Contacts of the helix formed by residues 459 - 464 (chain A) in PDB entry 5A63
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 THR 459 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A PRO* 3.5 25.6 - - + -
295A ALA* 3.3 12.4 - - - +
456A ILE 3.7 7.4 - - - +
457A TYR* 2.7 23.0 + - - +
458A ASP* 1.3 76.8 - - - +
460A ALA* 1.3 57.9 + - - +
461A GLU* 3.3 25.7 + - - +
462A ASN* 2.8 22.8 + - - +
463A ILE 3.1 8.8 + - - -
526A LEU* 5.6 0.7 - - - -
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Residues in contact with ALA 460 (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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295A ALA* 4.0 2.0 - - - +
459A THR* 1.3 72.4 - - - +
461A GLU* 1.3 53.7 + - + +
463A ILE* 3.1 13.1 + - - -
464A ASN 2.8 31.0 + - - -
465A VAL* 2.9 31.3 + - + +
526A LEU* 4.0 18.8 + - + +
527A ILE* 3.6 25.8 - - + -
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Residues in contact with GLU 461 (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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127A LYS* 3.8 20.7 - - - +
128A PRO 5.7 0.2 - - - +
129A SER* 4.9 6.8 + - - -
457A TYR 5.6 0.2 - - - +
459A THR* 3.1 14.3 + - - +
460A ALA* 1.3 78.0 - - + +
462A ASN* 1.3 61.5 + - - +
464A ASN* 3.5 11.0 + - - +
465A VAL 4.5 3.3 + - - +
466A SER* 6.4 1.1 - - - -
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Residues in contact with ASN 462 (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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295A ALA* 5.1 0.2 - - + -
296A GLU* 4.5 2.9 - - + +
370A LEU* 4.3 18.0 - - - +
450A ASN* 3.3 29.8 - - - +
451A LYS* 4.3 14.0 + - - +
452A TYR* 3.7 31.6 - - + +
457A TYR 4.0 6.4 + - - +
458A ASP* 3.3 11.4 + - - +
459A THR* 2.8 26.0 + - - +
461A GLU* 1.3 75.6 - - - +
463A ILE* 1.3 57.4 + - - +
464A ASN* 3.2 5.9 + - - +
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Residues in contact with ILE 463 (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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295A ALA* 4.2 10.3 - - + +
296A GLU* 4.7 6.5 - - + +
300A ALA* 3.1 23.8 - - + -
369A ALA* 2.9 38.8 - - + -
370A LEU* 4.9 4.9 - - + -
459A THR 3.1 3.9 + - - +
460A ALA* 3.1 10.5 + - - +
462A ASN* 1.3 76.5 - - - +
464A ASN* 1.3 60.3 + - - +
465A VAL* 3.4 23.8 - - + -
483A THR* 2.7 31.4 + - - +
487A LEU* 4.2 13.5 - - + -
522A LEU* 5.0 3.6 - - + -
526A LEU* 3.6 21.1 - - + -
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Residues in contact with ASN 464 (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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460A ALA 2.8 4.7 + - - -
461A GLU* 3.5 8.8 + - - +
462A ASN 3.2 6.8 - - - +
463A ILE* 1.3 80.5 - - - +
465A VAL* 1.3 60.4 + - - +
466A SER* 3.1 12.2 + - - -
481A THR* 4.1 4.9 + - - -
482A ASP* 5.9 0.6 - - - +
483A THR* 3.7 16.6 + - - +
1712A NAG 1.6 64.7 + - - +
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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