Contacts of the helix formed by residues 456 - 464 (chain A) in PDB entry 6E7P
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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444A TRP* 3.6 9.4 - - - +
455A ARG* 1.3 78.1 - - - +
457A LEU* 1.3 65.1 + - - +
458A SER* 3.1 22.0 + - - -
459A MET* 3.2 19.5 + - - +
460A VAL* 3.1 22.9 + - - +
88B GLN* 4.8 9.9 - - - +
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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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440A CYS* 5.1 11.4 - - + +
441A PHE* 3.7 32.8 - - + -
444A TRP* 3.5 50.0 - - + -
456A SER* 1.3 75.6 - - - +
458A SER* 1.3 58.5 + - - +
460A VAL* 3.9 7.1 - - - +
461A SER* 2.9 33.4 + - - -
81B ILE* 5.8 3.4 - - + -
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Residues in contact with SER 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* 3.1 15.3 + - - -
457A LEU* 1.3 77.3 - - - +
459A MET* 1.3 56.7 + - - +
461A SER* 4.3 4.3 - - - -
462A GLU* 3.2 20.8 + - - +
481D GLN* 3.1 28.5 + - - -
484D GLN* 4.3 13.8 + - - -
491D TRP* 4.3 21.5 - - - -
495D GLN* 4.8 3.4 + - - +
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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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452A VAL* 3.9 15.0 - - + +
453A LYS* 3.2 25.6 - - - +
455A ARG* 4.7 9.9 - - + -
456A SER* 3.2 19.7 + - - +
457A LEU 3.1 0.4 - - - -
458A SER* 1.3 79.4 + - - +
460A VAL* 1.3 53.8 + - - +
461A SER 3.3 0.4 - - - -
462A GLU* 3.0 8.3 + - - +
463A CYS* 2.6 37.9 + - - +
474D PHE* 4.7 9.2 - - + -
481D GLN* 3.3 28.7 - - + +
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Residues in contact with VAL 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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439A TYR 4.8 1.1 - - - +
440A CYS* 3.9 25.6 - - + +
443A GLY* 5.1 2.0 - - - -
444A TRP* 4.4 15.3 - - + +
454A PHE* 3.7 41.1 - - + +
456A SER 3.1 17.9 + - - +
457A LEU* 3.2 6.5 + - - +
459A MET* 1.3 76.1 - - - +
461A SER* 1.3 56.9 + - - +
463A CYS* 4.2 5.4 - - - +
464A LEU* 2.9 51.9 + - + +
497A TYR* 5.4 0.4 - - - +
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Residues in contact with SER 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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436A TYR* 2.8 32.0 + - - -
440A CYS* 4.3 12.0 - - - -
457A LEU 2.9 17.0 + - - -
458A SER* 4.8 4.9 - - - -
460A VAL* 1.3 76.4 - - - +
462A GLU* 1.3 53.6 + - - +
465A PHE* 3.3 9.1 - - - +
499D TYR* 2.8 29.5 + - - -
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Residues in contact with GLU 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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458A SER 3.2 15.7 + - - +
459A MET* 3.0 10.6 + - - +
461A SER* 1.3 76.4 - - - +
463A CYS* 1.3 58.3 + - - +
464A LEU 3.2 1.8 - - - -
465A PHE* 3.8 1.8 - - - +
466A SER* 2.9 34.2 + - - -
474D PHE* 4.2 11.4 - - + -
477D PHE* 3.4 53.5 - - + +
478D ALA* 4.4 1.6 + - - -
481D GLN* 3.3 22.1 + - - -
495D GLN* 3.2 30.1 + - - +
499D TYR* 3.7 12.1 - - - +
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Residues in contact with CYS 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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453A LYS* 3.7 34.1 - - - +
454A PHE* 3.5 32.5 - - + -
459A MET 2.6 21.1 + - - +
460A VAL 4.3 0.4 - - - +
462A GLU* 1.3 72.5 - - - +
464A LEU* 1.3 58.7 + - - +
466A SER* 3.7 8.6 + - - -
467A LEU* 3.2 23.9 - - - +
472A ASP* 5.5 2.1 - - - +
476A THR* 4.0 14.4 - - - -
474D PHE* 4.1 15.7 - - + -
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Residues in contact with LEU 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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436A TYR* 4.2 8.1 - - + -
439A TYR* 4.2 11.2 - - + +
440A CYS* 3.8 16.8 - - - -
454A PHE* 4.6 14.1 - - + -
460A VAL* 2.9 39.0 + - + +
463A CYS* 1.3 81.5 - - - +
465A PHE* 1.3 63.6 + - - +
466A SER 3.3 0.4 - - - -
467A LEU* 3.1 19.4 + - + +
468A ILE* 3.3 18.2 + - - +
497A TYR* 3.9 30.3 - - + +
498A LEU* 5.1 2.7 - - + -
501A PHE* 3.7 31.3 - - + -
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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