Contacts of the strand formed by residues 461 - 465 (chain D) in PDB entry 2QY0
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 461 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458D PHE* 3.0 18.0 + - + +
459D PRO 3.4 2.3 - - - +
460D TRP* 1.3 86.6 + - + +
462D VAL* 1.3 85.4 + - - +
471D GLY* 3.9 6.5 - - - -
472D GLY 3.5 16.1 + - - +
504D LEU* 4.0 7.8 - - - +
505D GLY 4.7 8.8 + - - -
506D HIS 5.7 1.2 - - - +
512D LEU* 5.7 1.6 - - - +
556D LEU* 5.4 0.9 - - - +
577D SER* 2.6 40.0 + - - +
578D GLY* 4.6 2.4 - - - -
579D PHE* 3.6 16.1 - - + -
590D LEU* 3.5 34.8 - - + -
639D GLY* 4.6 6.5 - - - -
640D VAL* 5.3 2.9 + - - +
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Residues in contact with VAL 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460D TRP 3.5 15.3 - - - +
461D GLN* 1.3 92.2 + - - +
463D PHE* 1.4 74.2 + - - +
464D THR* 4.1 10.3 - - + -
471D GLY* 3.3 3.6 - - - -
472D GLY* 2.9 32.9 + - - +
473D ALA 3.9 1.8 - - - +
474D LEU* 3.8 11.0 - - - +
480D ILE* 4.1 16.8 - - + -
502D VAL* 3.8 15.9 - - + -
503D PHE 3.9 0.2 - - - -
504D LEU* 3.0 31.9 - - + -
579D PHE* 3.8 4.0 - - - -
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Residues in contact with PHE 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462D VAL* 1.4 73.7 - - - +
464D THR* 1.3 78.9 + - - +
465D ASN* 4.1 11.0 - - + -
469D ARG* 3.5 41.7 - - + -
470D GLY 3.8 3.1 - - - -
502D VAL* 3.4 3.3 - - - -
503D PHE* 2.8 55.6 + + + +
509D VAL* 3.7 18.8 - - + -
512D LEU* 3.9 16.8 - - + +
513D MET* 3.6 30.7 - - + -
579D PHE* 3.5 33.2 - + + -
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Residues in contact with THR 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462D VAL* 4.1 12.3 - - + -
463D PHE* 1.3 86.8 - - - +
465D ASN* 1.3 61.5 + - - +
466D ILE* 4.0 18.7 + - + +
468D GLY 5.0 0.3 + - - -
469D ARG* 3.5 4.5 - - - -
470D GLY* 2.9 50.0 + - - +
471D GLY 3.8 9.6 + - - +
480D ILE* 5.5 2.0 - - + -
482D THR* 5.7 2.0 - - + +
486D THR* 4.2 12.7 - - + +
501D ASP 3.2 11.4 - - - +
502D VAL* 4.0 15.5 - - + -
544D LEU* 4.7 8.7 - - + -
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Residues in contact with ASN 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A TYR* 2.8 38.9 + - + +
463D PHE* 4.1 14.8 - - + -
464D THR* 1.3 74.1 - - - +
466D ILE* 1.3 61.3 + - - +
468D GLY* 3.5 25.1 + - - -
469D ARG* 4.0 1.9 + - + -
499D SER* 3.6 2.4 - - - +
501D ASP* 3.0 31.6 + - + +
503D PHE* 5.1 0.9 - - + -
513D MET* 6.0 0.2 - - - -
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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