Contacts of the strand formed by residues 236 - 240 (chain A) in PDB entry 3PU3
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 TYR 236 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A OGA 4.1 12.1 - - - +
193A THR 4.8 0.2 - - - +
194A ASN* 3.7 44.3 + - - -
195A LEU 3.2 3.4 - - - -
196A GLU* 3.7 16.6 - - + -
197A PHE* 3.6 3.0 - - - -
232A LYS 3.6 3.3 + - - -
233A VAL* 3.3 54.5 - - - +
235A LYS* 1.3 75.0 - - - +
237A CYS* 1.3 60.4 + - - +
238A LEU* 3.8 17.3 - - + -
332A PHE* 3.0 11.5 - - - +
333A ALA* 2.6 50.6 + - + +
334A GLY* 4.0 1.8 - - - -
335A HIS* 3.4 23.7 - + - -
361A THR* 5.3 4.7 + - - -
362A GLN 5.6 0.5 + - - -
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Residues in contact with CYS 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A VAL* 4.0 15.5 - - - -
192A VAL* 3.7 6.6 - - - +
195A LEU* 2.9 40.3 + - + +
197A PHE* 3.7 4.6 - - + -
202A MET* 3.7 31.9 - - + -
236A TYR* 1.3 73.8 - - - +
238A LEU* 1.3 65.5 + - - +
239A ILE* 4.1 8.3 - - - -
330A LEU* 3.5 25.8 - - - -
331A ALA 3.5 2.5 - - - -
332A PHE* 4.0 9.0 - - + -
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Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A OGA 4.1 13.0 - - - +
192A VAL 3.2 4.9 - - - +
193A THR* 3.9 33.7 - - + +
236A TYR* 3.8 28.3 - - + +
237A CYS* 1.3 79.4 - - - +
239A ILE* 1.3 62.9 + - - +
240A CYS* 4.0 8.3 - - - -
259A TYR* 3.8 27.1 - - + -
266A LYS* 4.6 10.7 + - - +
329A CYS 3.6 1.2 - - - +
330A LEU* 3.3 8.1 - - - +
331A ALA* 2.6 51.1 + - + +
333A ALA* 3.8 13.9 - - + -
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Residues in contact with ILE 239 (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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146A VAL* 3.8 34.8 - - + -
149A VAL* 4.5 15.0 - - + -
174A LEU* 5.0 8.1 - - + -
177A PHE* 3.8 33.0 - - + -
178A VAL* 6.1 0.2 - - + -
181A TYR* 3.9 16.6 - - + -
191A ASN* 3.4 4.5 - - - +
192A VAL* 2.8 47.6 + - + +
195A LEU* 5.1 1.3 - - + -
237A CYS* 4.1 12.6 - - - -
238A LEU* 1.3 76.5 - - - +
240A CYS* 1.3 61.5 - - - +
329A CYS 3.6 5.2 - - - +
330A LEU* 3.8 15.5 - - + -
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Residues in contact with CYS 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A OGA 5.7 0.4 - - - -
181A TYR* 4.9 1.4 - - - -
191A ASN* 3.3 28.7 - - - +
193A THR* 4.0 17.7 - - - -
238A LEU* 4.5 2.7 - - - -
239A ILE* 1.3 82.6 - - - +
241A VAL* 1.3 61.7 + - - +
244A SER* 3.4 0.4 - - - +
266A LYS* 2.8 36.6 - - - +
325A THR* 3.4 19.8 - - + +
328A ASP* 3.4 1.4 - - - +
329A CYS 2.8 35.7 + - - +
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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