Contacts of the strand formed by residues 823 - 827 (chain A) in PDB entry 2XY7
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 ARG 823 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491A ALA* 4.1 26.7 + - - +
643A SER* 3.0 21.6 + - - -
644A GLU* 2.8 28.5 + - - -
647A TRP* 3.8 14.5 - - - -
815A LEU* 4.9 1.8 - - - -
821A GLN 3.3 7.0 + - - +
822A ALA* 1.3 75.2 - - - +
824A LEU* 1.3 65.1 + - - +
825A LEU* 3.6 5.8 + - + +
834A LEU* 3.2 7.7 - - - -
835A GLU* 2.8 58.2 + - + +
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Residues in contact with LEU 824 (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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484A ILE* 4.0 23.8 - - + -
488A MET* 3.5 36.5 - - + +
491A ALA* 4.8 1.2 - - - +
808A MET* 4.7 13.0 - - + +
811A LEU* 3.7 36.3 - - + -
812A ASN* 4.6 10.3 - - - +
815A LEU* 4.9 5.6 - - + +
823A ARG* 1.3 78.7 - - - +
825A LEU* 1.3 66.0 + - - +
826A LEU 4.3 4.9 - - - +
832A LEU* 4.1 24.5 - - + -
833A ILE 3.7 13.7 - - - +
834A LEU* 4.1 6.8 - - + +
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Residues in contact with LEU 825 (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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488A MET* 3.3 32.5 - - - +
491A ALA* 4.3 6.3 - - + -
492A GLY 3.6 21.1 - - - +
493A VAL* 3.8 28.0 - - + -
494A LYS 5.9 0.2 - - - +
606A PHE* 4.1 3.3 - - - -
641A VAL 5.6 1.6 - - - +
649A ILE* 4.6 9.2 - - + -
823A ARG* 4.0 10.8 - - + +
824A LEU* 1.3 82.4 - - - +
826A LEU* 1.3 65.9 + - + +
833A ILE* 2.9 21.5 + - + +
834A LEU 4.5 3.6 - - - +
835A GLU* 3.5 53.2 - - + +
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Residues in contact with LEU 826 (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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488A MET* 4.2 4.3 - - - -
493A VAL* 4.2 19.5 - - + -
604A THR* 4.7 1.3 - - + -
606A PHE* 3.8 21.1 - - + -
623A LEU* 3.4 46.0 - - + +
640A PHE* 6.2 0.2 - - + -
824A LEU* 4.3 4.0 - - - +
825A LEU* 1.3 84.5 - - + +
827A GLN* 1.3 64.3 + - - +
828A VAL* 5.0 2.0 - - + -
832A LEU* 3.5 4.2 - - - +
833A ILE* 2.9 45.2 + - + +
872A TRP* 3.9 37.5 - - + -
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Residues in contact with GLN 827 (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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488A MET* 4.3 10.5 - - + +
606A PHE* 4.1 11.8 - - + -
616A LEU* 4.3 23.5 - - + +
624A GLN* 3.1 27.5 + - - +
804A ILE* 3.5 21.8 - - + +
805A LYS* 5.3 1.0 - - - +
808A MET* 3.2 27.5 - - + +
826A LEU* 1.3 74.8 - - - +
828A VAL* 1.3 68.9 + - - +
829A HIS* 2.7 33.6 + - - +
831A GLU 3.4 6.3 - - - +
832A LEU* 3.3 26.7 - - + -
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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