Contacts of the helix formed by residues 389 - 395 (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 LEU 389 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B SER* 3.6 15.3 + - - +
195B LEU* 3.8 33.7 - - + -
198B PHE* 3.9 13.9 - - + -
258B MET* 3.6 25.4 - - + -
360B PHE* 3.8 15.7 - - + -
363B PHE* 3.7 28.0 - - + -
385B MET 4.2 6.5 - - - +
386B LEU 4.2 4.5 + - - +
387B ASN 3.4 2.0 - - - -
388B SER* 1.3 76.3 - - - +
390B TYR* 1.3 68.8 + - - +
391B GLY 3.1 3.5 + - - -
392B LYS* 3.1 16.9 + - - +
393B PHE* 3.8 18.1 - - + -
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Residues in contact with TYR 390 (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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226B TYR* 3.9 15.1 + - - -
228B GLY* 6.0 1.2 - - - -
254B TYR* 3.6 54.4 + + + -
258B MET* 3.8 24.7 - - - +
386B LEU 5.3 1.0 + - - -
387B ASN* 4.5 14.1 + - - -
389B LEU* 1.3 79.6 - - - +
391B GLY* 1.3 71.8 + - - +
392B LYS 3.1 1.4 + - - -
393B PHE* 3.1 28.0 + - - +
394B ALA 4.4 1.0 + - - -
430B GLY* 4.7 6.6 - - - -
433B ILE* 3.8 24.9 - - + -
434B THR* 3.6 23.9 - - + +
4E C 5.7 1.3 - - - -
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Residues in contact with GLY 391 (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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226B TYR* 4.5 6.5 + - - -
388B SER 4.6 3.4 + - - -
389B LEU 3.1 1.4 + - - -
390B TYR* 1.3 98.0 - - - +
392B LYS* 1.3 61.4 + - - +
393B PHE 3.4 0.7 + - - -
394B ALA* 3.6 11.9 + - - +
395B SER 3.9 1.6 + - - -
4E C 3.3 42.1 - - - +
5E T 5.0 0.7 - - - +
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Residues in contact with LYS 392 (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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191B GLY* 3.5 35.9 - - - +
192B SER* 3.9 6.0 - - - +
195B LEU* 4.0 33.5 - - + +
388B SER 3.9 11.0 - - - +
389B LEU* 3.1 9.7 + - - +
390B TYR 3.1 0.4 + - - -
391B GLY* 1.3 74.9 - - - +
393B PHE* 1.3 63.2 + - - +
395B SER* 2.7 27.5 + - - +
425B VAL* 3.5 12.5 - - - +
3E A 4.3 16.6 + - - -
4E C 2.8 51.8 + - - +
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Residues in contact with PHE 393 (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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195B LEU* 4.6 4.5 - - + -
198B PHE* 4.0 17.5 - + - -
207B PHE* 4.3 10.5 - + - -
211B PHE* 4.1 28.5 - + - -
360B PHE* 3.8 34.5 - + - -
389B LEU* 3.8 24.2 - - + -
390B TYR* 3.1 20.9 + - - +
392B LYS* 1.3 80.1 - - + +
394B ALA* 1.3 58.7 + - - +
395B SER 3.4 1.1 + - - -
425B VAL* 3.7 10.7 + - + +
426B TYR* 2.9 52.2 + - + +
427B THR* 3.1 2.4 + - - -
429B MET* 3.8 24.0 - - + -
430B GLY 4.0 5.4 - - - +
433B ILE* 5.0 2.5 - - + -
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Residues in contact with ALA 394 (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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223B ARG* 2.8 17.5 + - - -
226B TYR* 3.4 46.0 - - + +
390B TYR 4.4 0.4 + - - -
391B GLY 3.6 7.2 + - - +
392B LYS 3.2 0.8 - - - -
393B PHE* 1.3 76.4 - - - +
395B SER* 1.3 66.3 + - - +
396B ASN 3.3 0.7 + - - -
427B THR* 3.9 22.4 - - + +
430B GLY* 4.5 4.9 - - - -
5E T 3.6 8.5 - - - +
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Residues in contact with SER 395 (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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223B ARG* 3.2 12.1 + - - -
391B GLY 3.9 0.8 + - - -
392B LYS* 2.7 37.0 + - - +
393B PHE 3.4 1.6 + - - -
394B ALA* 1.3 75.8 - - - +
396B ASN* 1.3 64.2 + - - +
397B PRO* 3.6 3.3 - - - +
423B ASP 6.1 0.4 - - - -
424B PRO* 4.7 9.4 - - - +
425B VAL* 4.1 16.2 + - - +
427B THR* 4.5 1.7 + - - -
4E C 3.6 27.5 + - - -
5E T 3.9 0.9 - - - -
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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