Contacts of the helix formed by residues 446 - 461 (chain A) in PDB entry 1OSH
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 446 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368A PRO* 5.6 0.2 - - - +
442A THR* 3.5 18.1 + - + +
443A GLU* 2.9 22.5 + - + +
444A LEU 3.2 0.4 - - - -
445A ARG* 1.3 77.5 - - - +
447A PHE* 1.3 68.2 + - - +
449A HIS* 3.0 24.4 + - - +
450A HIS* 3.1 35.4 + - - -
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Residues in contact with PHE 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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329A VAL* 3.4 5.8 - - + +
333A PHE* 3.4 57.4 - + + -
365A TYR* 4.6 3.1 - + - -
368A PRO* 3.3 28.3 - - + -
369A MET* 3.6 17.9 - - + -
372A PHE* 3.6 29.2 - + + -
443A GLU* 3.7 16.2 - - + -
444A LEU* 3.2 20.5 + - + +
445A ARG 3.0 1.6 - - - -
446A THR* 1.3 82.4 + - - +
448A ASN* 1.3 56.8 + - - +
450A HIS* 3.7 23.6 - + + +
451A HIS* 2.8 32.4 + - - +
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Residues in contact with ASN 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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326A GLY 4.5 9.1 - - - +
329A VAL* 3.7 24.7 - - - +
330A GLU* 2.8 36.0 + - - +
399A ARG* 4.7 2.4 - - - +
444A LEU 4.4 0.2 + - - -
445A ARG* 3.0 23.8 + - - +
447A PHE* 1.3 77.7 - - - +
449A HIS* 1.3 70.0 + - + +
451A HIS* 4.2 1.2 - - - +
452A ALA* 3.3 23.2 + - - +
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Residues in contact with HIS 449 (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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445A ARG 4.4 9.9 - - - -
446A THR* 3.0 14.2 + - - +
448A ASN* 1.3 81.1 - - + +
450A HIS* 1.3 69.6 + - + +
451A HIS 3.2 1.5 + - - -
452A ALA* 3.3 6.7 + - - +
453A GLU* 3.1 24.3 + - - +
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Residues in contact with HIS 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A GLU 3.9 15.0 + - - +
365A TYR* 3.5 18.2 - - + +
368A PRO* 3.7 24.3 - - + +
446A THR* 3.1 44.2 + - - +
447A PHE* 3.4 27.3 + + + +
449A HIS* 1.3 77.2 - - + +
451A HIS* 1.3 57.3 + - - +
453A GLU* 3.5 13.5 + - - +
454A MET* 3.0 30.3 + - - +
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Residues in contact with HIS 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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1A FEX 4.5 1.8 - + - -
329A VAL* 3.7 28.9 - - + -
332A MET* 3.6 22.0 - - + +
333A PHE* 4.5 1.2 - - + -
365A TYR* 2.7 30.8 + - + -
447A PHE 2.8 19.0 + - - +
448A ASN 4.2 1.8 - - - +
450A HIS* 1.3 76.3 - - - +
452A ALA* 1.3 59.8 + - - +
454A MET* 3.2 23.3 + - + +
455A LEU* 2.9 63.6 + - + +
473A TRP* 3.5 28.0 - + - -
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Residues in contact with ALA 452 (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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448A ASN 3.3 16.9 + - - +
449A HIS* 3.3 8.1 + - - +
451A HIS* 1.3 78.3 - - - +
453A GLU* 1.3 63.5 + - - +
455A LEU* 3.6 9.5 + - - +
456A MET* 3.4 30.8 + - + +
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Residues in contact with GLU 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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364A GLU* 2.4 36.6 - - - +
449A HIS 3.1 14.3 + - - +
450A HIS* 3.6 17.7 + - - +
452A ALA* 1.3 74.2 - - - +
454A MET* 1.3 66.5 + - - +
456A MET* 3.2 21.4 + - - +
457A SER* 4.3 1.7 + - - -
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Residues in contact with MET 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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1A FEX 3.5 24.0 - - + -
361A ILE* 4.1 17.9 - - + -
362A SER 5.6 1.1 - - - +
365A TYR* 3.5 33.4 - - + +
450A HIS 3.0 18.4 + - - +
451A HIS* 3.2 42.4 - - + +
453A GLU* 1.3 78.8 - - - +
455A LEU* 1.3 72.9 + - + +
456A MET 3.2 0.7 + - - -
457A SER* 3.8 8.1 + - - -
458A TRP* 3.3 33.0 + - - +
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Residues in contact with LEU 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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1A FEX 3.9 18.2 - - - -
451A HIS* 2.9 48.2 + - + +
452A ALA* 3.8 9.0 - - - +
454A MET* 1.3 101.0 - - + +
456A MET* 1.3 64.1 + - + +
458A TRP* 3.0 8.3 + - - +
459A ARG* 2.9 30.7 + - + +
465A PHE* 4.2 10.5 - - + -
473A TRP* 3.9 26.2 - - + +
475A VAL* 4.4 15.9 - - + -
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Residues in contact with MET 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 ALA* 3.4 19.3 + - + +
453A GLU* 3.2 16.7 + - - +
455A LEU* 1.3 79.1 - - + +
457A SER* 1.3 56.5 - - - +
459A ARG* 3.0 30.3 + - - +
460A VAL* 2.9 42.2 + - + +
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Residues in contact with SER 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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453A GLU 4.3 1.7 + - - -
454A MET 3.8 8.8 + - - -
455A LEU 3.3 0.8 - - - -
456A MET* 1.3 77.7 - - - +
458A TRP* 1.3 65.0 + - - +
460A VAL* 3.4 9.5 + - - +
461A ASN* 3.0 40.9 + - - -
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Residues in contact with TRP 458 (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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1A FEX 3.5 19.4 - - - -
287A ASN* 5.1 2.9 - - + -
288A PHE* 3.5 37.9 - + + -
291A LEU* 3.8 23.3 - - + -
359A SER 3.7 23.8 - - - -
360A GLY* 4.8 3.4 - - - -
361A ILE* 3.9 19.4 - - + +
454A MET* 3.3 41.1 + - - +
455A LEU* 3.0 7.7 + - - +
457A SER* 1.3 79.1 - - - +
459A ARG* 1.3 62.2 + - - +
462A ASP* 3.4 13.0 + - - +
463A HIS* 3.4 49.2 + + - +
465A PHE* 3.9 18.8 - - + -
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Residues in contact with ARG 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 LEU* 2.9 25.2 + - + +
456A MET* 3.0 30.2 + - - +
458A TRP* 1.3 78.6 - - - +
460A VAL* 1.3 63.2 + - + +
462A ASP* 3.0 29.9 + - - +
465A PHE* 4.1 15.9 - - + -
474A ASP 4.2 12.9 + - - -
475A VAL* 3.7 40.3 - - + +
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Residues in contact with VAL 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A MET* 2.9 34.9 + - + +
457A SER* 3.5 18.4 - - - +
459A ARG* 1.3 75.4 - - + +
461A ASN* 1.3 64.8 + - - +
462A ASP* 3.1 5.9 + - - -
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Residues in contact with ASN 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A SER* 3.0 34.6 + - - +
458A TRP 3.4 0.2 + - - -
459A ARG 3.2 0.8 - - - -
460A VAL* 1.3 83.7 - - - +
462A ASP* 1.3 64.8 - - - +
463A HIS* 3.5 25.6 + - + -
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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