Contacts of the strand formed by residues 324 - 329 (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 ALA 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288B ILE 3.9 0.9 - - - +
289B ARG* 3.2 5.9 - - - -
290B CYS* 2.7 40.2 + - - +
292B PHE* 3.5 31.2 - - + -
304B ILE* 4.4 11.0 - - + -
319B SER* 4.3 5.6 - - - -
322B GLU 3.4 2.8 + - - -
323B ILE* 1.3 73.8 - - - +
325B ASP* 1.3 59.6 + - - +
326B LEU* 3.9 14.4 - - + +
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Residues in contact with ASP 325 (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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272A GLU* 6.1 2.3 - - - +
287B HIS* 2.6 32.2 + - - -
288B ILE 3.8 1.8 - - - -
289B ARG* 3.1 34.6 + - + -
304B ILE* 5.1 2.8 - - - +
323B ILE* 3.7 5.2 + - + +
324B ALA* 1.3 72.1 - - - +
326B LEU* 1.3 65.5 + - - +
327B TRP* 4.6 4.9 + - - -
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Residues in contact with LEU 326 (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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227B ARG* 4.4 16.6 - - - +
286B GLN 3.5 1.2 - - - +
287B HIS* 3.4 4.0 - - - -
288B ILE* 2.9 47.7 + - + +
290B CYS* 4.9 3.6 - - - -
292B PHE* 4.5 2.7 - - + -
302B ILE* 4.2 14.4 - - + -
304B ILE* 3.1 35.7 - - + -
324B ALA* 4.2 17.7 - - + +
325B ASP* 1.3 79.6 + - - +
327B TRP* 1.3 64.7 + - - +
328B LEU* 4.0 15.9 - - + -
336B MET* 3.5 34.5 - - + -
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Residues in contact with TRP 327 (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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272A GLU* 6.3 0.4 - - - +
221B GLU* 3.5 53.2 - - + +
224B TYR* 3.4 51.2 + + + +
225B ALA* 3.3 23.5 - - - +
227B ARG* 4.6 4.5 + - - +
285B ILE* 3.9 21.1 - - + -
286B GLN 3.3 4.5 - - - -
287B HIS* 3.3 56.7 + + + -
325B ASP* 4.6 4.0 + - - -
326B LEU* 1.3 77.3 - - - +
328B LEU* 1.3 67.4 + - - +
349B SER* 4.2 10.1 - - - -
350B GLY* 4.6 13.0 - - - -
351B LEU* 4.7 9.6 - - + -
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Residues in contact with LEU 328 (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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225B ALA* 4.4 1.1 - - - +
227B ARG* 5.1 8.3 - - - +
285B ILE* 4.1 4.8 - - - +
286B GLN* 2.8 37.8 + - - +
288B ILE* 3.5 25.8 - - + -
302B ILE* 4.2 9.0 - - + -
326B LEU* 4.0 16.8 - - + -
327B TRP* 1.3 81.4 - - - +
329B SER* 1.3 70.3 + - - +
330B ASN* 4.7 0.5 - - - -
332B ASP* 4.3 13.5 - - + -
333B LEU* 3.9 19.6 - - + +
336B MET* 2.6 40.6 - - + -
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Residues in contact with SER 329 (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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225B ALA* 4.3 6.9 - - - +
284B HIS 3.4 7.6 - - - -
285B ILE* 4.2 4.7 - - - +
328B LEU* 1.3 74.3 - - - +
330B ASN* 1.3 60.2 + - - +
331B VAL* 3.5 2.8 + - - +
332B ASP* 2.7 35.3 + - - -
333B LEU* 2.8 25.8 + - - +
431B VAL* 4.1 17.9 - - - -
432B PHE* 3.8 22.0 - - - -
435B ALA* 3.5 9.4 - - - +
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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