Contacts of the helix formed by residues 460 - 469 (chain W) in PDB entry 6G0L
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 GLN 460 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-15J A 5.5 7.1 + - - -
459W ASN* 1.3 83.5 - - + +
461W LYS* 1.3 70.5 + - + +
463W ARG* 2.8 50.9 + - - +
464W ASP* 3.7 1.9 + - - +
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Residues in contact with LYS 461 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317W ASP* 3.3 41.4 + - + +
460W GLN* 1.3 76.9 - - + +
462W SER* 1.3 57.7 + - - +
464W ASP* 2.6 37.5 + - - +
465W THR* 3.5 8.7 + - + +
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Residues in contact with SER 462 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315W ASN* 3.1 34.9 + - - -
316W TYR* 4.2 4.9 + - - +
317W ASP* 4.6 4.4 + - - +
456W TYR* 5.4 2.0 - - - -
458W GLY* 3.2 23.7 - - - -
459W ASN 3.7 2.9 + - - +
460W GLN 3.4 1.2 - - - +
461W LYS* 1.3 77.1 - - - +
463W ARG* 1.3 66.7 + - - +
465W THR* 2.7 33.5 + - - -
466W ILE* 3.0 17.8 + - - +
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Residues in contact with ARG 463 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456W TYR* 4.1 22.0 - - + +
459W ASN 3.4 21.8 + - - +
460W GLN* 2.8 45.2 + - - +
462W SER* 1.3 79.8 - - - +
464W ASP* 1.3 56.2 + - - +
466W ILE* 3.9 3.1 + - - +
467W ARG* 3.0 44.3 + - - +
497W LYS* 4.0 25.1 - - - +
498W ASP* 4.2 17.7 + - - +
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Residues in contact with ASP 464 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460W GLN 3.7 1.9 + - - +
461W LYS* 2.6 17.9 + - - +
463W ARG* 1.3 71.0 - - - +
465W THR* 1.3 62.5 + - + +
466W ILE 3.2 1.8 - - - -
467W ARG* 3.0 10.0 + - - +
468W GLU* 2.8 30.3 + - - +
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Residues in contact with THR 465 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291W ILE* 5.6 5.2 - - - +
316W TYR* 3.1 53.6 - - + +
317W ASP* 5.2 2.2 - - - +
461W LYS* 4.2 11.0 - - + +
462W SER* 2.7 21.3 + - - -
464W ASP* 1.3 73.1 - - + +
466W ILE* 1.3 63.0 + - - +
467W ARG 3.1 0.2 - - - -
468W GLU* 3.5 18.2 + - - +
469W TYR* 3.5 14.4 + - - +
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Residues in contact with ILE 466 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316W TYR* 3.6 32.3 - - + -
454W ILE* 4.8 7.2 - - + -
455W CYS 3.4 25.6 - - - +
456W TYR* 3.4 36.8 - - + -
457W MET 5.5 0.7 - - - +
462W SER* 3.0 18.3 + - - +
463W ARG 3.9 5.2 - - - +
465W THR* 1.3 78.2 - - - +
467W ARG* 1.3 57.8 + - + +
469W TYR* 3.6 3.3 + - - +
470W GLU* 2.7 46.8 + - + +
488W LEU* 5.3 7.2 - - + -
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Residues in contact with ARG 467 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456W TYR* 6.4 0.4 - - - -
463W ARG* 3.0 33.3 + - - +
464W ASP* 3.0 11.6 + - - +
466W ILE* 1.3 83.1 - - + +
468W GLU* 1.3 64.3 - - - +
470W GLU* 3.2 20.4 + - + +
471W PHE* 3.3 22.8 + - + +
498W ASP* 3.8 16.4 + - - +
501W GLU* 3.4 43.8 + - - +
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Residues in contact with GLU 468 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291W ILE* 3.9 21.8 - - + +
292W ASP* 4.0 24.7 - - - +
308W LEU* 5.5 4.9 - - + -
464W ASP* 2.8 18.6 + - - +
465W THR* 3.6 13.2 - - - +
466W ILE 3.3 0.4 - - - -
467W ARG* 1.3 76.8 - - - +
469W TYR* 1.3 69.6 + - - +
471W PHE* 3.3 16.8 - - - +
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Residues in contact with TYR 469 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291W ILE* 4.7 17.7 - - + -
341W ARG* 4.0 21.1 + - - -
452W ASN* 2.9 24.8 + - - -
454W ILE* 4.1 32.5 - - + -
465W THR 3.5 11.0 + - - +
466W ILE* 4.2 3.1 - - - +
467W ARG 3.3 0.4 - - - -
468W GLU* 1.3 85.8 + - - +
470W GLU* 1.3 58.9 + - - +
471W PHE 3.1 8.5 + - - -
484W LYS* 2.7 59.8 + - + +
485W PHE* 4.1 15.4 - + + -
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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