Contacts of the helix formed by residues 453 - 470 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B GLU* 4.2 20.2 + - - +
376B LEU* 3.9 24.2 - - - +
379B ASN* 3.4 31.6 + - - +
383B ALA* 3.8 7.0 - - - -
451B VAL* 3.6 26.5 + - - +
452B PHE* 1.3 78.2 - - - +
454B ASP* 1.3 69.9 + - - +
455B HIS* 3.2 22.9 - - + +
456B HIS* 2.9 33.3 + - + +
457B ALA 3.2 8.3 + - - -
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Residues in contact with ASP 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ASN* 5.0 1.8 + - - -
382B HIS* 2.4 35.9 + - + +
383B ALA* 3.8 8.1 - - - +
386B VAL* 3.7 26.9 - - + -
453B ARG* 1.3 75.3 - - - +
455B HIS* 1.3 72.7 + - - +
457B ALA* 2.9 11.2 + - - +
458B HIS* 2.9 38.3 + - + +
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Residues in contact with HIS 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASP* 6.0 1.2 - - - +
13B TYR 5.7 1.8 + - - -
453B ARG* 3.8 16.6 - - + +
454B ASP* 1.3 86.3 + - - +
456B HIS* 1.3 94.8 + + - +
458B HIS* 3.6 11.3 + - + +
459B LEU* 3.0 30.3 + - + +
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Residues in contact with HIS 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASP* 2.9 23.8 + - + +
13B TYR 5.1 1.6 + - - -
55B ASN* 3.0 23.7 + - + -
56B TYR* 4.0 20.0 - - - -
66B LEU* 4.0 17.8 - - + +
451B VAL 3.5 7.9 - - - -
452B PHE* 3.6 20.4 - + + -
453B ARG* 2.9 30.0 + - + +
455B HIS* 1.3 106.6 + + - +
457B ALA* 1.3 60.1 + - - +
459B LEU* 3.2 7.5 + - + +
460B PHE* 2.9 30.5 + - - +
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Residues in contact with ALA 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ALA 4.1 2.7 - - - +
386B VAL* 3.9 19.1 - - + -
387B LEU* 4.0 20.2 - - + +
452B PHE* 3.5 26.6 - - + -
453B ARG 3.2 2.6 + - - -
454B ASP 2.9 11.3 + - - +
456B HIS* 1.3 76.9 - - - +
458B HIS* 1.3 52.4 + - - +
460B PHE* 3.2 6.5 + - - +
461B LEU* 2.8 40.1 + - + +
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Residues in contact with HIS 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B VAL* 3.4 28.1 - - + +
454B ASP* 2.9 33.0 + - + +
455B HIS* 3.8 9.6 - - + +
457B ALA* 1.3 70.8 - - - +
459B LEU* 1.3 66.8 + - - +
461B LEU* 3.8 11.6 - - + +
462B ASN* 3.0 35.7 + - - +
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Residues in contact with LEU 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASP 4.7 4.3 - - - +
15B GLY* 4.2 4.3 - - - -
16B PRO* 3.9 20.6 - - + -
56B TYR* 2.9 29.6 - - + +
66B LEU* 3.9 19.5 - - + -
434B VAL* 5.2 0.2 - - + -
455B HIS* 3.0 17.4 + - + +
456B HIS* 3.3 14.6 - - + +
458B HIS* 1.3 78.7 - - - +
460B PHE* 1.3 64.8 + - - +
462B ASN* 3.2 14.9 + - - +
463B ILE* 3.3 35.7 + - + +
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Residues in contact with PHE 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 4.1 6.3 - - + +
68B LEU* 3.9 18.2 - - + -
387B LEU* 3.8 24.5 - - + -
391B LEU* 4.1 5.6 - - + -
429B ALA* 5.9 0.4 - - + -
434B VAL* 3.9 24.2 - - + -
436B LEU* 4.1 12.3 - - + -
446B PHE* 3.3 35.2 - + - -
456B HIS 2.9 13.3 + - - +
457B ALA* 3.5 6.5 - - - +
459B LEU* 1.3 82.2 - - - +
461B LEU* 1.3 79.4 + - + +
462B ASN 3.1 0.5 + - - -
463B ILE* 3.1 5.2 + - - +
464B PHE* 2.9 62.3 + + + +
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Residues in contact with LEU 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B VAL* 3.8 15.5 - - + +
387B LEU* 4.1 8.5 - - + +
390B GLY* 3.5 44.6 - - - +
391B LEU* 3.7 4.3 - - + +
394B LEU* 4.0 17.2 - - + +
457B ALA 2.8 29.8 + - - +
458B HIS* 3.3 18.1 + - + +
460B PHE* 1.3 92.4 - - + +
462B ASN* 1.3 56.7 + - - +
464B PHE* 4.3 2.1 - - - +
465B SER* 3.0 29.5 + - - -
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Residues in contact with ASN 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B HIS* 3.0 24.5 + - - +
459B LEU* 3.4 11.7 - - - +
461B LEU* 1.3 75.8 - - - +
463B ILE* 1.3 68.6 - - + +
465B SER* 3.4 6.8 - - - -
466B ASP* 3.2 29.1 + - - +
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Residues in contact with ILE 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PRO* 4.1 13.0 - - + -
432B LYS* 3.9 43.7 - - + +
434B VAL* 4.3 16.8 - - + -
459B LEU* 3.3 35.2 + - + +
460B PHE 3.1 6.6 + - - +
462B ASN* 1.3 78.0 - - + +
464B PHE* 1.3 59.5 + - - +
466B ASP* 3.2 10.7 + - - +
467B ILE* 3.0 33.5 + - + +
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Residues in contact with PHE 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B LEU* 5.3 0.9 - - + -
394B LEU* 3.7 20.6 - - + -
402B ILE* 4.3 4.0 - - + -
414B PHE* 3.8 33.4 - + - -
425B LEU* 4.6 23.6 - - + -
429B ALA* 4.8 2.0 - - + -
436B LEU* 4.3 17.3 - - + -
444B ILE* 4.9 0.7 - - + -
460B PHE* 2.9 45.5 + + + +
461B LEU 4.3 1.8 - - - +
463B ILE* 1.3 77.7 - - - +
465B SER* 1.3 62.2 + - - +
467B ILE* 3.3 25.3 + - + +
468B LEU* 3.0 51.6 + - + +
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Residues in contact with SER 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LEU* 4.0 23.9 - - - +
398B TYR* 4.2 5.5 + - - -
461B LEU 3.0 21.9 + - - -
462B ASN* 3.4 9.4 - - - -
464B PHE* 1.3 76.7 - - - +
466B ASP* 1.3 64.5 + - - +
468B LEU* 3.2 5.2 + - - +
469B ALA* 3.1 21.3 + - - +
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Residues in contact with ASP 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B ASN* 3.2 16.5 + - - +
463B ILE* 3.2 9.8 + - - +
465B SER* 1.3 79.7 - - - +
467B ILE* 1.3 57.7 + - + +
469B ALA* 3.4 7.1 + - - +
470B ASP* 3.0 41.3 + - - +
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Residues in contact with ILE 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B LEU* 4.3 22.4 - - + +
428B ILE* 4.1 21.5 - - + -
429B ALA* 3.7 36.6 - - + +
432B LYS* 4.0 27.8 - - + +
463B ILE* 3.0 22.9 + - + +
464B PHE* 3.4 25.8 - - + +
465B SER 3.2 0.2 - - - -
466B ASP* 1.3 77.2 - - + +
468B LEU* 1.3 59.5 + - + +
470B ASP* 3.3 7.8 + - - +
471B PHE* 2.9 28.5 + - + +
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Residues in contact with LEU 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B LEU* 4.1 19.3 - - + -
398B TYR* 3.6 42.8 - - + -
401B PHE* 4.1 31.0 - - + -
402B ILE* 4.2 10.1 - - + -
425B LEU* 4.5 15.5 - - + -
464B PHE* 3.0 55.4 + - + +
465B SER 3.2 4.2 + - - +
467B ILE* 1.3 74.2 - - - +
469B ALA* 1.3 65.7 + - - +
471B PHE* 3.1 21.7 + - + +
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Residues in contact with ALA 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B TYR* 3.3 21.2 + - - +
465B SER 3.1 12.0 + - - +
466B ASP* 3.7 10.3 - - - +
467B ILE 3.3 0.2 - - - -
468B LEU* 1.3 77.4 - - - +
470B ASP* 1.3 65.6 + - - +
471B PHE 3.5 3.5 + - - +
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Residues in contact with ASP 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B LYS* 5.1 10.4 + - - -
466B ASP* 3.0 27.7 + - - +
467B ILE* 3.5 7.4 - - - +
469B ALA* 1.3 79.2 - - - +
471B PHE* 1.3 62.1 + - - +
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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