Contacts of the helix formed by residues 445 - 460 (chain A) in PDB entry 2WO6
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 445 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443A GLY* 5.5 3.4 - - - +
444A HIS* 1.3 83.3 - - - +
446A VAL* 1.3 63.8 + - - +
447A ALA* 3.5 10.3 + - - +
448A ASP* 2.7 43.3 + - - +
449A TYR* 3.0 23.6 + - - -
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Residues in contact with VAL 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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429A VAL* 3.5 23.1 - - + +
430A GLU* 3.2 41.3 - - - +
445A THR* 1.3 70.3 - - - +
447A ALA* 1.3 68.5 + - - +
449A TYR* 2.9 4.7 + - - +
450A LEU* 2.9 41.2 + - + +
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Residues in contact with ALA 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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445A THR* 3.5 8.4 + - - +
446A VAL* 1.3 81.2 - - - +
448A ASP* 1.3 63.5 + - - +
450A LEU* 3.3 9.2 + - - +
451A LYS* 3.2 42.6 + - - +
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Residues in contact with ASP 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LEU* 3.4 21.0 - - + +
260A ASN* 5.4 0.7 - - - +
263A ARG* 3.6 21.9 + - - +
443A GLY* 3.6 17.0 - - - +
445A THR* 2.7 49.6 + - - +
447A ALA* 1.3 74.1 - - - +
449A TYR* 1.3 61.8 + - - +
451A LYS* 3.5 13.0 + - - +
452A PHE* 3.1 23.2 + - - +
478A PHE* 4.2 3.4 - - - -
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Residues in contact with TYR 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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259A LEU* 4.1 13.7 - - + -
355A HIS* 2.7 40.0 + + - -
427A LEU* 3.8 24.4 - - + +
429A VAL* 4.0 37.0 - - + +
432A GLY* 4.9 1.8 - - - -
433A GLY* 3.4 28.3 - - - -
434A PRO* 3.7 0.7 - - - +
438A ARG* 3.7 3.1 - - - +
444A HIS* 3.4 38.2 - + + -
445A THR 3.0 21.4 + - - -
446A VAL 2.9 7.9 + - - +
448A ASP* 1.3 78.4 - - - +
450A LEU* 1.3 56.9 + - - +
452A PHE* 3.4 6.8 + + - +
453A LYS* 2.8 31.0 + - - +
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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
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424A HIS* 4.2 5.8 - - + -
429A VAL* 3.8 20.0 - - + -
430A GLU* 5.3 2.0 - - - +
446A VAL* 2.9 36.4 + - + +
447A ALA* 3.3 8.7 + - - +
449A TYR* 1.3 71.4 - - - +
451A LYS* 1.3 58.4 + - + +
453A LYS* 3.5 28.7 + - - +
454A ASP* 3.0 29.2 + - - +
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Residues in contact with LYS 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 ALA* 3.2 29.1 + - - +
448A ASP* 3.9 11.0 + - - +
450A LEU* 1.3 76.9 - - + +
452A PHE* 1.3 64.6 + - - +
454A ASP* 3.4 2.8 + - - -
455A LEU* 3.0 20.3 + - - +
476A HIS* 3.1 13.8 - - - -
477A SER* 3.4 42.4 + - - +
478A PHE* 3.9 17.9 - - + +
480A LYS* 5.2 5.7 + - - +
481A LYS 5.5 2.6 + - - -
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Residues in contact with PHE 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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259A LEU* 3.8 19.5 - - + -
262A THR* 3.9 19.7 - - + -
266A ALA* 5.8 0.2 - - + -
351A LEU* 3.8 34.5 - - + -
352A VAL* 4.3 0.7 - - - -
355A HIS* 4.5 7.4 - + + -
427A LEU* 3.8 36.6 - - + -
448A ASP 3.1 19.0 + - - +
449A TYR* 3.7 9.6 - + - +
451A LYS* 1.3 72.4 - - - +
453A LYS* 1.3 67.2 + - - +
455A LEU* 3.2 5.7 + - + +
456A ILE* 3.0 48.2 + - + +
478A PHE* 3.6 36.9 - + + -
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Residues in contact with LYS 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 4.1 14.1 - - + -
424A HIS* 2.9 56.2 + - + +
427A LEU* 4.0 15.5 - - + -
429A VAL* 4.4 3.6 - - + -
449A TYR 2.8 18.6 + - - +
450A LEU* 3.7 21.8 - - - +
452A PHE* 1.3 74.8 - - - +
454A ASP* 1.3 57.9 + - - +
456A ILE* 3.2 4.4 + - - +
457A LEU* 2.9 49.3 + - + +
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Residues in contact with ASP 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 3.0 18.2 + - - +
451A LYS* 3.6 6.3 - - - +
452A PHE 3.2 0.2 - - - -
453A LYS* 1.3 76.4 - - - +
455A LEU* 1.3 65.3 + - - +
457A LEU* 3.2 9.9 + - - +
458A ARG* 2.9 57.7 + - - +
476A HIS* 2.7 25.9 + - + +
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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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266A ALA* 5.1 2.7 - - + -
351A LEU* 5.4 2.0 - - + -
451A LYS 3.0 13.7 + - - +
452A PHE* 3.6 10.5 - - + +
454A ASP* 1.3 75.9 - - - +
456A ILE* 1.3 59.4 + - + +
458A ARG* 3.1 6.4 + - - +
459A MET* 2.9 55.2 + - + +
468A ILE* 4.0 17.0 - - + -
473A ALA* 4.3 7.0 - - + +
476A HIS* 3.5 35.7 + - + +
478A PHE* 3.8 29.2 - - + -
479A PHE* 3.9 19.3 - - + -
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Residues in contact with ILE 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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348A GLY* 3.5 25.8 - - - +
351A LEU* 4.0 21.8 - - + -
352A VAL* 3.7 17.5 - - + -
423A LEU* 3.5 23.3 - - + -
427A LEU* 5.4 0.2 - - + -
452A PHE* 3.0 35.2 + - + +
453A LYS* 3.5 7.4 - - - +
455A LEU* 1.3 77.9 - - + +
457A LEU* 1.3 57.3 + - - +
459A MET* 3.1 11.6 + - - +
460A LEU* 2.9 47.2 + - + +
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Residues in contact with LEU 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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376A VAL* 5.7 0.7 - - + -
377A LEU* 3.9 27.6 - - + -
423A LEU* 4.1 22.7 - - + -
453A LYS* 2.9 44.7 + - + +
454A ASP* 3.9 8.5 - - - +
456A ILE* 1.3 74.0 - - - +
458A ARG* 1.3 62.3 + - + +
460A LEU* 3.2 13.7 + - + +
461A ASP* 3.2 13.0 + - - +
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Residues in contact with ARG 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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454A ASP* 2.9 45.3 + - - +
455A LEU 3.5 7.9 - - - +
457A LEU* 1.3 78.9 - - + +
459A MET* 1.3 58.9 + - - +
460A LEU 3.5 0.2 + - - -
461A ASP* 3.6 10.0 - - - +
467A ARG* 3.6 4.5 - - - +
468A ILE* 3.1 55.3 + - + +
476A HIS* 3.9 10.1 + - - -
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Residues in contact with MET 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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266A ALA* 5.5 0.2 - - + -
270A CYS* 3.7 29.2 - - - -
344A MET* 3.8 25.1 - - + +
345A TRP* 3.7 12.6 + - - -
347A LEU* 3.8 10.5 - - + -
348A GLY* 3.8 28.7 - - - -
351A LEU* 3.9 15.9 - - + -
455A LEU* 2.9 42.3 + - + +
456A ILE* 3.1 14.1 + - - +
458A ARG* 1.3 77.2 - - - +
460A LEU* 1.3 57.9 + - - +
461A ASP 3.4 1.1 - - - -
467A ARG* 3.2 23.1 + - - -
468A ILE* 3.7 15.3 - - + -
473A ALA* 4.7 1.1 - - + -
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Residues in contact with LEU 460 (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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345A TRP* 3.5 58.9 - - + +
348A GLY* 4.3 2.7 - - - -
349A CYS* 4.0 13.2 - - - +
360A LEU* 3.7 24.2 - - + -
361A PHE* 4.4 7.4 - - + -
376A VAL* 5.9 1.8 - - + -
377A LEU* 3.5 33.0 - - + +
423A LEU* 5.1 4.9 - - + -
456A ILE* 2.9 38.1 + - + +
457A LEU* 3.2 7.6 + - - +
459A MET* 1.3 77.2 - - - +
461A ASP* 1.3 63.8 + - - +
462A TYR* 3.5 3.1 + - - -
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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
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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