 - - - +
281B ALA* 1.3 61.4 - - - +
283B LEU* 3.1 6.2 + - + +
284B LYS* 2.8 47.2 + - - +
312B ASN* 4.6 2.5 - - - -
375B TYR 5.9 0.4 - - - +
379B PRO* 3.9 26.0 - - + -
380B LEU* 3.7 28.3 - - + +
383B THR* 3.6 29.8 - - + +
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Residues in contact with ALA 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B MET 3.0 12.6 + - - +
278B ASN* 3.3 12.5 + - - +
280B LEU* 1.3 76.9 - - - +
282B ASP* 1.3 60.2 + - - +
284B LYS* 3.2 12.7 + - - +
285B THR* 3.0 31.6 + - - -
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Residues in contact with ASP 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ASN* 3.0 22.0 + - - +
279B LEU* 3.8 7.0 - - + +
281B ALA* 1.3 78.2 - - - +
283B LEU* 1.3 66.5 + - - +
285B THR* 3.5 8.5 + - - -
286B MET* 3.0 23.6 + - - +
308B GLN* 3.0 30.4 + - + +
312B ASN* 5.6 0.2 - - - +
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Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LEU 3.0 19.5 + - - +
280B LEU* 3.1 6.9 + - + +
282B ASP* 1.3 76.1 - - - +
284B LYS* 1.3 63.1 + - - +
286B MET* 3.3 13.2 + - + +
287B VAL* 3.0 29.8 + - + +
308B GLN* 5.2 4.3 - - + +
309B VAL* 5.3 2.9 - - + -
312B ASN* 3.7 36.1 - - + +
380B LEU* 4.5 11.2 - - + -
383B THR* 3.8 25.8 - - + -
384B TRP* 4.2 20.6 - - + +
387B LEU* 4.1 25.4 - - + -
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Residues in contact with LYS 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU* 2.8 37.6 + - + +
281B ALA* 3.3 13.7 - - - +
282B ASP 3.1 0.2 - - - -
283B LEU* 1.3 74.0 - - - +
285B THR* 1.3 65.8 + - - +
287B VAL* 3.0 6.3 + - - +
288B GLU* 2.9 38.7 + - + +
379B PRO* 5.2 5.9 - - - +
383B THR* 3.8 29.2 - - + -
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Residues in contact with THR 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ALA 3.0 15.3 + - - -
282B ASP* 3.8 9.5 + - - -
284B LYS* 1.3 77.2 - - - +
286B MET* 1.3 62.1 + - - +
288B GLU* 3.2 15.8 + - - +
289B THR* 3.0 35.5 + - + +
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Residues in contact with MET 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ASP 3.0 15.6 + - - +
283B LEU* 3.5 9.4 - - + +
285B THR* 1.3 77.6 - - - +
287B VAL* 1.3 57.0 + - - +
289B THR* 3.1 7.8 + - - +
290B LYS* 2.9 32.8 + - - +
298B LEU* 4.6 2.9 - - + -
300B LEU* 3.9 19.3 - - + -
305B ASP* 4.0 18.2 - - - +
308B GLN* 3.4 27.1 - - - +
309B VAL* 3.5 32.8 - - + -
387B LEU* 3.5 31.4 - - + -
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B LEU* 3.0 21.3 + - + +
284B LYS* 3.0 8.5 + - - +
286B MET* 1.3 72.9 - - - +
288B GLU* 1.3 65.0 + - + +
289B THR 3.3 0.5 + - - -
290B LYS* 3.3 22.1 + - + +
383B THR* 3.9 20.6 - - + +
386B ASP* 3.6 30.7 - - + +
387B LEU* 3.8 35.9 - - + +
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Residues in contact with GLU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LYS* 2.9 32.6 + - - +
285B THR* 3.6 14.3 + - + +
286B MET 3.2 0.4 - - - -
287B VAL* 1.3 80.3 - - + +
289B THR* 1.3 64.1 + - + +
290B LYS 3.5 0.6 + - - -
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Residues in contact with THR 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B THR* 3.0 27.1 + - + +
286B MET* 3.1 7.8 + - - +
288B GLU* 1.3 84.0 - - + +
290B LYS* 1.3 67.1 + - - +
291B LYS* 3.4 26.6 + - - +
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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