Contacts of the helix formed by residues 382 - 391 (chain A) in PDB entry 3OJW
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 ARG 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A THR* 6.1 2.8 - - - +
93A GLU* 3.9 15.7 + - - +
94A PHE* 5.8 1.0 - - - -
97A ARG* 3.2 18.6 - - - +
213A GLU* 3.0 33.5 + - - +
380A PRO 3.5 4.2 + - - +
381A PRO* 1.3 78.0 - - - +
383A THR* 1.3 66.0 + - - +
384A ASN* 3.1 33.2 - - - +
385A VAL* 3.1 23.3 + - + +
386A LEU* 3.2 11.8 + - - +
416A TYR* 3.5 6.1 - - - -
447A LEU 5.9 0.9 - - - -
449A PRO* 5.4 16.8 - - + -
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Residues in contact with THR 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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213A GLU* 5.4 8.1 - - - +
382A ARG* 1.3 74.5 - - - +
384A ASN* 1.3 58.6 + - - +
386A LEU* 3.1 5.8 + - - +
387A TYR* 2.9 24.1 + - - +
405A MET 4.0 8.7 - - - +
406A ALA* 3.3 28.7 + - - +
407A SER 5.7 0.9 - - - +
416A TYR* 3.7 44.0 + - + -
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Residues in contact with ASN 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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382A ARG* 3.1 47.5 - - - +
383A THR* 1.3 82.6 + - - +
385A VAL* 1.3 65.7 + - - +
387A TYR* 3.3 8.3 + - - +
388A GLU* 3.0 42.3 + - + +
447A LEU* 4.8 5.0 - - - +
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Residues in contact with VAL 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A PRO* 4.3 14.1 - - + -
382A ARG* 3.1 26.5 + - + +
384A ASN* 1.3 93.7 - - - +
386A LEU* 1.3 57.4 + - - +
388A GLU* 3.5 5.7 + - - +
389A LEU* 3.0 47.2 + - + +
427A ILE* 5.2 4.9 - - + -
444A LEU* 5.3 1.6 - - + -
447A LEU* 3.4 39.4 - - + +
448A LEU* 5.3 7.9 - - + -
449A PRO* 5.7 3.4 - - + -
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Residues in contact with LEU 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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381A PRO* 4.2 20.2 - - + +
382A ARG 3.2 9.8 + - - +
383A THR* 3.1 9.5 + - - +
385A VAL* 1.3 74.7 - - - +
387A TYR* 1.3 65.3 + - - +
389A LEU* 3.4 15.7 + - + +
390A ALA* 3.1 21.8 + - - +
402A LEU* 4.1 30.3 - - + +
405A MET* 4.2 17.7 - - + +
406A ALA* 4.3 3.6 - - + -
416A TYR* 3.8 33.2 - - + -
420A VAL* 4.1 13.7 - - + -
430A ILE* 4.2 20.9 - - + -
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Residues in contact with TYR 387 (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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383A THR 2.9 13.6 + - - +
384A ASN* 3.5 12.1 - - - +
385A VAL 3.2 0.4 - - - -
386A LEU* 1.3 77.4 - - - +
388A GLU* 1.3 82.3 + - - +
390A ALA* 3.2 21.4 + - - +
391A GLN* 4.2 1.9 + - - +
402A LEU 5.2 0.2 - - - -
403A HIS* 3.8 31.8 + + - -
406A ALA* 3.7 18.8 - - + +
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Residues in contact with GLU 388 (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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242A ILE 4.5 11.8 - - - +
384A ASN* 3.0 26.1 + - + +
385A VAL 3.9 3.6 - - - +
387A TYR* 1.3 99.5 - - - +
389A LEU* 1.3 61.9 + - - +
390A ALA 3.4 0.2 + - - -
391A GLN* 3.1 36.1 - - - +
392A TYR* 4.0 5.3 - - - -
443A HIS* 4.3 16.5 + - - +
447A LEU* 3.8 31.9 - - + +
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Residues in contact with LEU 389 (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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385A VAL* 3.0 45.1 + - + +
386A LEU* 3.8 20.0 - - + +
387A TYR 3.3 0.2 - - - -
388A GLU* 1.3 75.5 - - - +
390A ALA* 1.3 65.5 + - - +
392A TYR* 2.9 18.5 + - + +
402A LEU* 4.5 2.5 - - + -
427A ILE* 4.2 17.9 - - + -
430A ILE* 4.7 7.6 - - + -
431A LEU* 5.2 1.1 - - + -
437A LEU* 3.0 32.1 - - + +
439A PRO* 3.8 32.1 - - + -
444A LEU* 4.1 16.2 - - + -
447A LEU* 4.7 8.3 - - + -
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Residues in contact with ALA 390 (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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386A LEU 3.1 12.7 + - - +
387A TYR 3.2 11.1 + - - +
389A LEU* 1.3 76.7 - - - +
391A GLN* 1.3 61.2 + - - +
392A TYR 3.0 1.4 + - - -
393A ALA* 3.1 12.5 + - - +
399A GLN* 3.3 20.9 - - - +
402A LEU* 3.9 24.7 - - + -
403A HIS* 3.2 37.5 - - + +
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Residues in contact with GLN 391 (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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387A TYR 4.2 1.9 + - - +
388A GLU* 3.1 31.0 + - - +
389A LEU 3.1 0.4 + - - -
390A ALA* 1.3 77.3 - - - +
392A TYR* 1.3 94.3 + - + +
393A ALA 3.5 1.9 + - - +
399A GLN* 5.2 4.9 - - - +
403A HIS* 5.0 2.4 - - - -
443A HIS* 4.6 6.8 - - - -
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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