Contacts of the strand formed by residues 520 - 525 (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 ILE 520 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480D ILE* 4.4 1.1 - - + -
500D LEU* 3.5 42.7 + - + +
502D VAL* 3.9 25.8 - - + -
518D HIS 3.6 5.4 - - - +
519D PRO* 1.3 72.2 - - - +
521D ARG* 1.3 62.1 + - - +
522D ARG 3.2 30.5 - - - +
523D VAL* 4.0 2.2 - - + -
544D LEU* 4.1 19.3 - - + -
545D GLU 3.4 7.2 - - - +
546D LEU* 3.3 31.4 - - + -
547D GLU* 5.0 1.1 - - - -
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Residues in contact with ARG 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478D ARG* 4.3 16.4 - - - +
520D ILE* 1.3 73.4 - - - +
522D ARG* 1.3 59.8 + - + +
545D GLU* 2.7 30.8 + - - +
546D LEU 4.1 2.2 - - - +
547D GLU* 3.5 48.3 - - - +
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Residues in contact with ARG 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479D TRP* 4.3 12.5 - - - -
520D ILE* 3.2 8.2 - - - +
521D ARG* 1.3 85.0 - - + +
523D VAL* 1.3 77.6 + - - +
524D SER* 3.1 25.6 + - - -
543D LEU 4.6 0.2 - - - -
544D LEU* 3.5 0.9 - - - -
545D GLU* 2.8 51.8 + - + +
683D GLU* 3.1 30.3 + - - +
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Residues in contact with VAL 523 (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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487D LEU* 3.4 31.6 - - + -
488D TYR* 5.3 4.7 - - + +
500D LEU* 3.3 34.8 - - + -
520D ILE* 4.0 0.2 - - + -
522D ARG* 1.3 87.8 - - - +
524D SER* 1.3 66.7 + - - +
525D VAL* 4.2 13.0 + - + -
543D LEU 3.4 3.8 - - - +
544D LEU* 3.8 10.5 - - + -
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Residues in contact with SER 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479D TRP* 5.3 2.9 - - - -
522D ARG* 3.1 19.8 + - - -
523D VAL* 1.3 75.3 + - - +
525D VAL* 1.3 63.3 + - - +
542D ALA* 3.2 5.2 - - - +
543D LEU* 2.8 48.5 + - - +
679D TRP* 3.8 10.4 - - - -
683D GLU* 2.8 34.3 + - - +
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Residues in contact with VAL 525 (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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484D ALA* 3.8 21.8 - - + -
487D LEU* 4.1 8.3 - - + -
488D TYR* 3.6 35.7 - - + -
523D VAL* 4.1 5.3 + - + -
524D SER* 1.3 75.2 - - - +
526D HIS* 1.3 75.8 + - - +
527D PRO* 3.5 5.4 - - - +
529D TYR* 4.2 13.5 - - + -
542D ALA* 4.1 15.3 - - + -
679D TRP* 4.1 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