Contacts of the strand formed by residues 520 - 525 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480B ILE* 4.7 0.2 - - + -
500B LEU* 3.7 42.9 + - + +
502B VAL* 3.9 26.0 - - + -
518B HIS 3.7 6.3 - - - +
519B PRO* 1.3 73.6 - - - +
521B ARG* 1.3 62.9 - - - +
522B ARG 3.6 22.2 - - - +
523B VAL* 4.1 4.7 - - + -
544B LEU* 4.1 21.3 - - + -
545B GLU 3.6 4.7 - - - +
546B LEU* 3.3 31.6 - - + -
547B GLU* 4.5 1.1 - - - -
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Residues in contact with ARG 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B ARG* 4.5 9.9 - - - +
520B ILE* 1.3 75.4 - - - +
522B ARG* 1.3 76.8 + - + +
545B GLU* 2.8 41.5 + - - +
546B LEU 4.2 1.6 - - - +
547B GLU* 3.4 44.6 - - - +
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Residues in contact with ARG 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B TRP* 3.2 34.7 - - + -
520B ILE* 3.6 5.4 - - - +
521B ARG* 1.3 98.4 - - + +
523B VAL* 1.3 75.5 + - - +
524B SER* 4.6 7.4 + - - +
543B LEU 4.0 0.5 - - - +
544B LEU* 3.7 0.5 - - - -
545B GLU* 2.9 50.9 + - + +
683B GLU* 3.5 22.8 + - - +
686B GLU* 4.4 21.0 - - - +
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Residues in contact with VAL 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B LEU* 3.5 26.7 - - + -
488B TYR* 4.9 9.2 - - + +
500B LEU* 3.4 33.7 - - + -
520B ILE* 4.1 1.1 - - + -
522B ARG* 1.3 85.0 - - - +
524B SER* 1.3 67.7 + - - +
525B VAL* 4.0 14.8 + - + +
543B LEU 3.6 4.5 - - - +
544B LEU* 3.9 11.7 - - + -
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Residues in contact with SER 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B TRP* 5.3 3.8 - - - -
522B ARG* 4.6 10.4 + - - +
523B VAL* 1.3 77.7 + - - +
525B VAL* 1.3 62.7 + - - +
542B ALA* 3.1 2.9 - - - -
543B LEU* 2.7 54.2 + - - +
679B TRP* 3.5 6.8 - - - -
683B GLU* 2.5 39.5 + - - +
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Residues in contact with VAL 525 (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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484B ALA* 3.7 24.7 - - + -
487B LEU* 4.2 2.5 - - + -
488B TYR* 3.6 35.2 - - + -
523B VAL* 4.0 13.6 - - + +
524B SER* 1.3 77.2 - - - +
526B HIS* 1.3 75.5 + - - +
527B PRO* 3.6 4.2 - - - +
529B TYR* 4.1 12.6 - - + +
542B ALA* 4.0 13.5 - - + -
679B TRP* 3.7 6.5 - - - -
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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