Contacts of the helix formed by residues 364 - 376 (chain A) 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 SER 364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A ASN 5.3 0.5 + - - -
363A ALA* 1.3 76.4 - - - +
365A VAL* 1.3 66.4 + - - +
366A GLU* 3.2 7.4 - - - -
367A LYS* 3.2 36.4 + - - +
368A SER* 3.0 27.8 + - - -
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Residues in contact with VAL 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A THR* 3.9 27.1 - - + -
337A MET* 3.9 36.1 - - + +
341A PHE* 4.6 10.5 - - + -
363A ALA* 3.9 3.3 + - + -
364A SER* 1.3 71.9 - - - +
366A GLU* 1.3 70.3 + - - +
368A SER* 3.4 5.9 + - - -
369A GLN* 3.0 29.7 + - + +
406A TYR* 4.5 9.9 - - + +
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Residues in contact with GLU 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A SER* 4.3 4.9 - - - -
365A VAL* 1.3 90.3 + - - +
367A LYS* 1.3 62.9 + - + +
369A GLN* 3.4 3.3 + - - +
370A VAL* 3.1 29.8 + - - +
405A TRP* 5.9 0.4 - - + -
406A TYR* 3.8 29.9 - - + +
409A THR* 3.2 38.3 - - - +
410A ILE* 4.1 15.5 - - - +
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Residues in contact with LYS 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A SER* 3.2 30.1 + - - +
366A GLU* 1.3 76.2 - - - +
368A SER* 1.3 65.8 + - - +
370A VAL* 3.2 8.5 + - + +
371A GLY* 3.0 21.1 + - - -
410A ILE* 4.5 22.9 - - + +
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Residues in contact with SER 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A MET* 5.7 4.7 - - - +
357A MET* 3.2 39.1 - - - +
364A SER* 3.0 24.0 + - - -
365A VAL* 3.7 6.5 - - - -
367A LYS* 1.3 76.8 - - - +
369A GLN* 1.3 60.8 + - - +
371A GLY* 3.3 1.3 + - - -
372A PHE* 2.8 30.6 + - - +
501A 2SR 3.3 9.5 - - - +
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Residues in contact with GLN 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A TYR* 2.3 40.6 + - - +
333A THR* 3.9 31.2 - - + +
336A ILE* 5.0 4.2 - - - +
337A MET* 5.0 6.7 - - - -
357A MET* 5.9 0.4 - - - -
365A VAL 3.0 20.6 + - - +
366A GLU 3.7 4.5 - - - +
368A SER* 1.3 77.8 - - - +
370A VAL* 1.3 58.9 + - - +
372A PHE* 3.4 15.2 + - - +
373A ILE* 2.9 36.2 + - - +
406A TYR* 4.0 21.8 - - + -
501A 2SR 3.0 27.5 + - - -
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Residues in contact with VAL 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A GLU 3.1 17.7 + - - +
367A LYS* 3.2 8.9 + - - +
369A GLN* 1.3 74.7 - - - +
371A GLY* 1.3 61.3 + - - +
373A ILE* 3.3 5.5 + - - +
374A ASP* 2.8 50.6 + - - +
403A ARG* 3.8 20.9 - - - +
406A TYR* 4.1 7.2 - - + -
407A GLN* 3.7 49.1 - - + +
410A ILE 5.5 1.1 - - - +
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Residues in contact with GLY 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A LYS 3.0 13.8 + - - -
368A SER* 3.8 2.5 - - - -
370A VAL* 1.3 74.2 - - - +
372A PHE* 1.3 60.2 + - - +
374A ASP* 4.4 1.3 - - - -
375A TYR* 2.8 57.5 + - - +
376A ILE* 5.3 0.2 - - - +
501A 2SR 4.7 3.8 - - - -
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Residues in contact with PHE 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A MET* 5.3 0.9 - - + -
319A LEU* 4.3 11.4 - - + -
322A PRO* 4.3 15.9 - - + -
368A SER 2.8 17.9 + - - +
369A GLN* 3.4 18.6 - - - +
371A GLY* 1.3 75.4 - - - +
373A ILE* 1.3 57.6 + - - +
376A ILE* 3.0 45.0 + - + +
377A VAL* 3.0 36.5 + - + -
501A 2SR 3.3 89.8 - + + +
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Residues in contact with ILE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A PRO* 4.1 21.5 - - + -
329A TYR* 3.6 26.2 - - + +
369A GLN* 2.9 20.9 + - + +
370A VAL* 3.8 3.4 - - - +
372A PHE* 1.3 77.0 - - + +
374A ASP* 1.3 67.3 + - - +
375A TYR 3.3 0.3 + - - -
377A VAL* 4.0 5.8 - - + -
378A HIS* 2.7 45.8 + - + +
379A PRO* 3.5 0.7 - - - +
399A LEU* 4.0 18.4 - - + +
402A ASN* 4.8 0.4 - - + +
403A ARG* 3.7 47.3 - - + +
406A TYR* 5.4 2.0 - - + -
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Residues in contact with ASP 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A VAL* 2.8 31.5 + - - +
371A GLY* 4.1 2.8 + - - +
373A ILE* 1.3 76.1 - - - +
375A TYR* 1.3 76.9 + - + +
378A HIS* 4.6 4.0 - - - +
379A PRO* 3.4 16.6 - - - +
403A ARG* 2.8 46.2 + - - +
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Residues in contact with TYR 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A HIS* 4.8 1.4 + - - -
277A MET* 4.7 10.0 - - - +
371A GLY* 2.8 44.8 + - - +
374A ASP* 1.3 88.1 - - + +
376A ILE* 1.3 68.3 + - + +
379A PRO* 3.7 11.8 - - - +
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Residues in contact with ILE 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A MET* 4.2 6.3 - - + -
276A HIS* 3.7 37.3 + - + +
277A MET* 5.1 7.0 - - + -
319A LEU* 4.0 18.8 - - + -
372A PHE* 3.0 30.1 + - + +
374A ASP 3.6 0.4 - - - -
375A TYR* 1.3 89.7 - - + +
377A VAL* 1.3 69.2 + - - +
379A PRO* 3.3 4.0 - - - +
380A LEU* 3.3 22.0 + - - +
501A 2SR 3.2 41.3 - - + -
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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