Contacts of the strand formed by residues 479 - 482 (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 TRP 479 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474D LEU* 3.4 8.8 - - - +
475D LEU* 2.7 47.0 + - + +
476D GLY* 5.5 1.3 - - - -
478D ARG* 1.3 100.5 - - + +
480D ILE* 1.3 60.9 + - - +
481D LEU 4.2 0.2 - - - -
522D ARG* 4.3 13.7 - - - -
524D SER* 5.3 2.9 - - - -
543D LEU* 3.9 29.6 - - + -
544D LEU 3.4 18.4 - - - -
545D GLU* 3.5 46.4 - - + -
546D LEU 5.1 0.2 - - - +
683D GLU* 3.3 28.3 - - + -
684D MET* 3.5 46.4 + - + +
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Residues in contact with ILE 480 (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 33.4 - - + -
464D THR* 5.5 1.1 - - + -
472D GLY* 4.4 2.5 - - - -
473D ALA 3.5 3.1 - - - +
474D LEU* 4.6 8.3 - - + -
479D TRP* 1.3 78.5 - - - +
481D LEU* 1.3 72.9 + - - +
482D THR* 4.1 2.2 + - - -
502D VAL* 3.4 31.9 - - + -
504D LEU* 4.7 3.8 - - + -
520D ILE* 4.4 6.1 - - + -
543D LEU* 3.4 7.4 - - - +
544D LEU* 2.7 57.6 + - + +
546D LEU* 3.7 27.1 - - + -
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Residues in contact with LEU 481 (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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472D GLY* 3.2 5.7 - - - -
473D ALA* 2.9 40.2 + - + +
475D LEU* 4.0 25.0 - - + +
479D TRP 4.2 0.4 - - - -
480D ILE* 1.3 73.2 - - - +
482D THR* 1.3 61.0 + - - +
541D ILE* 3.8 23.3 - - + -
542D ALA 3.6 16.2 - - - +
543D LEU* 3.6 15.7 - - + +
561D LEU* 4.3 15.5 - - + -
638D GLY 3.8 1.2 - - - +
640D VAL* 4.9 4.2 - - + +
653D ALA* 4.7 9.4 - - + -
656D ILE* 3.7 20.2 - - + -
673D VAL* 4.5 9.9 - - + -
680D ILE* 4.1 13.0 - - + -
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Residues in contact with THR 482 (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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464D THR* 5.9 2.0 - - + -
471D GLY 2.7 25.0 + - - -
472D GLY* 4.2 1.6 - - - -
480D ILE* 4.9 2.2 - - + -
481D LEU* 1.3 76.4 - - - +
483D ALA* 1.4 71.8 + - - +
486D THR* 4.1 14.3 - - + +
487D LEU* 4.9 2.0 - - + -
541D ILE* 3.5 4.3 - - - -
542D ALA* 2.8 41.3 + - + +
544D LEU* 4.4 27.8 - - + -
638D GLY* 3.0 13.8 - - - -
656D ILE* 3.6 13.5 - - - +
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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