Contacts of the strand formed by residues 668 - 672 (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 GLY 668 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622B CYS* 3.1 7.3 - - - +
623B ALA 2.9 36.7 + - - -
624B GLY* 5.1 0.2 - - - -
631B ASP* 4.5 17.1 + - - -
659B TRP 4.1 4.9 - - - -
660B GLY* 5.1 1.1 - - - -
666B GLY 4.2 0.8 + - - -
667B TYR* 1.3 74.1 - - - +
669B PHE* 1.3 60.4 + - - -
670B TYR* 3.4 14.7 - - - -
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Residues in contact with PHE 669 (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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603B CYS* 4.3 10.8 - - + -
606B TRP* 4.0 14.4 - + - -
607B LEU* 4.0 16.6 - - + -
616B PHE* 3.8 46.9 - + - -
620B MET* 5.2 2.9 - - + -
621B PHE 3.4 2.5 - - - -
622B CYS* 4.3 8.3 - - + -
657B VAL* 5.4 0.5 - - - +
658B SER* 3.2 22.5 + - - -
659B TRP* 2.9 81.1 + + - +
660B GLY* 4.3 1.3 - - - -
667B TYR* 3.5 22.2 - - + -
668B GLY* 1.3 74.8 - - - -
670B TYR* 1.3 66.8 + - - +
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Residues in contact with TYR 670 (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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576B VAL* 3.6 7.1 - - + +
595B LEU* 3.3 24.9 - - - +
620B MET* 3.2 8.2 - - - +
621B PHE* 2.9 55.9 + + + +
623B ALA* 3.6 19.0 + - + -
631B ASP* 4.4 9.2 + - - -
632B ALA* 4.7 5.9 - - + +
641B PHE* 3.7 32.3 - + + -
656B ILE 3.2 9.9 - - - +
657B VAL* 3.7 39.9 - - + -
658B SER* 4.2 1.8 - - - -
659B TRP* 6.3 0.2 - - - -
668B GLY* 3.4 29.3 - - - -
669B PHE* 1.3 79.3 - - - +
671B THR* 1.3 63.5 + - - +
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Residues in contact with THR 671 (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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537B PHE 5.0 0.3 + - - -
539B GLY 5.4 0.2 - - - +
540B ASP* 2.6 44.7 + - - +
541B ILE* 4.2 9.6 - - + -
619B ASN 3.8 6.3 - - - +
620B MET* 4.5 4.6 - - + +
655B GLY* 3.1 21.0 - - - -
656B ILE* 3.0 20.2 + - + -
658B SER* 3.9 8.6 - - - -
670B TYR* 1.3 69.6 - - - +
672B LYS* 1.3 58.7 + - - +
673B VAL* 3.1 9.2 + - - +
676B TYR* 3.4 38.8 - - + +
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Residues in contact with LYS 672 (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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565B ASP* 3.3 26.5 + - - -
568B TYR* 3.9 39.1 - - + +
618B GLN 3.6 19.3 + - - +
619B ASN* 2.8 25.8 + - - +
620B MET* 3.8 13.4 + - - +
621B PHE* 4.0 8.1 - - + +
654B THR 3.9 3.6 - - - -
670B TYR 3.2 2.6 + - - -
671B THR* 1.3 66.8 - - - +
673B VAL* 1.3 66.4 + - - +
674B LEU* 3.0 3.8 + - - +
675B ASN* 3.1 31.2 + - - +
676B TYR* 3.5 13.2 - - - -
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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