Contacts of the helix formed by residues 464 - 469 (chain B) 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 LEU 464 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436B TYR* 4.2 8.5 - - + -
439B TYR* 4.2 11.2 - - + +
440B CYS* 3.8 17.0 - - - -
454B PHE* 4.6 13.9 - - + -
460B VAL* 2.9 39.0 + - + +
463B CYS* 1.3 80.4 - - - +
465B PHE* 1.3 63.7 + - - +
466B SER 3.3 0.2 - - - -
467B LEU* 3.1 19.5 + - + +
468B ILE* 3.3 18.9 + - - +
497B TYR* 3.9 31.2 - - + +
498B LEU* 5.1 2.7 - - + -
501B PHE* 3.7 31.5 - - + -
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Residues in contact with PHE 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473A MET* 5.0 0.9 - - - -
477A PHE* 4.9 7.4 - + - -
499A TYR* 3.7 26.9 - + + -
502A ILE* 3.5 34.3 - - + -
503A SER* 4.2 20.4 - - - -
507A TYR* 4.5 18.6 - + - -
436B TYR* 3.4 21.0 + + - +
461B SER 3.3 20.2 - - - +
462B GLU 3.4 3.3 + - - +
464B LEU* 1.3 79.7 - - - +
466B SER* 1.3 62.1 + - - +
467B LEU 3.1 1.0 + - - -
468B ILE* 3.6 21.4 - - + +
469B ASN* 3.2 27.2 + - - -
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Residues in contact with SER 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A MET* 3.7 24.7 - - - -
474A PHE* 3.5 35.5 - - - +
477A PHE* 5.1 3.4 - - - -
462B GLU 2.9 23.7 + - - -
463B CYS* 3.7 8.3 + - - -
465B PHE* 1.3 76.9 - - - +
467B LEU* 1.3 58.0 + - - +
468B ILE 3.6 0.4 - - - -
469B ASN* 4.1 3.0 + - - +
470B GLY 3.9 2.4 + - - -
471B ASP* 2.9 33.9 + - - +
472B ASP* 5.2 0.5 - - - +
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Residues in contact with LEU 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B PHE* 5.6 1.3 - - + -
463B CYS* 3.2 24.0 - - - +
464B LEU* 3.1 13.1 + - + +
466B SER* 1.3 78.7 + - - +
468B ILE* 1.3 59.7 + - - +
469B ASN 3.2 1.3 - - - -
470B GLY 3.1 13.9 + - - -
471B ASP 3.9 6.7 - - - +
472B ASP 4.3 9.0 - - - +
473B MET* 3.4 24.3 - - + +
476B THR* 4.0 24.7 - - + +
477B PHE* 5.9 2.2 - - + -
498B LEU* 4.7 19.5 - - + -
501B PHE* 4.6 12.3 - - + -
502B ILE* 3.2 42.9 - - + +
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Residues in contact with ILE 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507A TYR* 3.5 22.7 - - - +
436B TYR* 5.9 2.0 - - + -
464B LEU 3.7 11.0 - - - +
465B PHE* 3.6 26.5 - - + +
467B LEU* 1.3 76.5 - - - +
469B ASN* 1.3 68.2 + - - +
470B GLY 3.2 0.6 + - - -
501B PHE* 3.7 17.5 - - + +
502B ILE* 3.7 12.3 - - + -
505B PHE* 3.6 48.7 - - + +
506B ILE* 3.6 21.7 - - + +
510B LEU* 5.9 1.2 - - - +
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Residues in contact with ASN 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A ASN 4.7 2.6 - - - +
470A GLY* 4.3 13.0 - - - +
473A MET* 3.2 42.3 - - + +
502A ILE* 4.0 9.5 - - - +
506A ILE* 3.5 28.5 - - + +
507A TYR* 3.7 17.5 + - - -
465B PHE* 3.2 24.5 + - - -
466B SER 4.4 2.2 - - - +
467B LEU 3.2 0.6 - - - -
468B ILE* 1.3 78.8 - - - +
470B GLY* 1.3 60.6 + - - +
506B ILE* 5.8 0.9 - - - -
469C ASN 4.7 4.0 - - - +
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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