Contacts of the strand formed by residues 527 - 531 (chain B) in PDB entry 1XR2
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 LYS 527 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407B THR* 3.4 21.0 + - - +
408B THR 2.8 21.8 + - - -
409B ILE* 3.5 10.9 - - - +
457B VAL* 3.6 20.6 - - + -
458B LEU 2.8 12.5 + - - +
459B VAL* 4.1 7.5 - - + -
460B HIS* 4.7 1.6 + - - -
515B ILE* 3.9 11.0 - - - +
526B VAL* 1.3 82.0 - - - +
528B GLY* 1.3 66.5 + - - +
529B MET* 3.6 25.6 + - + +
571B ILE* 4.4 0.9 - - - -
573B ILE* 3.4 19.1 - - + +
575B GLN* 2.8 32.2 + - + +
616B HIS* 4.1 23.0 + - - -
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Residues in contact with GLY 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B ILE* 4.1 16.4 - - - -
526B VAL 3.8 0.6 + - - -
527B LYS* 1.3 77.9 - - - +
529B MET* 1.3 58.9 + - - -
530B LEU* 4.1 0.7 - - - -
566B LEU* 4.4 14.1 - - - -
571B ILE* 3.9 5.8 - - - +
573B ILE 2.8 15.3 + - - -
574B VAL* 4.3 7.0 - - - -
575B GLN* 2.9 29.0 + - - +
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Residues in contact with MET 529 (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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409B ILE 5.2 0.2 - - - -
410B GLY* 5.2 6.1 - - - +
459B VAL* 3.8 26.2 - - + -
460B HIS* 4.0 12.8 - - + +
462B GLU* 3.4 32.5 - - - +
465B ARG* 2.9 34.4 + - - +
472B PHE* 3.8 0.7 - - - -
511B THR* 4.5 0.8 + - - +
515B ILE* 4.2 6.9 - - - +
527B LYS* 3.6 36.2 + - + +
528B GLY* 1.3 70.9 - - - -
530B LEU* 1.3 69.4 + - - +
566B LEU* 5.3 0.2 - - - +
575B GLN* 3.7 35.2 - - - +
577B ASP* 4.7 8.3 - - - +
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Residues in contact with LEU 530 (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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465B ARG* 5.3 0.4 - - - -
472B PHE* 3.9 21.1 - - + -
510B MET* 5.1 1.3 - - + -
511B THR* 4.1 11.0 - - - +
529B MET* 1.3 84.2 - - - +
531B THR* 1.3 67.5 + - - +
559B ILE* 4.3 13.7 - - + -
562B GLU* 3.7 25.6 - - + -
563B VAL* 3.7 30.1 - - + -
566B LEU* 4.0 11.4 - - + -
574B VAL* 3.7 17.9 - - + -
575B GLN 2.8 15.4 + - - +
576B ILE* 3.3 9.3 - - + -
577B ASP* 2.8 32.5 + - - +
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Residues in contact with THR 531 (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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465B ARG* 5.4 0.5 + - - -
468B MET* 2.7 48.7 + - + +
469B VAL* 4.2 2.9 - - + -
472B PHE* 3.5 16.7 - - - -
530B LEU* 1.3 76.8 + - - +
532B GLY* 1.3 70.6 + - - +
535B THR* 3.9 19.3 - - + -
536B ILE* 3.8 14.8 - - + +
559B ILE* 3.0 23.8 - - - +
576B ILE* 4.1 2.6 - - - +
577B ASP* 3.6 11.8 + - - +
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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