Contacts of the strand formed by residues 528 - 531 (chain A) 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 GLY 528 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515A ILE* 4.1 16.6 - - - -
527A LYS* 1.3 75.6 - - - +
529A MET* 1.3 59.4 + - - +
530A LEU 4.1 0.4 - - - -
566A LEU* 4.2 18.6 - - - -
571A ILE* 3.8 3.5 - - - +
573A ILE 2.7 15.0 + - - -
574A VAL* 4.2 6.3 - - - -
575A GLN* 2.8 28.3 + - - +
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Residues in contact with MET 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ILE* 3.7 0.9 - - - -
410A GLY* 3.5 28.0 - - - +
459A VAL* 3.9 20.0 - - + -
460A HIS* 4.3 9.6 - - + -
462A GLU* 3.8 22.9 - - + +
465A ARG* 3.0 38.0 + - - +
472A PHE* 3.8 1.2 - - - -
511A THR* 4.5 0.6 + - - +
515A ILE* 4.2 6.1 - - - +
527A LYS* 3.8 18.8 + - - +
528A GLY* 1.3 79.5 - - - +
530A LEU* 1.3 71.6 + - - +
566A LEU* 5.2 0.2 - - - +
575A GLN* 3.1 40.2 - - - +
577A ASP* 4.6 6.7 - - - +
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Residues in contact with LEU 530 (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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465A ARG* 5.7 0.2 - - - -
472A PHE* 3.9 21.3 - - + -
510A MET* 5.3 1.1 - - + -
511A THR* 4.3 8.7 - - - +
529A MET* 1.3 84.8 - - - +
531A THR* 1.3 66.2 + - - +
559A ILE* 4.2 17.5 - - + +
562A GLU* 3.7 24.2 - - + -
563A VAL* 3.6 31.0 - - + -
566A LEU* 4.3 10.1 - - + -
574A VAL* 3.7 17.3 - - + -
575A GLN 2.8 12.7 + - - +
576A ILE* 3.4 9.7 - - + -
577A ASP* 2.9 32.0 + - - +
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Residues in contact with THR 531 (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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468A MET* 2.6 45.8 + - - +
469A VAL* 4.1 2.2 - - + -
472A PHE* 3.6 18.1 - - - -
530A LEU* 1.3 74.6 + - - +
532A GLY* 1.3 72.1 + - - +
535A THR* 3.8 24.0 - - + -
536A ILE* 3.8 14.8 - - + +
559A ILE* 2.9 25.1 - - - +
576A ILE* 4.3 2.0 - - - -
577A ASP* 3.5 7.8 + - - +
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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