Contacts of the strand formed by residues 324 - 329 (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 ALA 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A ILE 3.7 1.4 - - - +
289A ARG* 3.2 6.2 - - - -
290A CYS* 2.8 39.1 + - - +
292A PHE* 3.7 29.4 - - + -
304A ILE* 3.9 18.6 - - + -
322A GLU 3.4 4.3 + - - +
323A ILE* 1.3 72.1 - - - +
325A ASP* 1.3 60.5 + - - +
326A LEU* 3.9 16.0 - - + +
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Residues in contact with ASP 325 (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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287A HIS* 2.6 34.8 + - - -
288A ILE 3.8 2.0 - - - -
289A ARG* 2.7 39.5 + - - +
304A ILE* 5.7 1.1 - - - +
323A ILE 3.7 4.0 + - - +
324A ALA* 1.3 72.3 - - - +
326A LEU* 1.3 64.3 + - - +
327A TRP* 4.3 7.6 + - - -
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Residues in contact with LEU 326 (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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227A ARG* 3.9 18.6 - - - +
286A GLN 3.5 1.2 - - - +
287A HIS* 3.3 4.0 - - - -
288A ILE* 2.8 43.3 + - + +
290A CYS* 4.7 5.2 - - - -
302A ILE* 4.7 13.7 - - + -
303A GLN 5.3 2.0 - - - +
304A ILE* 4.4 23.8 - - + -
324A ALA* 4.1 21.8 - - + +
325A ASP* 1.3 82.1 + - - +
327A TRP* 1.3 64.4 + - - +
328A LEU* 4.0 20.6 - - + -
336A MET* 3.9 27.6 - - - -
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Residues in contact with TRP 327 (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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221A GLU* 3.5 51.4 - - + +
224A TYR* 3.4 56.0 + + + +
225A ALA* 3.2 11.4 - - - +
227A ARG* 3.0 25.0 + - - +
285A ILE* 3.9 17.5 - - + -
286A GLN 3.4 4.7 - - - -
287A HIS* 3.3 52.7 + + + -
325A ASP* 4.3 5.7 + - - -
326A LEU* 1.3 77.3 - - - +
328A LEU* 1.3 59.5 + - - +
349A SER* 3.8 13.5 - - - -
350A GLY* 4.5 4.3 - - - -
351A LEU* 3.9 11.4 - - + -
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Residues in contact with LEU 328 (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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225A ALA* 4.5 0.2 - - - -
227A ARG* 3.6 32.1 - - - +
285A ILE* 3.2 4.6 - - - +
286A GLN* 2.8 38.7 + - + +
288A ILE* 4.1 10.1 - - + -
326A LEU* 4.0 15.7 - - + -
327A TRP* 1.3 75.7 - - - +
329A SER* 1.3 72.0 + - - +
332A ASP* 4.2 14.4 - - + +
333A LEU* 4.0 24.8 - - + +
336A MET* 3.7 38.1 - - + -
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Residues in contact with SER 329 (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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225A ALA* 4.2 8.1 + - - +
284A HIS 3.4 7.0 - - - -
285A ILE* 4.2 4.7 - - - -
328A LEU* 1.3 74.7 - - - +
330A ASN* 1.3 58.6 + - - +
331A VAL 3.5 1.6 + - - -
332A ASP* 2.7 37.3 + - - -
333A LEU* 2.8 25.8 + - - +
431A VAL* 4.1 16.8 - - - -
432A PHE* 3.8 22.7 - - - -
435A ALA* 3.4 10.9 - - - +
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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