Contacts of the strand formed by residues 660 - 665 (chain A) in PDB entry 2Y48
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 ASN 660 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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658A ASN* 3.5 9.9 + - - -
659A LEU* 1.3 77.0 - - - +
661A LYS* 1.3 69.0 + - - +
706A LEU* 3.5 5.4 - - - -
707A VAL* 3.0 48.8 + - + +
712A ALA 3.9 9.7 + - - -
715A MET* 6.5 0.2 - - + -
716A GLU* 2.9 37.8 + - - +
748A VAL* 5.7 2.0 - - + -
749A SER* 2.4 37.9 + - - +
751A TRP* 3.2 17.5 + - - -
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Residues in contact with LYS 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A ASP 3.5 20.6 + - - +
329A LEU* 4.0 22.5 - - + +
330A GLY 3.2 22.9 + - - -
332A MET* 3.3 38.5 - - - +
538A PHE* 6.2 1.4 - - - -
659A LEU* 5.2 4.7 - - - -
660A ASN* 1.3 80.6 - - - +
662A VAL* 1.3 65.8 + - - +
663A VAL* 4.1 0.7 - - + -
704A LEU* 3.7 21.1 - - + -
705A ALA 3.6 3.1 - - - -
706A LEU* 4.4 13.0 - - + -
747A VAL 3.9 0.7 - - - +
748A VAL* 3.5 5.4 - - - +
749A SER* 2.7 37.5 + - - +
900A FAD 3.9 21.8 + - + -
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Residues in contact with VAL 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661A LYS* 1.3 78.3 - - - +
663A VAL* 1.3 69.6 + - - +
664A LEU* 4.4 11.5 - - + +
691A LEU* 4.0 11.4 - - + -
703A LEU 3.6 1.2 - - - +
704A LEU* 3.4 6.6 - - - +
705A ALA* 2.9 47.7 + - + +
707A VAL* 4.1 10.5 - - + -
723A ILE* 3.7 28.9 - - + -
724A VAL* 4.6 5.6 - - + -
727A CYS* 4.3 11.9 - - - -
747A VAL 3.5 2.5 - - - +
748A VAL* 3.7 23.6 - - + -
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Residues in contact with VAL 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A PHE* 4.6 8.7 - - + -
327A ALA* 3.8 24.0 - - + +
328A ASP 5.0 1.1 - - - +
329A LEU* 3.9 28.9 - - + -
661A LYS* 5.2 0.4 - - + -
662A VAL* 1.3 76.2 - - - +
664A LEU* 1.3 64.5 + - - +
665A CYS* 4.1 13.7 - - - -
702A ILE* 3.5 24.0 - - + -
703A LEU 3.9 1.8 - - - -
704A LEU* 4.4 12.3 - - + -
746A THR* 3.2 12.8 - - - -
747A VAL* 2.9 41.9 + - + +
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Residues in contact with LEU 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662A VAL* 4.4 13.2 - - + +
663A VAL* 1.3 81.1 - - - +
665A CYS* 1.3 62.4 - - - +
666A PHE* 4.0 21.1 + - + -
694A PHE* 4.6 7.6 - - + -
701A PRO 4.0 0.3 - - - +
702A ILE* 3.1 6.6 - - - +
703A LEU* 2.7 49.0 + - + +
705A ALA* 5.3 0.7 - - + -
724A VAL* 3.5 31.4 - - + -
727A CYS* 3.7 31.0 - - + -
728A LEU* 5.2 1.8 - - + -
731A LEU* 4.3 18.8 - - + -
743A PRO* 4.4 6.3 - - + -
745A GLU 4.1 0.2 - - - -
746A THR* 3.9 7.6 - - + -
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Residues in contact with CYS 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A PHE* 4.4 6.3 - - - -
325A TYR* 3.5 51.6 - - + -
663A VAL* 4.1 14.1 - - - -
664A LEU* 1.3 72.6 - - - +
666A PHE* 1.3 59.6 + - - +
701A PRO 4.0 2.9 - - - -
702A ILE* 3.8 13.2 - - - -
743A PRO* 3.5 5.0 - - - +
744A LYS* 2.7 33.8 + - - +
745A GLU* 2.9 31.3 + - + +
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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