Contacts of the helix formed by residues 444 - 459 (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 THR 444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441A ASP* 4.4 15.9 + - - +
442A GLY 3.4 0.2 - - - -
443A ALA* 1.3 84.4 - - - +
445A ASP* 1.3 74.7 + - + +
448A GLU* 3.9 14.6 + - - +
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Residues in contact with ASP 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ASP 2.9 24.3 - - - +
442A GLY* 3.2 7.6 - - - -
444A THR* 1.3 82.5 - - + +
446A TYR* 1.3 71.6 + - - +
447A LEU 3.0 2.4 + - - -
448A GLU* 3.2 11.1 + - - +
449A ARG* 3.2 27.1 + - + +
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Residues in contact with TYR 446 (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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442A GLY* 3.0 21.8 + - - +
445A ASP* 1.3 80.5 + - - +
447A LEU* 1.3 64.7 + - + +
449A ARG* 3.3 7.3 + - + +
450A LEU* 2.9 52.3 + - + +
453A ARG* 4.7 6.7 + - - -
505A GLU* 3.3 49.5 + - + +
506A LEU* 4.3 1.1 + - + -
509A TYR* 3.7 47.5 - + + +
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Residues in contact with LEU 447 (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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442A GLY 3.5 1.0 + - - -
443A ALA* 3.8 24.7 - - + +
445A ASP 3.3 1.0 - - - -
446A TYR* 1.3 84.4 - - + +
448A GLU* 1.3 62.4 + - - +
449A ARG 3.2 0.4 - - - -
450A LEU* 3.5 2.9 + - + +
451A GLU* 3.0 29.4 + - - +
465A VAL* 3.8 34.8 - - + +
466A GLY* 6.3 0.7 - - - -
473A TYR* 3.8 29.2 - - + +
506A LEU* 4.2 3.6 - - + -
509A TYR* 3.5 38.6 - - + +
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Residues in contact with GLU 448 (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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444A THR 3.9 10.0 + - - +
445A ASP* 3.2 8.8 + - - +
447A LEU* 1.3 79.1 - - - +
449A ARG* 1.3 57.3 + - + +
451A GLU* 3.3 13.1 + - + +
452A VAL* 3.0 50.7 + - + +
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Residues in contact with ARG 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ASP* 3.2 27.5 + - + +
446A TYR* 3.6 10.1 - - + +
447A LEU 3.2 0.6 - - - -
448A GLU* 1.3 75.4 - - + +
450A LEU* 1.3 65.6 + - - +
451A GLU 3.1 1.1 - - - -
452A VAL* 3.3 4.2 + - - +
453A ARG* 2.9 32.9 + - - +
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Residues in contact with LEU 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A TYR* 2.9 37.9 + - + +
447A LEU* 4.0 2.9 - - + +
449A ARG* 1.3 75.3 - - - +
451A GLU* 1.3 62.8 + - - +
453A ARG* 3.7 22.4 - - - +
454A GLU* 3.1 39.0 + - + +
465A VAL* 4.3 18.3 - - + +
475A ILE* 5.1 4.9 - - + -
503A ILE* 4.6 8.5 - - + -
505A GLU* 3.6 21.8 - - - +
506A LEU* 3.7 33.2 - - + -
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Residues in contact with GLU 451 (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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447A LEU 3.0 19.7 + - - +
448A GLU* 3.4 14.9 - - - +
449A ARG 3.1 0.2 - - - -
450A LEU* 1.3 76.3 - - - +
452A VAL* 1.3 55.8 + - - +
454A GLU* 3.2 2.3 + - - -
455A ARG* 2.8 61.4 + - - +
463A LEU* 3.8 9.9 - - + +
464A LYS* 3.9 15.0 - - - +
465A VAL* 3.1 47.0 + - + +
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Residues in contact with VAL 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A GLU* 3.0 35.2 + - + +
449A ARG* 4.1 3.8 - - - +
451A GLU* 1.3 81.2 - - + +
453A ARG* 1.3 58.7 + - - +
455A ARG* 3.8 33.5 - - - +
456A GLU* 3.0 32.5 + - + +
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Residues in contact with ARG 453 (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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446A TYR* 4.7 6.7 + - - -
449A ARG* 2.9 25.0 + - - +
450A LEU* 3.7 26.0 - - - +
452A VAL* 1.3 79.2 - - - +
454A GLU* 1.3 75.5 + - - +
456A GLU* 3.9 3.5 - - - +
457A ARG* 3.0 33.4 + - + +
505A GLU* 3.2 39.3 + - - -
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Residues in contact with GLU 454 (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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450A LEU* 3.1 38.9 + - + +
451A GLU 3.9 2.2 - - - +
453A ARG* 1.3 89.6 + - - +
455A ARG* 1.3 55.9 + - - +
457A ARG* 2.9 41.2 + - - -
458A THR* 2.6 37.8 + - - +
463A LEU* 3.8 11.7 - - + +
475A ILE* 4.9 5.2 - - + -
489A TYR* 2.5 35.9 + - - +
503A ILE* 4.9 7.9 - - - +
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Residues in contact with ARG 455 (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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451A GLU* 2.8 51.6 + - - +
452A VAL* 3.8 30.1 - - - +
453A ARG 3.3 0.2 - - - -
454A GLU* 1.3 75.6 - - - +
456A GLU* 1.3 59.0 + - - +
458A THR* 4.1 2.9 - - - -
459A GLY* 3.0 27.0 + - - -
460A LEU 3.5 18.0 + - - +
461A ASP* 3.7 22.6 - - - +
463A LEU* 3.5 23.8 + - + +
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Residues in contact with GLU 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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452A VAL* 3.0 22.0 + - + +
453A ARG* 3.9 4.3 - - - +
455A ARG* 1.3 74.0 - - - +
457A ARG* 1.3 63.7 + - - +
459A GLY* 3.3 11.3 + - - -
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Residues in contact with ARG 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A ARG* 3.0 23.1 + - + +
454A GLU* 2.9 43.6 + - - +
456A GLU* 1.3 79.0 - - - +
458A THR* 1.3 64.3 + - - +
486A PRO* 4.0 17.6 - - - +
488A ASN* 5.9 2.6 + - - +
489A TYR* 4.0 13.7 + - - -
503A ILE* 6.1 0.4 - - - +
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Residues in contact with THR 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A GLU* 2.6 23.0 + - - +
455A ARG 3.8 0.5 + - - -
457A ARG* 1.3 88.5 - - - +
459A GLY* 1.3 64.7 + - - +
460A LEU* 3.3 37.2 + - + +
463A LEU* 3.8 7.3 - - + +
484A LEU* 5.6 2.9 - - - +
486A PRO* 4.0 29.6 - - + -
489A TYR* 4.1 13.0 - - + +
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Residues in contact with GLY 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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455A ARG 3.0 12.5 + - - -
456A GLU* 3.3 10.4 + - - -
457A ARG 3.4 0.2 - - - -
458A THR* 1.3 78.6 - - - +
460A LEU* 1.3 66.0 + - - +
461A ASP* 3.7 4.5 + - - +
481A GLN* 5.3 0.9 + - - -
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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