Contacts of the helix formed by residues 334 - 339 (chain B) in PDB entry 3PI5
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 GLY 334 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B ASP 3.2 11.9 - - - -
231B THR* 3.1 16.8 - - - -
233B ASN 3.2 21.3 + - - -
234B LEU* 4.5 1.2 - - - +
332B VAL 3.2 1.4 + - - -
333B MET* 1.3 77.7 - - - +
335B ALA* 1.3 60.3 + - - -
336B VAL 3.1 3.4 - - - -
337B ILE* 2.9 19.7 + - - +
338B MET* 3.1 12.8 + - - +
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Residues in contact with ALA 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR* 4.5 13.9 - - + -
154B LEU* 4.7 5.6 - - + -
228B ASP 4.1 1.4 + - - -
229B SER 4.9 4.7 + - - +
231B THR 2.7 15.7 + - - +
232B THR* 3.4 12.5 + - + +
334B GLY* 1.3 70.7 - - - -
336B VAL* 1.3 63.4 + - - +
338B MET* 3.8 10.3 - - - -
339B GLU* 2.9 50.0 + - + +
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Residues in contact with VAL 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B THR* 3.0 26.0 + - + +
233B ASN* 3.3 6.1 - - - +
234B LEU* 3.0 42.8 - - + +
300B ILE* 4.3 3.0 - - + +
304B GLN* 3.5 46.5 + - + +
305B TYR* 4.7 3.8 - - + -
307B ARG* 5.7 2.9 - - + -
323B ALA* 3.4 33.2 - - + +
334B GLY 4.2 1.6 - - - +
335B ALA* 1.3 77.1 - - - +
337B ILE* 1.3 66.5 + - + +
339B GLU* 4.2 7.1 - - - +
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Residues in contact with ILE 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 4.0 28.9 - - + -
285B LEU* 3.5 26.5 - - + -
298B ILE* 4.0 11.9 - - + -
300B ILE* 3.5 28.7 - - + -
304B GLN* 3.9 0.3 + - - -
333B MET* 3.8 36.6 - - + -
334B GLY 2.9 7.9 + - - +
336B VAL* 1.3 85.7 - - + +
338B MET* 1.3 67.6 - - + +
339B GLU 3.1 6.2 - - - +
341B PHE* 3.0 27.7 - - + -
354B PHE* 4.6 6.1 - - + -
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Residues in contact with MET 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU* 4.0 14.1 - - + +
154B LEU* 4.1 23.5 + - + +
227B VAL* 3.8 18.2 - - + -
228B ASP 4.1 3.6 - - - +
229B SER* 3.5 45.5 - - - -
333B MET 4.1 6.1 - - - +
334B GLY 3.1 12.0 + - - +
335B ALA* 4.2 1.6 - - - +
337B ILE* 1.3 82.6 - - + +
339B GLU* 1.3 58.7 + - - +
341B PHE* 2.9 30.2 + - - +
343B VAL* 4.2 23.1 - - + +
345B PHE* 3.9 26.5 - - + -
354B PHE* 5.7 0.4 - - + -
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Residues in contact with GLU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR* 2.6 31.8 + - - +
154B LEU* 3.0 19.5 - - + +
156B GLY* 3.9 21.2 - - - +
170B VAL* 5.4 1.9 - - - +
304B GLN* 3.1 35.1 + - + +
335B ALA* 2.9 43.7 + - + +
336B VAL* 4.5 8.2 - - - +
337B ILE 3.1 6.3 + - - +
338B MET* 1.3 71.6 - - - +
340B GLY* 1.3 60.2 + - - +
361B VAL* 5.6 7.0 - - + +
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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
------------------------------------------------------------
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