Contacts of the helix formed by residues 441 - 446 (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 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435A LEU* 4.3 2.5 - - - -
439A GLU 4.1 0.4 + - - -
440A TYR* 1.3 78.9 - - - +
442A ARG* 1.3 64.0 + - - +
443A GLU* 3.7 10.0 + - - +
444A GLU* 3.0 46.0 + - - +
445A ILE* 3.4 11.4 + - - +
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Residues in contact with ARG 442 (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 PHE* 5.4 5.0 - - - -
430A ALA* 2.8 31.5 + - + +
431A SER* 4.3 0.2 - - - +
432A ASP* 2.8 36.7 + - - +
435A LEU* 3.5 37.4 - - + +
441A SER* 1.3 73.6 - - - +
443A GLU* 1.3 76.2 + - - +
445A ILE* 3.3 2.6 + - - +
446A LEU* 2.9 52.4 + - + +
584A SER* 4.4 27.0 - - - +
586A ASN* 6.3 1.1 - - - -
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Residues in contact with GLU 443 (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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441A SER* 3.3 8.3 + - - +
442A ARG* 1.3 95.9 + - - +
444A GLU* 1.3 65.1 + - - +
445A ILE 3.3 0.5 + - - -
446A LEU* 3.4 5.8 - - + +
564A ILE* 5.7 2.0 - - + -
567A THR* 3.9 13.2 + - - +
568A THR* 3.5 33.5 - - + +
582A ASN 5.6 0.9 - - - -
583A TYR* 4.2 26.9 - - + -
584A SER 5.6 1.9 + - - +
1727A CA 2.6 28.8 - - - -
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Residues in contact with GLU 444 (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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439A GLU 4.7 0.2 - - - +
440A TYR* 3.5 15.0 - - + -
441A SER* 3.0 43.7 + - - +
443A GLU* 1.3 80.0 - - - +
445A ILE* 1.3 64.7 + - + +
448A ARG* 3.0 28.5 + - - +
485A LYS* 2.7 35.7 + - - -
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Residues in contact with ILE 445 (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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427A ILE* 3.5 27.6 - - + +
430A ALA* 3.5 31.4 - - + -
434A PHE* 4.3 12.1 - - + -
435A LEU* 4.6 5.8 - - + -
440A TYR* 3.3 40.4 - - + -
441A SER 3.4 8.5 + - - +
442A ARG 3.3 3.3 + - - +
443A GLU 3.2 0.2 - - - -
444A GLU* 1.3 82.1 - - - +
446A LEU* 1.3 73.2 + - + +
448A ARG* 3.1 27.7 + - - +
452A PHE* 3.5 26.5 - - + -
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Residues in contact with LEU 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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427A ILE* 3.4 26.0 - - + +
428A ILE 3.9 4.0 - - - +
429A PHE* 3.8 19.5 - - - +
430A ALA* 3.9 8.7 - - + +
442A ARG* 2.9 36.1 + - + +
443A GLU* 3.4 3.0 - - + +
445A ILE* 1.3 83.9 - - + +
447A GLY* 1.3 55.5 + - - +
448A ARG* 4.3 2.8 - - - +
581A ASP* 3.8 1.1 - - - -
582A ASN 3.3 26.7 - - - +
583A TYR* 3.6 14.1 - - + -
584A SER* 3.4 24.5 - - - +
1727A CA 2.5 29.2 - - - -
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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