Contacts of the helix formed by residues 456 - 467 (chain A) in PDB entry 2WTJ
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 SER 456 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A GLU* 2.7 34.8 + - - -
454A GLU 4.2 0.8 + - - -
455A VAL* 1.3 86.3 - - - +
457A GLU* 1.3 62.7 + - - +
458A LYS* 3.4 10.0 + - - +
459A ALA* 3.0 17.3 + - - +
460A LEU* 3.4 11.1 + - - +
485A TRP* 3.9 1.2 - - - -
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Residues in contact with GLU 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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455A VAL 3.7 1.7 + - - -
456A SER* 1.3 70.4 - - - +
458A LYS* 1.3 59.9 + - - +
460A LEU* 3.8 8.1 - - - +
461A ASP* 2.9 29.6 + - - +
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Residues in contact with LYS 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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456A SER* 3.2 8.9 + - - +
457A GLU* 1.3 76.1 - - + +
459A ALA* 1.3 65.3 + - - +
461A ASP* 3.3 4.9 + - - -
462A LEU 3.2 17.2 + - - -
483A HIS* 3.3 13.8 - - + -
484A PRO* 4.0 37.5 + - + +
485A TRP* 3.8 18.6 - - + +
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Residues in contact with ALA 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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321A GLU* 3.7 3.4 - - - +
417A LEU* 4.5 0.9 - - - +
421A LEU* 3.8 16.1 - - + +
455A VAL* 3.6 21.1 - - + -
456A SER* 3.0 17.7 + - - +
458A LYS* 1.3 74.9 - - - +
460A LEU* 1.3 64.9 + - - +
462A LEU* 3.1 13.9 + - - +
463A VAL* 3.2 15.1 + - - +
485A TRP* 3.5 31.9 - - + +
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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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418A PHE* 5.7 0.2 - - + -
445A TYR* 5.1 6.3 - - + +
447A PHE* 3.8 31.9 - - + -
452A TRP* 3.8 42.2 - - + -
455A VAL* 4.6 0.8 - - - +
456A SER 3.4 10.3 + - - +
457A GLU* 3.9 9.9 - - - +
458A LYS 3.3 0.4 - - - -
459A ALA* 1.3 79.9 - - - +
461A ASP* 1.3 61.7 + - - +
463A VAL* 3.2 9.4 + - + +
464A LYS* 3.1 52.0 + - + +
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Residues in contact with ASP 461 (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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457A GLU 2.9 18.4 + - - +
458A LYS* 3.5 8.3 - - - +
459A ALA 3.2 0.4 - - - -
460A LEU* 1.3 77.4 - - - +
462A LEU* 1.3 60.8 + - - +
464A LYS* 3.2 17.8 + - - +
465A LYS* 2.6 56.2 + - - +
483A HIS* 2.7 18.1 + - + +
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Residues in contact with LEU 462 (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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328A PHE* 4.0 16.4 - - + -
417A LEU* 4.0 3.8 - - + -
458A LYS 3.2 3.1 + - - +
459A ALA 3.1 10.1 + - - +
461A ASP* 1.3 75.3 - - - +
463A VAL* 1.3 68.1 + - - +
465A LYS* 3.0 11.5 + - - +
466A LEU* 3.1 22.1 + - + +
475A PHE* 3.9 26.2 - - + -
480A ALA* 4.0 14.8 - - + +
483A HIS* 3.7 30.4 + - + +
485A TRP* 3.7 17.9 - - + -
486A LEU* 3.6 29.2 - - + -
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Residues in contact with VAL 463 (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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414A GLY 4.3 3.1 - - - +
417A LEU* 3.6 29.6 - - + -
418A PHE* 3.8 26.9 - - + +
421A LEU* 3.8 12.6 - - + -
445A TYR* 5.9 2.7 - - + -
452A TRP* 4.4 6.5 - - + -
459A ALA 3.2 12.9 + - - +
460A LEU* 3.5 14.6 - - + +
462A LEU* 1.3 76.2 - - - +
464A LYS* 1.3 59.8 + - + +
466A LEU* 2.9 8.5 + - - +
467A LEU* 2.9 52.7 + - + +
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Residues in contact with LYS 464 (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 TYR* 3.6 30.5 - - + +
447A PHE* 6.1 0.2 - - - -
460A LEU* 3.1 49.8 + - + +
461A ASP* 3.5 17.0 + - - +
462A LEU 3.2 0.2 - - - -
463A VAL* 1.3 78.4 - - + +
465A LYS* 1.3 61.6 + - + +
466A LEU 3.4 0.5 + - - -
467A LEU* 3.7 11.3 + - - +
468A VAL* 3.3 16.1 - - - +
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Residues in contact with LYS 465 (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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461A ASP* 2.6 44.1 + - - +
462A LEU 3.0 8.5 + - - +
464A LYS* 1.3 78.7 - - + +
466A LEU* 1.3 60.2 + - - +
468A VAL* 3.5 16.9 - - + +
473A ALA 5.0 0.2 - - - +
475A PHE* 3.1 71.9 + - + -
483A HIS* 3.9 9.9 + - + -
484A PRO* 5.9 0.6 - - - +
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Residues in contact with LEU 466 (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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328A PHE* 3.7 31.2 - - + -
332A LEU* 5.7 2.0 - - + -
410A CYS* 3.7 22.2 - - + +
411A TRP* 3.9 8.5 - - - -
413A LEU* 5.2 1.8 - - + -
414A GLY* 3.7 23.1 - - - +
417A LEU* 4.5 2.9 - - + -
462A LEU* 3.1 32.1 + - + +
463A VAL 2.9 6.4 + - - +
465A LYS* 1.3 78.1 - - - +
467A LEU* 1.3 57.5 + - - +
468A VAL 3.0 10.1 + - - -
474A ARG* 3.3 23.5 + - - -
475A PHE* 3.8 29.8 - - + +
480A ALA* 4.6 9.9 - - + -
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Residues in contact with LEU 467 (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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411A TRP* 3.5 37.6 - - + +
414A GLY* 3.8 6.5 - - - +
415A VAL* 3.7 36.3 - - + +
418A PHE* 4.1 14.6 - - + -
426A PRO* 4.4 13.5 - - + -
427A PHE* 4.5 3.6 - - + -
443A GLY* 4.8 8.4 - - - +
445A TYR* 4.4 22.0 - - + -
463A VAL* 2.9 39.4 + - + +
464A LYS* 3.7 9.9 + - - +
466A LEU* 1.3 74.6 - - - +
468A VAL* 1.3 60.2 + - - +
469A VAL* 3.9 3.8 + - - +
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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