Contacts of the helix formed by residues 375 - 386 (chain A) in PDB entry 1OJ7
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 THR 375 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A THR* 3.2 10.3 - - - +
367A GLN* 3.5 27.8 - - - +
373A ASP 3.2 9.7 + - - +
374A ILE* 1.3 75.8 - - - +
376A LEU* 1.3 61.7 + - - +
377A ASP* 2.2 30.9 + - - +
378A VAL* 3.1 11.3 + - - +
379A SER* 2.9 27.2 + - - -
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Residues in contact with LEU 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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357A LEU* 3.7 37.9 - - + +
360A LEU* 4.0 22.2 - - + -
361A GLU* 3.8 36.1 - - + +
365A MET 4.2 11.0 - - - +
366A THR* 4.1 19.7 + - + -
375A THR* 1.3 74.6 - - - +
377A ASP* 1.3 57.8 + - - +
379A SER* 4.2 3.4 - - - -
380A ARG* 2.9 29.4 + - - +
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Residues in contact with ASP 377 (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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375A THR* 2.2 33.4 + - - +
376A LEU* 1.3 75.8 - - - +
378A VAL* 1.3 70.1 + - - +
380A ARG* 3.6 11.6 + - - +
381A ARG* 3.2 35.7 + - - +
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Residues in contact with VAL 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLU* 3.9 27.8 - - + +
296A LYS* 4.8 4.7 - - + +
373A ASP 3.9 9.0 - - - +
374A ILE* 3.8 22.4 - - + -
375A THR* 3.1 30.8 + - - +
377A ASP* 1.3 80.8 - - - +
379A SER* 1.3 59.2 + - - +
381A ARG* 3.1 24.7 + - - +
382A ILE* 2.9 30.2 + - + +
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Residues in contact with SER 379 (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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269A LEU* 3.4 28.0 - - - +
357A LEU* 4.0 2.9 - - - -
360A LEU* 3.9 17.4 - - - +
365A MET 4.9 1.4 + - - -
368A LEU* 4.2 4.9 - - - +
374A ILE* 3.5 15.5 + - - +
375A THR 2.9 18.3 + - - -
376A LEU* 3.7 6.6 - - - -
378A VAL* 1.3 77.4 - - - +
380A ARG* 1.3 62.2 + - - +
382A ILE* 3.3 7.2 + - - +
383A TYR* 3.0 30.7 + - - -
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Residues in contact with ARG 380 (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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353A ILE* 4.0 10.2 - - + +
354A PRO* 4.0 29.7 - - - +
357A LEU* 3.5 33.8 - - + +
376A LEU 2.9 17.7 + - - +
377A ASP* 3.6 11.2 - - - +
379A SER* 1.3 75.1 - - - +
381A ARG* 1.3 58.2 + - - +
383A TYR* 3.4 1.9 + - - +
384A GLU* 2.9 61.9 + - - +
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Residues in contact with ARG 381 (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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295A GLU* 3.0 39.7 + - - +
377A ASP* 3.2 25.4 + - - +
378A VAL* 3.1 32.5 + - - +
380A ARG* 1.3 79.1 - - - +
382A ILE* 1.3 57.6 + - - +
384A GLU* 3.4 11.2 + - + +
385A ALA* 2.9 31.7 + - + +
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Residues in contact with ILE 382 (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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269A LEU* 4.1 19.1 - - + -
288A VAL* 4.2 12.3 - - + -
291A ALA* 3.5 8.5 - - + +
292A LEU* 3.9 45.5 - - + +
295A GLU* 3.9 25.6 - - + -
296A LYS* 5.2 0.4 - - + -
374A ILE* 4.2 14.4 - - + -
378A VAL* 2.9 33.3 + - + +
379A SER* 3.3 6.7 + - - +
381A ARG* 1.3 73.5 - - - +
383A TYR* 1.3 66.7 + - + +
385A ALA* 3.2 5.4 + - - -
386A ALA* 3.1 21.2 + - + +
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Residues in contact with TYR 383 (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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269A LEU* 2.6 55.0 + - + +
272A GLU* 3.7 14.0 - - - +
273A LEU* 4.0 25.4 - - + -
287A ILE* 6.3 0.2 - - + -
288A VAL* 4.4 8.5 - - + -
343A LEU* 3.7 14.6 - - + +
353A ILE* 3.7 28.5 - - + +
356A LEU* 3.9 27.1 - - + -
357A LEU* 4.2 9.2 - - + -
360A LEU* 4.0 20.6 - - + +
379A SER 3.0 23.0 + - - +
380A ARG 3.8 2.0 - - - +
382A ILE* 1.3 78.5 - - + +
384A GLU* 1.3 63.5 + - - +
386A ALA* 3.1 18.2 + - + +
387A ARG* 3.5 7.3 + - - -
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Residues in contact with GLU 384 (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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353A ILE* 3.8 17.9 - - + +
380A ARG* 2.9 49.1 + - + +
381A ARG* 3.7 12.3 - - + +
383A TYR* 1.3 76.9 - - - +
385A ALA* 1.3 60.6 + - - +
387A ARG* 3.0 55.3 + - - +
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Residues in contact with ALA 385 (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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291A ALA* 4.1 18.2 - - + +
294A ASN* 5.8 5.8 - - - +
331A ARG* 5.7 2.6 + - - -
342A HIS* 4.8 5.5 + - - -
381A ARG* 2.9 19.5 + - + +
382A ILE* 3.2 6.5 + - - +
384A GLU* 1.3 76.0 - - - +
386A ALA* 1.3 57.8 + - - +
387A ARG 3.3 4.4 + - - +
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Residues in contact with ALA 386 (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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287A ILE* 3.6 35.0 - - + +
288A VAL* 5.0 4.0 - - + -
291A ALA* 4.0 8.1 - - + -
331A ARG* 6.3 0.4 - - - +
341A THR 5.1 0.9 - - - -
342A HIS* 3.4 11.8 - - - -
343A LEU* 2.9 26.2 + - + +
382A ILE 3.1 11.8 + - - +
383A TYR* 3.1 15.6 + - + +
385A ALA* 1.3 75.7 - - - +
387A ARG* 1.3 61.0 + - - +
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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