Contacts of the helix formed by residues 372 - 384 (chain A) in PDB entry 1OZG
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 HIS 372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A LEU* 4.5 16.8 + - + +
368A GLN* 3.5 39.7 + - + +
370A ALA 3.8 1.0 + - - -
371A LEU* 1.3 74.5 - - - +
373A PRO* 1.3 82.8 - - + +
374A LEU* 3.0 43.1 + - + +
375A ARG* 2.7 24.9 + - + +
376A ILE* 3.2 9.5 + - - +
400A TRP* 4.1 17.7 - + - -
542A ASP 5.3 1.3 - - - -
545A ASP* 2.7 32.8 + - + +
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Residues in contact with PRO 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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371A LEU 3.7 3.1 - - - +
372A HIS* 1.3 95.8 - - + +
374A LEU* 1.3 56.0 + - - +
376A ILE* 3.3 5.8 + - + +
377A VAL* 2.8 35.5 + - - +
400A TRP* 3.4 45.5 - - + +
472A TRP* 3.8 16.1 - - + -
541A VAL* 3.8 12.3 - - + -
542A ASP 3.3 23.6 - - - +
543A TYR* 4.1 7.4 - - + -
545A ASP* 5.8 1.6 - - + +
546A ASN* 4.4 1.3 - - - +
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Residues in contact with LEU 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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359A LEU 4.8 0.4 - - - +
361A ARG* 3.3 50.4 - - + +
366A LEU* 4.1 16.4 - - + +
372A HIS* 2.9 22.0 + - + +
373A PRO* 1.3 78.4 - - - +
375A ARG* 1.3 57.5 + - - +
377A VAL* 3.5 5.3 + - + +
378A ARG* 3.0 28.6 + - - +
400A TRP* 3.3 29.6 - - + -
404A TYR* 3.2 31.9 - - + +
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Residues in contact with ARG 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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365A GLN* 3.0 19.8 + - - +
366A LEU* 2.7 55.9 + - + +
367A ASN* 3.7 9.7 - - - +
371A LEU* 4.6 8.7 - - + -
372A HIS* 2.7 23.9 + - + +
374A LEU* 1.3 71.7 - - - +
376A ILE* 1.3 57.8 + - - +
378A ARG* 3.3 26.5 + - - +
379A ALA* 3.0 25.8 + - - +
518A ALA* 3.4 21.9 + - + +
519A GLU* 4.2 6.9 + - - +
521A LEU* 4.0 11.2 - - + -
522A GLU* 3.0 37.1 + - - -
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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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371A LEU* 3.9 28.0 - - + -
372A HIS 3.2 10.0 + - - +
373A PRO 3.7 5.2 - - - +
375A ARG* 1.3 73.7 - - - +
377A VAL* 1.3 60.4 + - - +
379A ALA* 3.0 3.4 + - + +
380A MET* 2.8 36.2 + - + +
472A TRP* 3.5 40.4 - - + +
521A LEU* 3.8 8.1 - - + -
525A LEU* 6.2 0.2 - - + -
539A ILE* 3.7 36.8 - - + -
541A VAL* 4.0 28.0 - - + -
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Residues in contact with VAL 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A PRO 2.8 24.1 + - - +
374A LEU* 3.7 8.1 - - + +
376A ILE* 1.3 76.6 - - - +
378A ARG* 1.3 60.7 + - - +
380A MET* 3.3 8.6 + - - +
381A GLN* 3.0 46.3 + - - +
400A TRP* 4.2 22.7 - - + +
401A ILE* 4.8 5.6 - - + +
404A TYR* 3.9 24.7 - - + -
408A PHE* 4.2 8.2 - - + -
472A TRP* 4.1 17.3 - - + -
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Residues in contact with ARG 378 (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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361A ARG* 3.1 25.0 + - + +
362A ARG* 4.2 16.9 + - - +
364A ALA 2.6 32.3 + - - +
365A GLN 4.3 2.2 + - - -
366A LEU* 3.8 11.9 - - + +
374A LEU 3.0 18.4 + - - +
375A ARG* 3.6 37.0 - - - +
377A VAL* 1.3 78.1 - - - +
379A ALA* 1.3 62.9 + - - +
381A GLN* 3.2 24.3 + - + +
382A ASP* 3.2 30.3 + - - +
522A GLU* 4.6 6.3 + - - -
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Residues in contact with ALA 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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375A ARG 3.0 6.9 + - - +
376A ILE* 3.0 7.4 + - - +
378A ARG* 1.3 76.2 - - - +
380A MET* 1.3 62.9 + - - +
382A ASP* 3.1 25.7 + - - +
383A ILE* 3.6 6.8 + - - +
521A LEU* 3.5 30.1 - - + -
522A GLU* 3.7 16.8 - - + +
525A LEU* 3.6 24.5 - - + +
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Residues in contact with MET 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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376A ILE* 2.8 26.2 + - + +
377A VAL* 3.6 7.0 - - - +
378A ARG 3.2 0.2 - - - -
379A ALA* 1.3 76.8 - - - +
381A GLN* 1.3 61.6 + - - +
382A ASP 3.2 0.3 + - - -
383A ILE* 3.2 9.8 + - + +
384A VAL* 3.2 30.3 + - + +
390A LEU* 4.4 13.0 - - + -
401A ILE* 3.5 30.5 - - + -
408A PHE* 3.9 17.9 - - + -
442A VAL* 5.4 1.1 - - + -
444A VAL* 4.0 15.9 - - + -
470A LEU* 3.6 26.5 - - + -
472A TRP* 3.9 31.2 - - - -
525A LEU* 4.7 2.5 - - + -
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Residues in contact with GLN 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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377A VAL* 3.0 41.6 + - - +
378A ARG* 3.2 17.7 + - - +
380A MET* 1.3 75.7 - - - +
382A ASP* 1.3 63.4 + - - +
384A VAL 3.4 17.0 - - - +
404A TYR* 3.8 8.3 - - - +
407A THR* 2.5 54.5 + - - +
408A PHE* 3.9 19.6 - - + +
409A ARG* 4.8 10.3 + - - +
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Residues in contact with ASP 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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378A ARG* 3.2 29.5 - - - +
379A ALA* 3.1 14.7 + - - +
380A MET 3.1 0.8 - - - -
381A GLN* 1.3 82.4 - - - +
383A ILE* 1.3 62.0 + - + +
384A VAL 4.9 0.6 - - - -
385A ASN* 5.4 2.9 + - - +
522A GLU* 4.5 12.6 - - + +
526A ARG* 4.6 5.9 + - - -
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Residues in contact with ILE 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ALA 3.6 9.4 + - - +
380A MET* 3.3 17.0 - - - +
382A ASP* 1.3 82.7 - - + +
384A VAL* 1.3 67.6 + - + +
385A ASN* 3.6 10.0 + - - +
388A VAL* 3.9 2.1 - - - +
442A VAL* 4.3 12.1 - - + -
468A LEU* 4.0 16.4 - - + -
470A LEU* 4.6 9.2 - - + -
522A GLU 5.7 0.2 - - - +
525A LEU* 4.2 35.0 - - + +
526A ARG* 4.2 18.5 + - + +
529A MET* 3.2 50.3 - - + +
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A MET* 3.2 21.1 + - + +
381A GLN 3.4 13.6 - - - +
382A ASP 5.2 0.4 - - - -
383A ILE* 1.3 85.3 - - + +
385A ASN* 1.3 60.3 + - - +
388A VAL* 4.2 14.4 - - + +
390A LEU* 4.4 27.8 - - + -
408A PHE* 4.4 15.4 - - + -
409A ARG* 3.9 12.4 + - - +
410A ALA* 3.3 35.4 - - + +
442A VAL* 4.6 13.2 - - + -
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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