Contacts of the helix formed by residues 431 - 439 (chain A) in PDB entry 2WKP
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 431 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408A LEU 5.7 0.4 - - - -
411A ILE 4.7 3.8 - - - -
413A LYS 2.7 28.9 + - - -
415A PHE* 3.0 40.2 + - - -
429A PHE* 3.9 10.3 - - - -
430A ALA* 1.3 75.8 - - - +
432A ASP* 1.3 64.9 + - - +
433A SER* 3.6 1.7 + - - -
434A PHE* 3.1 20.7 + - - +
435A LEU* 3.1 12.6 + - - +
442A ARG* 3.7 0.7 - - - +
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Residues in contact with ASP 432 (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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409A GLU* 6.0 2.5 - - - +
412A GLU* 5.4 7.4 - - - +
431A SER* 1.3 73.2 - - - +
433A SER* 1.3 63.0 + - - +
435A LEU* 3.1 11.6 + - - +
436A GLN* 2.9 39.0 + - - +
442A ARG* 2.8 32.3 + - - +
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Residues in contact with SER 433 (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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412A GLU* 3.8 28.6 + - - +
413A LYS* 3.6 16.9 + - - -
414A ASN* 3.1 21.2 - - - +
431A SER* 3.2 1.8 + - - -
432A ASP* 1.3 78.2 - - - +
434A PHE* 1.3 58.9 + - - +
436A GLN* 3.2 16.8 + - - +
437A LEU* 2.8 26.3 + - - +
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Residues in contact with PHE 434 (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 ASN* 3.4 10.0 + - + -
415A PHE 3.8 9.6 - - - +
416A VAL* 3.7 26.9 - - + -
430A ALA* 4.3 1.8 - - + -
431A SER* 3.1 22.2 + - - +
433A SER* 1.3 76.2 - - - +
435A LEU* 1.3 69.2 + - + +
437A LEU* 3.3 4.4 + - + +
438A THR* 2.8 64.4 + - + +
445A ILE* 4.3 15.3 - - + -
450A CYS* 3.9 8.7 - - - -
452A PHE* 4.4 9.2 - + - -
453A LEU* 3.8 19.1 - - + -
513A GLN* 3.3 42.2 - - + -
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Residues in contact with LEU 435 (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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430A ALA* 3.8 23.8 - - + +
431A SER 3.1 14.7 + - - +
432A ASP* 3.3 11.7 - - - +
434A PHE* 1.3 82.1 - - + +
436A GLN* 1.3 55.2 + - + +
438A THR* 3.5 5.3 + - - +
439A GLU* 2.8 34.5 + - - -
440A TYR 3.4 21.2 + - - +
441A SER* 5.0 0.7 - - - -
442A ARG* 3.5 58.6 - - + +
445A ILE* 4.6 6.5 - - + -
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Residues in contact with GLN 436 (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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432A ASP* 2.9 27.4 + - - +
433A SER* 3.5 20.7 + - - +
435A LEU* 1.3 80.8 - - + +
437A LEU* 1.3 62.2 + - - +
439A GLU* 3.7 10.1 + - - +
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Residues in contact with LEU 437 (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 ASN* 3.8 31.2 - - + +
433A SER 2.8 20.5 + - - +
434A PHE* 3.6 5.4 - - + +
436A GLN* 1.3 75.3 - - - +
438A THR* 1.3 70.8 + - + +
439A GLU* 4.1 2.6 - - - +
484A THR* 3.4 18.7 - - + +
490A PHE* 4.0 37.5 - - + -
513A GLN* 4.6 9.4 - - + -
515A ASP* 3.7 32.5 - - + +
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Residues in contact with THR 438 (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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434A PHE* 2.8 57.9 + - + +
435A LEU* 3.5 4.7 + - - -
437A LEU* 1.3 89.1 - - + +
439A GLU* 1.3 70.5 + - - +
440A TYR* 3.2 28.0 + - - +
453A LEU* 3.8 19.3 - - + -
484A THR* 4.1 6.5 - - - +
485A LYS 2.9 22.5 + - - -
490A PHE* 4.8 3.6 - - + -
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Residues in contact with GLU 439 (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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435A LEU 2.8 11.5 + - - -
436A GLN* 4.3 7.2 - - - +
437A LEU 3.4 6.0 - - - +
438A THR* 1.3 77.8 - - - +
440A TYR* 1.3 61.9 + - - +
441A SER 4.1 0.3 + - - -
444A GLU* 4.7 0.2 - - - +
484A THR* 2.9 26.8 + - - +
485A LYS* 3.8 17.6 + - + +
486A SER* 2.7 39.4 + - - -
488A LYS* 3.4 19.3 + - - +
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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