Contacts of the helix formed by residues 453 - 470 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374D GLU* 4.6 20.0 + - - +
376D LEU* 3.8 26.0 - - - +
379D ASN* 3.7 25.5 + - - +
383D ALA* 3.8 7.4 - - - -
451D VAL* 3.4 36.8 + - - +
452D PHE* 1.3 79.2 - - - +
454D ASP* 1.3 69.2 + - - +
455D HIS* 3.2 33.4 - - + +
456D HIS* 2.9 20.9 + - + +
457D ALA 3.2 8.1 + - - -
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Residues in contact with ASP 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379D ASN* 5.1 0.8 + - - -
382D HIS* 2.7 37.8 + - + +
383D ALA* 3.8 8.9 - - - +
386D VAL* 3.7 20.9 - - + -
453D ARG* 1.3 76.1 - - - +
455D HIS* 1.3 89.1 + - - +
457D ALA* 3.0 23.6 + - - +
458D HIS* 3.2 16.5 + - + +
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Residues in contact with HIS 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ASP* 5.0 0.4 + - - -
453D ARG* 3.5 28.1 - - + +
454D ASP* 1.3 89.5 + - - +
456D HIS* 1.3 84.0 + + - +
458D HIS* 3.3 11.7 + - + +
459D LEU* 3.1 33.7 + - + +
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Residues in contact with HIS 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ASP* 2.6 25.6 + - - -
13D TYR 5.0 1.6 + - - -
55D ASN* 3.1 22.6 + - - -
56D TYR* 3.7 23.7 + + - -
66D LEU* 3.7 23.0 - - + +
451D VAL 3.6 7.6 - - - -
452D PHE* 3.5 20.1 - - + -
453D ARG* 2.9 31.8 + - + +
455D HIS* 1.3 100.4 + + - +
457D ALA* 1.3 65.4 + - - +
459D LEU* 3.4 9.1 - - + +
460D PHE* 3.2 18.7 + - - +
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Residues in contact with ALA 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D ALA 4.1 2.2 - - - +
386D VAL* 3.9 19.3 - - + -
387D LEU* 4.0 19.9 - - - +
452D PHE* 3.5 22.7 - - + -
453D ARG 3.2 5.3 + - - -
454D ASP* 3.0 19.0 + - - +
456D HIS* 1.3 77.2 - - - +
458D HIS* 1.3 55.3 + - - +
460D PHE* 3.4 5.0 + - - +
461D LEU* 3.0 31.9 + - + +
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Residues in contact with HIS 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D VAL* 3.5 24.0 - - + +
454D ASP* 3.2 25.5 + - + +
455D HIS* 3.8 9.6 - - + +
456D HIS 3.3 0.2 - - - -
457D ALA* 1.3 73.2 - - - +
459D LEU* 1.3 68.8 + - - +
461D LEU* 4.1 15.7 - - + +
462D ASN* 2.8 40.8 + - - +
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Residues in contact with LEU 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ASP 4.3 12.6 - - - +
15D GLY* 4.4 0.4 - - - -
16D PRO* 3.3 34.5 - - + -
56D TYR* 3.3 22.7 - - - +
66D LEU* 4.1 9.0 - - + -
455D HIS* 3.1 20.8 + - + +
456D HIS* 3.4 20.2 - - + +
458D HIS* 1.3 76.8 - - - +
460D PHE* 1.3 60.8 + - - +
462D ASN* 3.6 6.8 + - - +
463D ILE* 3.2 33.7 + - + +
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Residues in contact with PHE 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D LEU* 4.2 7.3 - - + +
68D LEU* 3.9 19.5 - - + -
387D LEU* 3.9 8.5 - - + -
391D LEU* 3.8 8.1 - - + -
414D PHE* 4.9 0.7 - + - -
429D ALA* 5.7 0.7 - - + -
434D VAL* 3.8 23.3 - - + -
436D LEU* 3.7 21.3 - - + -
446D PHE* 3.1 38.6 - + - -
456D HIS 3.2 8.7 + - - +
457D ALA* 3.5 7.0 - - - +
458D HIS 3.1 0.4 - - - -
459D LEU* 1.3 79.2 - - - +
461D LEU* 1.3 85.8 + - + +
463D ILE* 3.3 6.3 + - + +
464D PHE* 2.8 59.9 + + + +
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Residues in contact with LEU 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386D VAL 4.0 13.2 - - - +
387D LEU* 4.1 9.2 - - + +
390D GLY* 3.6 42.2 - - - -
391D LEU* 3.7 5.6 - - + +
394D LEU* 3.9 15.9 - - + +
457D ALA* 3.0 28.8 + - + +
458D HIS* 3.0 20.6 + - + +
460D PHE* 1.3 96.3 - - + +
462D ASN* 1.3 62.2 + - - +
464D PHE* 3.8 1.8 - - - +
465D SER* 2.8 31.2 + - - -
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Residues in contact with ASN 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458D HIS* 2.8 31.6 + - - +
459D LEU* 3.8 5.6 - - - +
461D LEU* 1.3 76.7 - - - +
463D ILE* 1.3 65.3 + - + +
465D SER* 3.5 6.2 + - - -
466D ASP* 3.2 31.3 + - - +
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Residues in contact with ILE 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D PRO* 4.3 8.7 - - + -
429D ALA* 4.9 1.3 - - + +
432D LYS* 3.7 41.0 - - + +
434D VAL* 3.3 33.9 - - + -
459D LEU* 3.2 32.7 + - + +
460D PHE* 3.7 6.5 - - + +
462D ASN* 1.3 77.1 - - + +
464D PHE* 1.3 58.9 + - + +
466D ASP* 3.3 10.3 + - - +
467D ILE* 3.1 34.4 + - + +
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Residues in contact with PHE 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D LEU* 5.4 0.9 - - + -
394D LEU* 4.0 11.9 - - + -
402D ILE* 4.0 5.8 - - + -
414D PHE* 3.7 31.0 - + - -
425D LEU* 4.1 36.1 - - + -
429D ALA* 4.8 1.3 - - + -
436D LEU* 4.3 17.3 - - + -
444D ILE* 4.6 0.4 - - + -
460D PHE* 2.8 44.6 + + + +
461D LEU 4.1 2.7 - - - +
463D ILE* 1.3 75.5 - - + +
465D SER* 1.3 65.6 + - - +
467D ILE* 3.2 22.1 + - + +
468D LEU* 3.0 56.9 + - + +
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Residues in contact with SER 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394D LEU* 4.0 23.5 - - - +
398D TYR* 4.2 7.9 + - - -
461D LEU 2.8 20.5 + - - -
462D ASN* 3.7 7.6 - - - -
464D PHE* 1.3 76.4 - - - +
466D ASP* 1.3 66.8 + - - +
468D LEU* 3.2 5.0 + - - +
469D ALA* 3.0 24.1 + - - +
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Residues in contact with ASP 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432D LYS* 6.0 6.3 - - + +
462D ASN* 3.2 16.0 + - - +
463D ILE* 3.5 11.2 - - - +
465D SER* 1.3 78.5 + - - +
467D ILE* 1.3 62.7 + - + +
469D ALA* 3.3 15.1 + - - +
470D ASP* 3.5 18.5 + - - +
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Residues in contact with ILE 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425D LEU* 3.7 29.4 - - + +
428D ILE* 3.7 26.0 - - + -
429D ALA* 3.5 39.7 - - + +
432D LYS* 4.4 13.5 - - + +
463D ILE* 3.1 30.7 + - + +
464D PHE* 3.2 20.2 + - + +
466D ASP* 1.3 76.3 - - + +
468D LEU* 1.3 58.1 + - + +
470D ASP* 3.4 8.7 + - - +
471D PHE* 3.0 27.1 + - + +
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Residues in contact with LEU 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394D LEU* 4.1 20.2 - - + -
398D TYR* 3.5 43.1 - - + -
401D PHE* 3.9 41.8 - - + -
402D ILE* 4.2 10.3 - - + -
425D LEU* 4.6 11.2 - - + -
464D PHE* 3.0 55.0 + - + +
465D SER 3.7 2.9 - - - +
467D ILE* 1.3 74.2 - - - +
469D ALA* 1.3 65.6 + - - +
470D ASP 3.2 0.5 + - - -
471D PHE* 3.4 11.3 + - - +
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Residues in contact with ALA 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398D TYR* 3.3 22.3 + - - +
465D SER 3.0 15.2 + - - +
466D ASP* 3.6 9.2 - - - +
467D ILE 3.3 0.4 - - - -
468D LEU* 1.3 78.6 - - - +
470D ASP* 1.3 58.5 + - + +
471D PHE 5.4 0.2 - - - +
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Residues in contact with ASP 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428D ILE* 6.1 0.7 - - - +
432D LYS* 6.1 0.5 - - - -
466D ASP* 3.5 14.5 + - - +
467D ILE* 3.4 10.5 + - - +
468D LEU 3.2 0.2 - - - -
469D ALA* 1.3 78.7 - - + +
471D PHE* 1.3 64.3 + - - +
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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
------------------------------------------------------------
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