Contacts of the strand formed by residues 452 - 456 (chain B) 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 ILE 452 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B TRP* 4.0 24.5 - - + -
234B ASN* 3.0 27.5 + - - +
236B ARG* 5.0 0.2 + - - -
237B PHE* 3.4 7.8 - - - -
299B ILE* 4.5 1.1 - - + -
445B ALA* 3.8 32.1 - - + +
448B CYS 3.0 9.0 + - - +
449B TYR* 3.4 35.0 + - + +
451B ARG* 1.3 76.2 - - - +
453B ILE* 1.3 58.5 + - - +
454B TYR 3.8 15.0 - - - +
455B CYS* 4.1 2.5 - - - -
460B ILE* 4.0 9.4 - - + -
461B HIS 3.5 16.4 - - - +
462B LEU* 3.7 15.0 - - + -
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Residues in contact with ILE 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B TRP* 4.9 0.2 - - - -
233B LEU* 3.5 3.6 - - + +
234B ASN* 2.9 30.2 + - - +
237B PHE* 3.8 19.5 - - + -
242B ILE* 3.7 32.3 - - + -
452B ILE* 1.3 76.2 - - - +
454B TYR* 1.3 66.5 + - + +
461B HIS* 2.8 14.5 + - + +
462B LEU* 3.6 24.5 - - - +
463B THR* 3.7 24.5 - - + +
489B PHE* 3.9 17.7 - - + -
494B TYR* 3.8 23.3 - - + +
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Residues in contact with TYR 454 (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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231B THR* 3.8 3.0 - - + +
232B TRP* 3.2 26.9 - - - -
233B LEU* 4.0 12.6 - - + -
452B ILE* 3.8 5.2 - - - +
453B ILE* 1.3 81.4 - - + +
455B CYS* 1.3 75.7 + - - +
456B ASP* 3.6 26.5 + - + +
460B ILE* 3.5 2.4 - - - -
461B HIS* 2.9 55.6 + + + +
494B TYR* 3.8 24.9 - + + -
496B ARG 4.6 2.2 - - - -
497B GLN* 4.0 11.0 - - - -
498B LYS* 2.8 42.6 + - - +
500B TYR* 3.6 23.7 - + - -
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Residues in contact with CYS 455 (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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230B PHE* 3.7 36.8 - - + +
231B THR* 3.3 1.2 - - - -
232B TRP* 2.9 39.1 + - - +
299B ILE* 5.1 0.2 - - - -
441B THR* 4.1 6.3 - - + -
445B ALA* 3.5 31.6 - - - -
452B ILE* 4.1 4.5 - - - -
454B TYR* 1.3 86.6 - - - +
456B ASP* 1.3 63.1 + - - +
459B SER 3.2 8.5 - - - +
460B ILE* 4.0 9.4 - - - -
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Residues in contact with ASP 456 (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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230B PHE 3.5 2.0 - - - -
231B THR* 2.8 27.2 + - + -
454B TYR* 3.6 25.5 + - + +
455B CYS* 1.3 74.7 - - - +
457B THR* 1.3 67.3 + - - +
458B ASP* 2.7 22.7 + - - +
459B SER* 3.0 22.1 + - - -
461B HIS* 5.7 0.2 - - - +
498B LYS* 3.9 20.0 - - - +
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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