Contacts of the helix formed by residues 453 - 470 (chain A) in PDB entry 1OHV
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 453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374A GLU* 4.7 18.0 + - - +
376A LEU* 3.9 23.2 - - - +
379A ASN* 3.8 32.1 + - - +
383A ALA* 3.9 7.9 - - - -
451A VAL* 3.5 34.4 + - - +
452A PHE* 1.3 77.1 - - - +
454A ASP* 1.3 69.9 + - - +
455A HIS* 3.2 34.5 - - + +
456A HIS* 3.0 22.6 + - + +
457A ALA 3.2 8.0 + - - -
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Residues in contact with ASP 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ASN* 5.2 0.4 + - - -
382A HIS* 2.6 38.2 + - + +
383A ALA* 3.9 9.7 - - - +
386A VAL* 3.7 20.5 - - + +
453A ARG* 1.3 74.5 - - - +
455A HIS* 1.3 85.8 + - - +
457A ALA* 3.1 20.2 + - - +
458A HIS* 3.1 21.1 + - + -
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Residues in contact with HIS 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASP* 5.2 0.2 + - - -
453A ARG* 3.4 29.4 - - + +
454A ASP* 1.3 84.7 + - - +
456A HIS* 1.3 86.5 + + - +
458A HIS* 3.4 10.9 + - - +
459A LEU* 3.0 35.4 + - + +
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Residues in contact with HIS 456 (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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12A ASP* 2.8 23.0 + - - -
13A TYR 4.9 1.8 + - - -
55A ASN* 3.0 23.0 + - - -
56A TYR* 3.7 22.8 - + - -
66A LEU* 3.7 20.2 - - + +
451A VAL 3.7 5.8 - - - -
452A PHE* 3.6 19.5 - - + -
453A ARG* 3.0 31.6 + - + +
455A HIS* 1.3 100.9 + + - +
457A ALA* 1.3 60.2 + - - +
459A LEU* 3.2 10.0 - - + +
460A PHE* 2.9 30.3 + - - +
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Residues in contact with ALA 457 (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 ALA 4.3 2.0 - - - +
386A VAL* 4.1 9.9 - - + -
387A LEU* 4.1 26.7 - - + +
452A PHE* 3.5 26.6 - - + -
453A ARG 3.2 2.6 + - - -
454A ASP 3.1 14.2 + - - +
456A HIS* 1.3 79.6 - - - +
458A HIS* 1.3 57.1 + - - +
460A PHE* 3.4 5.8 + - - +
461A LEU* 2.9 36.1 + - + +
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Residues in contact with HIS 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A VAL* 3.6 23.8 - - + +
454A ASP* 3.1 27.8 + - + +
455A HIS* 3.8 10.1 - - - +
456A HIS 3.3 0.2 - - - -
457A ALA* 1.3 71.5 - - - +
459A LEU* 1.3 61.5 + - - +
461A LEU* 3.6 15.6 - - + +
462A ASN* 2.8 48.6 + - - +
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Residues in contact with LEU 459 (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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14A ASP 4.2 14.1 - - - +
15A GLY* 4.7 0.4 - - - -
16A PRO* 3.4 31.2 - - + -
56A TYR* 3.4 23.3 - - - +
66A LEU* 4.5 7.6 - - + -
455A HIS* 3.0 20.6 + - + +
456A HIS* 3.2 18.4 - - + +
458A HIS* 1.3 77.7 - - - +
460A PHE* 1.3 61.8 + - - +
462A ASN* 4.0 7.4 - - - +
463A ILE* 3.3 33.7 + - + +
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Residues in contact with PHE 460 (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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66A LEU* 4.0 9.6 - - + +
68A LEU* 3.9 16.6 - - + -
387A LEU* 4.0 11.2 - - + -
391A LEU* 4.2 7.6 - - + -
434A VAL* 3.7 27.8 - - + -
436A LEU* 3.9 18.8 - - + -
446A PHE* 3.4 33.9 - + - -
456A HIS 2.9 15.6 + - - +
457A ALA* 3.7 7.9 - - - +
459A LEU* 1.3 75.1 - - - +
461A LEU* 1.3 79.3 + - + +
463A ILE* 3.3 1.3 + - - +
464A PHE* 2.9 71.2 + + + +
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Residues in contact with LEU 461 (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 VAL 4.1 12.1 - - - +
387A LEU* 4.4 7.0 - - + +
390A GLY* 3.6 43.3 - - - +
391A LEU* 3.9 4.5 - - + +
394A LEU* 3.6 21.3 - - + +
457A ALA* 2.9 29.3 + - + +
458A HIS* 3.0 21.3 + - + +
460A PHE* 1.3 93.9 - - + +
462A ASN* 1.3 59.8 + - - +
464A PHE* 3.9 1.8 - - - +
465A SER* 2.9 31.5 + - - -
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Residues in contact with ASN 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A HIS* 2.8 31.9 + - - +
459A LEU* 4.0 6.8 - - - +
461A LEU* 1.3 79.6 - - - +
463A ILE* 1.3 62.6 + - + +
465A SER* 3.5 5.8 + - - -
466A ASP* 3.2 27.9 + - - +
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Residues in contact with ILE 463 (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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16A PRO* 4.1 20.6 - - + -
429A ALA* 5.1 0.9 - - + +
432A LYS* 3.7 45.3 - - + +
434A VAL* 3.8 25.6 - - + -
459A LEU* 3.3 22.6 + - + +
460A PHE* 3.3 6.4 + - + +
461A LEU 3.3 0.2 - - - -
462A ASN* 1.3 75.7 - - + +
464A PHE* 1.3 66.7 + - + +
466A ASP* 3.1 11.1 + - - +
467A ILE* 3.0 27.2 + - + +
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Residues in contact with PHE 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A LEU* 5.6 0.7 - - + -
394A LEU* 4.3 10.5 - - + -
402A ILE* 4.3 4.0 - - + -
414A PHE* 3.7 32.1 - + - -
425A LEU* 4.2 39.0 - - + -
429A ALA* 4.4 2.2 - - + -
436A LEU* 4.1 17.3 - - + -
444A ILE* 4.5 1.3 - - + -
460A PHE* 2.9 50.0 + + + +
461A LEU* 4.2 2.5 - - - +
463A ILE* 1.3 74.2 - - + +
465A SER* 1.3 57.9 + - - +
467A ILE* 3.1 24.6 + - + +
468A LEU* 2.9 66.5 + - + +
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Residues in contact with SER 465 (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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394A LEU* 4.0 24.8 - - - +
398A TYR* 4.2 7.7 + - - -
461A LEU 2.9 20.9 + - - -
462A ASN* 3.6 8.3 - - - -
464A PHE* 1.3 77.3 - - - +
466A ASP* 1.3 59.0 + - - +
468A LEU* 3.3 5.7 + - - +
469A ALA* 3.0 27.6 + - - +
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Residues in contact with ASP 466 (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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432A LYS* 6.2 3.8 - - - -
462A ASN* 3.2 11.2 + - - +
463A ILE* 3.1 12.1 + - - +
465A SER* 1.3 78.7 + - - +
467A ILE* 1.3 67.9 + - + +
469A ALA* 3.3 16.9 + - - +
470A ASP* 3.4 19.8 + - - +
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Residues in contact with ILE 467 (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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425A LEU* 4.1 25.4 - - + -
428A ILE* 3.6 31.4 - - + -
429A ALA* 3.5 35.4 - - + -
432A LYS* 3.8 23.1 - - + +
463A ILE* 3.0 26.6 + - + +
464A PHE* 3.1 20.8 + - + +
466A ASP* 1.3 78.3 - - + +
468A LEU* 1.3 62.6 + - - +
470A ASP* 3.7 6.5 - - - +
471A PHE* 3.1 23.9 + - + +
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Residues in contact with LEU 468 (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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394A LEU* 4.4 16.6 - - + -
398A TYR* 3.8 40.2 - - + -
401A PHE* 4.1 35.5 - - + -
402A ILE* 4.5 13.2 - - + -
425A LEU* 4.2 19.5 - - + -
464A PHE* 2.9 51.1 + - + +
465A SER 3.7 4.3 - - - +
466A ASP 3.3 0.2 - - - -
467A ILE* 1.3 75.8 - - + +
469A ALA* 1.3 62.4 + - - +
471A PHE* 3.4 15.9 + - + +
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Residues in contact with ALA 469 (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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398A TYR* 3.6 18.4 + - - +
465A SER* 3.0 13.9 + - - +
466A ASP* 3.5 15.7 - - - +
467A ILE 3.2 0.6 - - - -
468A LEU* 1.3 77.3 - - - +
470A ASP* 1.3 60.0 + - + +
471A PHE 3.9 0.5 + - - -
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Residues in contact with ASP 470 (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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432A LYS* 6.1 1.0 - - - -
466A ASP* 3.4 16.2 + - - +
467A ILE* 4.0 4.7 - - - +
468A LEU 3.4 0.2 - - - -
469A ALA* 1.3 78.4 - - + +
471A PHE* 1.3 61.3 + - - +
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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