Contacts of the strand formed by residues 459 - 463 (chain A) in PDB entry 2PY5
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 SER 459 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A VAL* 4.6 5.0 - - - +
248A PHE 3.2 9.6 - - - -
249A ASP* 3.2 18.0 + - - +
441A THR* 4.3 1.6 + - - +
455A CYS* 3.3 5.9 - - - +
456A ASP* 3.0 31.5 + - - -
457A THR 3.6 0.8 - - - -
458A ASP* 1.3 92.9 + - - +
460A ILE* 1.3 66.5 + - - +
461A HIS* 4.3 17.9 - - - -
486A GLU* 5.0 1.6 + - - -
9010A EDO 3.5 9.7 + - - -
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Residues in contact with ILE 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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246A MET 4.0 0.5 - - - +
247A VAL* 3.5 1.7 - - - -
248A PHE* 2.9 56.6 + - + +
441A THR* 4.0 13.7 - - + +
444A ALA* 4.1 29.2 - - + +
445A ALA* 4.1 5.2 - - + +
448A CYS* 4.7 1.3 - - - -
452A ILE* 4.0 8.7 - - + -
454A TYR 3.5 3.4 - - - -
455A CYS* 3.9 18.6 - - - -
459A SER* 1.3 78.8 - - - +
461A HIS* 1.3 65.4 + - - +
462A LEU* 4.5 14.6 - - + -
471A ILE* 4.6 15.5 - - + -
483A TRP* 3.9 20.6 - - + -
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Residues in contact with HIS 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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246A MET 3.4 6.7 - - - +
247A VAL* 3.9 23.0 - - + +
452A ILE* 3.6 4.5 - - - +
453A ILE* 2.9 29.9 + - + +
454A TYR* 2.9 43.1 + + + +
456A ASP* 5.5 0.6 - - - +
459A SER* 4.3 10.2 - - - -
460A ILE* 1.3 86.7 - - - +
462A LEU* 1.3 60.3 + - - +
489A PHE* 5.1 0.9 - - + -
494A TYR* 2.7 29.4 + - - +
500A TYR* 3.6 31.6 + + - -
502A GLN* 3.3 14.8 + - - -
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Residues in contact with LEU 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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245A GLY* 3.1 3.8 - - - -
246A MET* 2.8 38.7 + - + +
248A PHE* 3.9 26.2 - - + -
448A CYS* 3.8 23.6 - - + -
451A ARG* 3.2 15.9 - - + +
452A ILE* 3.7 27.4 - - + -
453A ILE* 3.5 9.2 - - - +
460A ILE* 4.5 8.1 - - + -
461A HIS* 1.3 80.8 - - - +
463A THR* 1.3 68.6 + - - +
468A PRO* 3.4 34.5 - - + -
471A ILE* 5.1 0.2 - - + -
489A PHE* 4.2 0.2 - - - -
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Residues in contact with THR 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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236A ARG* 5.1 1.1 + - - +
237A PHE* 3.5 38.7 - - + -
242A ILE* 4.5 9.0 - - + -
244A GLU 3.8 7.0 - - - -
245A GLY* 4.1 0.4 - - - -
450A ASP 4.7 1.4 + - - -
451A ARG* 2.8 59.5 + - - +
453A ILE* 3.6 12.1 - - + +
462A LEU* 1.3 73.9 - - - +
464A GLY* 1.3 61.0 + - - +
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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