Contacts of the helix formed by residues 361 - 374 (chain A) in PDB entry 1OH7
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 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A GLU* 3.1 39.3 + - - +
121A ASP* 4.6 17.0 + - - +
354A ARG* 5.7 3.1 - - - +
359A THR 3.9 9.6 + - - +
360A ALA* 1.3 72.9 - - - +
362A PRO* 1.3 79.1 - - + +
363A ARG* 3.3 5.4 - - + +
364A ASP* 3.1 27.2 + - - +
365A LEU* 3.2 11.3 + - - +
417A VAL* 3.5 24.3 - - - +
418A LEU* 3.1 32.2 - - - +
528A TYR* 2.8 8.6 + - - -
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Residues in contact with PRO 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ARG* 1.3 90.4 - - + +
363A ARG* 1.3 57.2 + - - +
365A LEU* 3.1 7.1 + - + +
366A ALA* 2.9 24.8 + - - +
411A ILE* 4.5 4.7 - - + +
415A PRO* 3.7 21.6 - - + +
416A PRO 3.5 11.9 - - - +
417A VAL 3.6 11.0 - - - +
418A LEU* 3.7 25.4 - - - +
419A VAL* 3.7 13.5 - - + +
424A VAL* 3.7 18.2 - - + -
528A TYR* 3.2 14.8 - - + +
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Residues in contact with ARG 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ARG* 3.3 3.6 - - + +
362A PRO* 1.3 75.6 - - - +
364A ASP* 1.3 59.1 + - - +
366A ALA* 3.5 9.0 - - + +
367A ARG* 3.0 45.9 + - + +
414A THR* 6.2 2.2 - - - -
415A PRO* 3.1 34.2 + - + +
416A PRO* 3.8 15.8 - - - +
417A VAL* 3.8 33.0 + - - +
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Residues in contact with ASP 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU* 4.7 1.2 - - - +
351A ILE* 3.5 20.4 - - + +
354A ARG* 2.6 44.7 + - - -
360A ALA* 4.0 10.3 - - + -
361A ARG* 3.1 40.5 + - - +
363A ARG* 1.3 75.9 - - - +
365A LEU* 1.3 63.4 + - - +
367A ARG* 3.0 22.0 + - - +
368A MET* 3.1 22.7 + - - +
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Residues in contact with LEU 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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355A LEU* 4.4 2.0 - - + -
360A ALA* 4.5 6.3 - - + -
361A ARG 3.2 10.1 + - - +
362A PRO* 3.1 8.7 + - + +
364A ASP* 1.3 74.0 - - - +
366A ALA* 1.3 60.5 + - - +
368A MET* 3.7 27.1 - - + -
369A ARG* 2.9 24.1 + - - +
407A LEU* 3.1 23.0 - - + +
411A ILE* 4.4 12.6 - - + -
528A TYR* 4.0 24.5 - - + +
531A LEU* 4.1 32.8 - - + -
532A PHE* 4.4 16.4 - - + -
535A LEU* 3.9 13.5 - - + -
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Residues in contact with ALA 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A PRO 2.9 12.7 + - - +
363A ARG* 3.5 15.3 - - + +
365A LEU* 1.3 76.7 - - - +
367A ARG* 1.3 60.8 + - + +
369A ARG* 3.0 33.9 + - - +
370A HIS* 2.8 28.3 + - - +
411A ILE* 5.4 1.7 - - + +
413A ASP 5.1 1.6 - - - +
415A PRO* 4.3 14.4 - - + -
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Residues in contact with ARG 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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122A GLU* 2.9 41.4 + - - -
344A GLN 5.1 0.9 - - - +
345A VAL 4.5 5.9 - - - +
347A ASP* 5.3 9.5 + - - +
351A ILE* 3.7 35.8 - - + +
354A ARG* 4.9 0.8 - - - +
363A ARG* 3.0 25.6 + - + +
364A ASP* 3.0 26.0 + - - +
366A ALA* 1.3 80.3 - - + +
368A MET* 1.3 56.4 + - - +
370A HIS* 3.7 9.6 - - + +
371A ALA* 3.0 26.9 + - - +
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Residues in contact with MET 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 4.1 16.2 - - + -
351A ILE* 3.8 22.1 - - + +
352A LEU* 4.4 10.3 - - + -
355A LEU* 4.1 19.7 - - + -
364A ASP 3.1 13.5 + - - +
365A LEU* 3.5 28.5 - - + +
366A ALA 3.1 0.2 - - - -
367A ARG* 1.3 75.3 - - - +
369A ARG* 1.3 64.7 + - - +
371A ALA* 3.1 15.5 + - - +
372A PHE* 3.1 49.2 + - + -
407A LEU* 4.2 4.3 - - - -
535A LEU* 3.9 24.0 - - + -
542A LEU* 5.2 1.3 - - - -
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Residues in contact with ARG 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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365A LEU 2.9 13.0 + - - +
366A ALA* 3.2 28.0 + - - +
368A MET* 1.3 75.2 - - - +
370A HIS* 1.3 61.6 + - - +
372A PHE* 3.3 13.2 + - - +
373A GLN* 3.2 33.9 + - - +
404A ARG* 4.1 4.3 - - + +
407A LEU* 3.0 43.8 + - + +
408A GLU* 3.7 23.8 - - + +
411A ILE* 2.9 35.0 + - - +
412A ILE 3.2 10.7 + - - -
413A ASP* 3.2 33.3 + - - +
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Residues in contact with HIS 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLN* 3.1 52.7 + - + +
366A ALA 2.8 18.0 + - - +
367A ARG* 3.7 12.3 - - + +
369A ARG* 1.3 74.8 - - - +
371A ALA* 1.3 59.4 + - - +
373A GLN* 3.3 19.1 + - - -
374A GLN* 2.9 37.9 + - - -
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Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLN 4.1 8.7 - - - -
345A VAL* 3.9 30.9 - - + +
348A LEU* 4.4 15.9 - - + -
367A ARG 3.0 15.6 + - - +
368A MET* 3.1 12.5 + - - +
370A HIS* 1.3 72.3 - - - +
372A PHE* 1.3 68.4 + - + +
373A GLN 2.9 2.7 + - - -
374A GLN* 2.9 20.9 + - - +
375A LEU* 3.6 10.9 + - + +
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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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348A LEU* 5.0 12.3 - - + -
368A MET* 3.1 46.0 + - + -
369A ARG* 3.3 11.4 + - - +
371A ALA* 1.3 78.2 - - + +
373A GLN* 1.3 61.6 + - - +
375A LEU* 3.3 27.1 + - + +
376A PRO* 3.5 5.4 - - - +
399A GLU 4.4 7.6 - - - +
400A PHE* 4.1 21.8 - + + -
403A LEU* 4.1 23.3 - - + -
404A ARG* 3.6 39.7 - - + -
407A LEU* 4.3 6.1 - - + -
535A LEU* 5.1 0.7 - - + -
542A LEU* 3.8 29.4 - - + -
545A SER* 5.9 0.4 - - - -
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Residues in contact with GLN 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ARG* 3.2 22.9 + - - +
370A HIS* 3.5 28.6 + - - +
371A ALA 2.9 1.4 + - - -
372A PHE* 1.3 77.5 - - - +
374A GLN* 1.3 67.3 + - - +
375A LEU 3.4 0.2 - - - -
376A PRO* 3.4 14.7 - - - +
377A GLU* 5.1 2.4 + - - +
404A ARG* 3.7 18.4 - - - +
408A GLU* 2.6 34.1 + - - +
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Residues in contact with GLN 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A VAL* 3.9 24.8 - - + +
344A GLN* 3.4 43.7 - - + +
345A VAL* 4.2 9.4 - - + -
370A HIS* 2.9 33.6 + - - +
371A ALA 2.9 8.5 + - - +
373A GLN* 1.3 89.3 + - - +
375A LEU* 1.3 56.8 + - - +
376A PRO* 3.4 2.2 - - - -
377A GLU* 3.5 7.9 + - - +
378A LEU* 3.0 31.5 + - + +
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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