Contacts of the helix formed by residues 389 - 394 (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 LEU 389 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A SER* 3.7 29.4 + - - +
195A LEU* 3.8 19.5 - - + -
198A PHE* 3.9 15.0 - - + -
258A MET* 3.8 22.2 - - + -
360A PHE* 3.8 15.3 - - + -
363A PHE* 3.7 28.7 - - + -
385A MET 4.1 6.7 - - - +
386A LEU 4.4 5.4 - - - +
387A ASN 3.4 2.6 - - - -
388A SER* 1.3 75.8 - - - +
390A TYR* 1.3 68.7 + - - +
391A GLY 3.2 2.0 - - - -
392A LYS* 3.1 17.0 + - + +
393A PHE* 3.7 20.9 - - + -
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Residues in contact with TYR 390 (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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226A TYR* 3.8 14.8 + - - -
254A TYR* 3.6 53.3 + + + -
258A MET* 3.9 14.4 - - - +
386A LEU 5.3 0.6 + - - -
387A ASN* 4.3 16.3 + - - -
389A LEU* 1.3 78.9 - - - +
391A GLY* 1.3 71.6 + - - +
393A PHE* 3.1 28.9 + - - +
394A ALA 4.3 1.4 + - - -
430A GLY* 4.5 7.6 - - - -
433A ILE* 3.8 29.8 - - + -
434A THR* 3.6 28.3 - - + +
4D C 5.6 1.8 - - - -
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Residues in contact with GLY 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A TYR* 4.2 6.5 + - - -
388A SER 4.4 3.5 + - - -
389A LEU 3.2 1.2 - - - +
390A TYR* 1.3 97.2 - - - +
392A LYS* 1.3 61.4 + - - +
393A PHE 3.2 0.6 + - - -
394A ALA* 3.5 10.7 + - - +
395A SER 3.9 1.4 + - - -
4D C 3.3 43.2 - - - +
5D T 5.0 0.2 - - - +
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Residues in contact with LYS 392 (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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191A GLY* 3.3 41.5 - - - +
192A SER* 3.9 10.9 - - - +
195A LEU* 4.1 31.9 - - + -
388A SER 3.8 6.9 + - - +
389A LEU* 3.1 10.3 + - - +
391A GLY* 1.3 75.2 - - - +
393A PHE* 1.3 65.0 + - - +
395A SER* 2.7 27.4 + - - +
425A VAL* 3.4 14.4 - - - +
3D A 4.3 14.5 + - - -
4D C 2.8 50.7 + - - +
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Residues in contact with PHE 393 (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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195A LEU* 4.7 3.8 - - + -
198A PHE* 3.8 26.5 - + - -
207A PHE* 4.3 9.9 - + - -
211A PHE* 4.1 25.1 - + - -
360A PHE* 3.8 26.5 - + - -
389A LEU* 3.7 24.9 - - + -
390A TYR* 3.1 21.9 + - - +
392A LYS* 1.3 81.1 - - + +
394A ALA* 1.3 55.6 + - - +
395A SER 3.4 2.0 + - - -
425A VAL* 3.6 11.8 + - + +
426A TYR* 2.9 51.2 + - + +
427A THR* 3.1 2.8 + - - -
429A MET* 3.8 22.2 - - + -
430A GLY 3.9 11.0 - - - +
433A ILE* 5.0 0.4 - - + -
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Residues in contact with ALA 394 (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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223A ARG* 2.8 29.8 + - - -
226A TYR* 3.5 45.8 - - + +
390A TYR 4.3 0.4 + - - +
391A GLY 3.5 7.0 + - - +
392A LYS 3.2 0.6 - - - -
393A PHE* 1.3 75.1 - - - +
395A SER* 1.3 60.3 + - - +
396A ASN 3.3 0.3 + - - -
427A THR* 3.8 23.8 - - + +
430A GLY* 4.5 4.7 - - - -
5D T 3.5 7.2 - - - +
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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