Contacts of the helix formed by residues 453 - 471 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C GLU* 4.8 16.0 + - - +
376C LEU* 4.1 23.3 - - - +
379C ASN* 3.6 31.4 + - - +
383C ALA* 3.7 9.0 - - - -
451C VAL* 3.8 27.6 + - - +
452C PHE* 1.3 81.6 - - - +
454C ASP* 1.3 68.2 + - - +
455C HIS* 3.3 34.8 - - + +
456C HIS* 3.0 15.2 + - + +
457C ALA 3.2 15.8 + - - -
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Residues in contact with ASP 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379C ASN* 5.2 0.4 + - - -
382C HIS* 2.8 30.6 + - + +
383C ALA* 3.9 7.4 - - - +
386C VAL* 3.7 26.2 - - + -
453C ARG* 1.3 72.1 - - - +
455C HIS* 1.3 79.3 + - - +
457C ALA* 3.1 9.6 + - - +
458C HIS* 3.1 33.5 + - + +
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Residues in contact with HIS 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453C ARG* 3.6 25.7 - - + +
454C ASP* 1.3 88.2 + - - +
456C HIS* 1.3 87.0 + + - +
458C HIS* 3.6 10.2 + - - +
459C LEU* 3.0 31.2 + - + +
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Residues in contact with HIS 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ASP* 3.2 31.3 + - - -
13C TYR 5.0 1.6 + - - -
55C ASN* 3.3 13.0 + - - -
56C TYR* 3.7 22.8 + + - -
66C LEU* 3.9 18.8 - - + +
451C VAL 3.9 5.6 - - - -
452C PHE* 3.5 23.6 - + + -
453C ARG* 3.0 26.9 + - + +
454C ASP 3.2 0.4 - - - -
455C HIS* 1.3 100.6 + + - +
457C ALA* 1.3 66.5 + - - +
459C LEU* 3.1 10.1 + - + +
460C PHE* 2.9 24.3 + - - +
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Residues in contact with ALA 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C ALA 4.2 2.2 - - - +
386C VAL* 3.9 19.3 - - + -
387C LEU* 4.0 20.9 - - - +
452C PHE* 3.5 24.3 - - + -
453C ARG 3.2 6.6 + - - +
454C ASP 3.1 10.0 + - - +
456C HIS* 1.3 80.2 - - - +
458C HIS* 1.3 57.1 + - - +
460C PHE* 3.3 4.4 + - - +
461C LEU* 2.8 33.4 + - + +
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Residues in contact with HIS 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C VAL* 3.4 25.8 - - + +
454C ASP* 3.1 30.8 + - + +
455C HIS* 3.8 9.0 - - - +
457C ALA* 1.3 75.9 - - - +
459C LEU* 1.3 56.7 + - - +
461C LEU* 3.7 13.5 - - + +
462C ASN* 2.8 49.8 + - - +
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Residues in contact with LEU 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ASP 4.4 6.1 - - - +
15C GLY* 4.2 5.6 - - - -
16C PRO* 3.7 22.0 - - + -
56C TYR* 3.3 26.0 - - - +
66C LEU* 4.4 10.3 - - + -
455C HIS* 3.0 18.8 + - + +
456C HIS* 3.2 17.7 - - + +
458C HIS* 1.3 77.1 - - - +
460C PHE* 1.3 63.1 + - - +
462C ASN* 3.5 7.8 + - - +
463C ILE* 3.3 41.9 + - + +
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Residues in contact with PHE 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 4.1 8.2 - - + +
68C LEU* 3.9 19.1 - - + -
387C LEU* 4.0 8.1 - - + -
391C LEU* 4.1 7.4 - - + -
414C PHE* 5.2 0.2 - + - -
429C ALA* 5.7 0.7 - - + -
434C VAL* 3.8 27.4 - - + -
436C LEU* 3.9 17.0 - - + -
446C PHE* 3.3 38.4 - + - -
456C HIS 2.9 11.2 + - - +
457C ALA* 3.6 7.0 - - - +
459C LEU* 1.3 77.5 - - - +
461C LEU* 1.3 84.9 + - + +
463C ILE* 3.2 2.8 + - + +
464C PHE* 3.0 63.3 + + + +
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Residues in contact with LEU 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C VAL* 3.9 14.1 - - + +
387C LEU* 4.2 8.3 - - + +
390C GLY* 3.6 42.6 - - - -
391C LEU* 3.8 5.2 - - + +
394C LEU* 3.8 21.0 - - + +
457C ALA* 2.8 30.3 + - + +
458C HIS* 3.3 18.8 + - + +
460C PHE* 1.3 95.0 - - + +
462C ASN* 1.3 63.8 + - - +
464C PHE* 4.4 1.1 - - - +
465C SER* 3.2 25.8 + - - -
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Residues in contact with ASN 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C HIS* 2.8 31.4 + - - +
459C LEU* 3.7 8.0 - - - +
461C LEU* 1.3 79.3 - - - +
463C ILE* 1.3 63.2 + - + +
465C SER* 3.6 5.2 + - - -
466C ASP* 3.3 29.0 + - - +
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Residues in contact with ILE 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C PRO* 4.2 9.4 - - + -
429C ALA* 5.2 0.4 - - + +
432C LYS* 3.8 43.9 - - + +
434C VAL* 4.1 21.3 - - + -
459C LEU* 3.3 36.2 + - + +
460C PHE* 3.2 5.4 + - + +
462C ASN* 1.3 79.3 - - + +
464C PHE* 1.3 59.1 + - + +
466C ASP* 3.3 12.1 + - - +
467C ILE* 3.2 31.1 + - + +
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Residues in contact with PHE 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C LEU* 5.5 0.4 - - + -
394C LEU* 4.1 11.4 - - + -
402C ILE* 4.2 4.3 - - + -
414C PHE* 3.8 31.2 - + - -
425C LEU* 4.2 39.3 - - + -
429C ALA* 4.7 4.3 - - + -
436C LEU* 4.5 9.6 - - + -
444C ILE* 4.7 0.9 - - + -
460C PHE* 3.0 45.7 + + + +
461C LEU 4.4 2.0 - - - +
463C ILE* 1.3 76.0 - - + +
465C SER* 1.3 65.6 + - - +
467C ILE* 3.2 20.0 + - + +
468C LEU* 3.0 61.2 + - + +
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Residues in contact with SER 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C LEU* 3.9 25.4 - - - +
398C TYR* 4.0 9.1 + - - -
461C LEU 3.2 21.3 + - - -
462C ASN* 3.6 7.2 - - - -
464C PHE* 1.3 77.8 - - - +
466C ASP* 1.3 63.5 + - - -
468C LEU* 3.5 4.7 + - - +
469C ALA* 3.1 23.2 + - - +
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Residues in contact with ASP 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432C LYS* 6.3 3.1 - - - -
462C ASN* 3.3 17.5 + - - +
463C ILE* 3.3 12.3 + - - +
464C PHE 3.2 0.6 - - - -
465C SER* 1.3 77.9 + - - +
467C ILE* 1.3 64.8 + - + +
469C ALA* 3.5 7.5 + - - +
470C ASP* 3.4 27.7 + - - +
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Residues in contact with ILE 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425C LEU* 4.0 24.9 - - + -
428C ILE* 3.7 30.3 - - + -
429C ALA* 3.6 31.9 - - + +
432C LYS* 4.1 19.5 - - + +
463C ILE* 3.2 21.7 + - + +
464C PHE* 3.2 26.9 + - + +
466C ASP* 1.3 74.5 - - + +
468C LEU* 1.3 61.1 + - - +
470C ASP* 3.2 6.4 + - - +
471C PHE* 2.9 28.7 + - + +
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Residues in contact with LEU 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394C LEU* 4.3 14.4 - - + -
398C TYR* 3.6 48.2 - - + -
401C PHE* 4.0 32.4 - - + -
402C ILE* 4.3 11.0 - - + -
425C LEU* 4.3 13.5 - - + -
464C PHE* 3.0 54.1 + - + +
465C SER 3.9 4.3 - - - +
467C ILE* 1.3 75.3 - - - +
469C ALA* 1.3 62.3 + - - +
471C PHE* 3.2 21.3 + - + +
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Residues in contact with ALA 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C TYR* 3.6 18.6 + - - +
465C SER 3.1 18.0 + - - +
466C ASP* 3.6 10.5 - - - +
467C ILE 3.2 0.2 - - - -
468C LEU* 1.3 78.1 - - - +
470C ASP* 1.3 61.8 + - - +
471C PHE 5.0 0.9 - - - +
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Residues in contact with ASP 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466C ASP* 3.4 13.5 + - - +
467C ILE* 3.2 8.5 + - - +
469C ALA* 1.3 80.0 - - - +
471C PHE* 1.3 62.8 + - - +
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Residues in contact with PHE 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C PHE* 3.5 54.6 - + + -
421C ILE* 3.8 37.7 - - + -
424C LYS* 4.1 28.7 - - + -
425C LEU* 4.0 26.0 - - + -
428C ILE* 5.1 8.1 - - + -
467C ILE* 2.9 19.3 + - + +
468C LEU* 3.2 18.6 + - - +
469C ALA 5.0 1.0 - - - +
470C ASP* 1.3 82.2 - - - +
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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
------------------------------------------------------------
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