Contacts of the helix formed by residues 471 - 481 (chain A) in PDB entry 5KE6
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 ARG 471 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A ARG* 3.3 48.3 - - + +
452A ARG* 5.5 1.6 - - - +
460A PHE* 3.6 9.7 - - - -
469A PHE* 3.4 6.7 - - - +
470A SER* 1.3 91.7 + - - +
472A SER* 1.3 63.7 + - - +
473A ASP* 2.9 36.8 + - - +
474A HIS* 3.3 41.5 + - - +
475A LEU 3.3 8.7 + - - -
2B A 3.6 13.1 + - - +
3B G 2.8 48.7 + - - -
7C C 3.7 1.4 - - - +
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Residues in contact with SER 472 (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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460A PHE* 3.4 29.0 - - - -
471A ARG* 1.3 72.7 - - - +
473A ASP* 1.3 61.1 + - - +
475A LEU* 3.3 4.7 + - - +
476A ALA* 2.9 28.6 + - - +
5C C 2.9 49.2 + - - +
6C A 5.0 5.0 + - - -
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Residues in contact with ASP 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ARG* 2.9 48.3 + - - +
472A SER* 1.3 74.5 + - - +
474A HIS* 1.3 72.1 + - - +
476A ALA* 3.8 7.6 - - - +
477A LEU* 3.1 28.2 + - - +
2B A 5.4 0.2 + - - -
6C A 4.3 24.5 - - + +
7C C 2.9 24.4 + - + -
8C C 4.4 3.3 + - - -
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Residues in contact with HIS 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A PHE* 3.8 22.6 - + + +
470A SER* 4.2 10.6 + - - -
471A ARG* 3.3 42.3 + - + +
472A SER 3.3 0.2 - - - -
473A ASP* 1.3 96.3 + - - +
475A LEU* 1.3 62.5 + - - +
477A LEU* 3.4 9.9 + - + +
478A HIS* 3.1 21.5 + - - +
1B G 3.6 43.7 + + - -
2B A 3.0 35.3 + + - -
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Residues in contact with LEU 475 (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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460A PHE* 3.9 27.6 - - + +
461A GLN 4.0 15.0 - - - +
462A CYS* 3.6 33.7 - - + -
469A PHE* 3.8 25.0 - - + -
471A ARG 3.3 8.0 + - - +
472A SER* 3.3 7.7 + - - +
473A ASP 3.3 0.4 - - - -
474A HIS* 1.3 76.2 - - - +
476A ALA* 1.3 57.8 + - - +
478A HIS* 3.0 4.5 + - + +
479A MET* 2.7 50.1 + - + +
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Residues in contact with ALA 476 (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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472A SER 2.9 17.0 + - - +
473A ASP* 3.8 8.3 - - - +
475A LEU* 1.3 78.4 - - - +
477A LEU* 1.3 64.5 + - - +
479A MET* 3.5 8.6 + - - +
480A LYS* 3.4 31.0 + - - +
6C A 5.6 5.6 - - - +
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Residues in contact with LEU 477 (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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473A ASP 3.1 19.2 + - - +
474A HIS* 3.7 9.6 - - + +
475A LEU 3.2 0.2 - - - -
476A ALA* 1.3 74.1 - - - +
478A HIS* 1.3 67.5 + - - +
480A LYS* 3.2 35.0 + - + +
481A ARG* 3.9 7.9 + - - +
1B G 6.0 5.2 - - - +
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Residues in contact with HIS 478 (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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462A CYS* 3.8 9.0 - - + -
465A CYS* 3.3 4.3 - - - -
467A ARG* 3.7 31.6 + - - +
469A PHE* 3.5 34.3 - + + -
474A HIS 3.1 5.7 + - - +
475A LEU* 3.0 7.7 + - + +
477A LEU* 1.3 76.9 - - - +
479A MET* 1.3 61.8 + - - +
481A ARG* 2.8 50.8 + - + +
482A HIS* 3.0 11.6 + + - -
501A ZN 2.1 36.9 - - - -
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Residues in contact with MET 479 (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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462A CYS* 3.5 27.4 - - - -
463A GLN* 4.1 13.7 - - + +
464A LYS* 4.4 11.7 - - + +
475A LEU* 2.7 36.6 + - + +
476A ALA* 3.7 9.6 - - - +
478A HIS* 1.3 73.1 - - - +
480A LYS* 1.3 61.8 + - - +
482A HIS* 3.1 26.8 + - - +
483A PHE* 3.3 33.1 - - + -
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Residues in contact with LYS 480 (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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476A ALA* 3.4 20.0 + - - +
477A LEU* 3.2 25.0 + - + +
478A HIS 3.0 0.8 + - - -
479A MET* 1.3 79.3 - - - +
481A ARG* 1.3 58.0 + - + +
482A HIS 3.1 4.4 + - - -
483A PHE* 3.3 23.7 + - - +
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Residues in contact with ARG 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ARG* 5.6 4.8 - - - +
477A LEU 3.9 8.5 - - - +
478A HIS* 2.8 43.0 + - + +
480A LYS* 1.3 73.0 - - + +
482A HIS* 1.3 60.7 + - + +
483A PHE 3.4 2.0 - - - -
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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