Contacts of the helix formed by residues 233 - 237 (chain A) in PDB entry 1P9B
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 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A GLY* 3.6 11.0 - - - +
23A GLN 3.2 8.1 - - - +
24A TRP* 4.0 0.7 - - - -
25A GLY 3.1 27.6 - - - +
27A GLU* 3.1 15.0 - - - +
231A ALA 3.4 1.4 + - - -
232A ASN* 1.3 83.0 - - - +
234A ALA* 1.3 58.7 + - - +
235A MET 3.4 0.7 - - - -
236A LEU* 2.9 22.1 + - + +
237A ASP 3.3 1.6 + - - -
251A THR* 2.6 24.7 + - - -
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Residues in contact with ALA 234 (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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21A GLY 3.1 16.3 + - - +
22A ALA 4.1 2.9 - - - +
233A ALA* 1.3 74.1 - - - +
235A MET* 1.3 59.9 + - - +
237A ASP* 3.0 25.3 + - - +
240A PHE* 4.2 3.8 - - - +
241A GLY 3.9 4.2 + - - -
251A THR* 3.6 8.2 + - - -
252A THR* 4.0 12.7 - - + +
326A VAL* 3.8 35.4 - - + -
329A ILE* 5.9 0.9 - - + -
330A ASN* 3.8 10.3 - - - +
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Residues in contact with MET 235 (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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22A ALA 4.0 3.8 - - - +
23A GLN 2.9 22.5 + - - +
24A TRP* 3.3 29.4 + - + +
234A ALA* 1.3 72.8 - - - +
236A LEU* 1.3 56.7 + - - +
237A ASP 3.4 0.2 - - - -
240A PHE 4.6 1.6 - - - +
241A GLY* 3.1 17.8 - - - -
242A THR* 3.1 19.9 + - + -
246A VAL* 3.8 0.2 - - - +
322A MET* 3.7 36.1 - - + -
325A TYR* 3.7 34.1 - - + -
326A VAL* 4.0 7.2 - - - -
369A TYR* 3.6 37.0 - - + -
371A VAL* 4.1 10.1 - - + -
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Residues in contact with LEU 236 (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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24A TRP* 3.7 45.1 - - + +
25A GLY 4.3 0.2 - - - +
232A ASN* 4.2 0.9 - - + -
233A ALA 2.9 22.0 + - - +
235A MET* 1.3 78.6 - - - +
237A ASP* 1.3 66.0 + - - +
245A TYR 4.0 6.5 - - - +
246A VAL* 3.5 7.2 - - - -
247A THR* 2.7 40.6 + - + +
280A ARG* 3.8 15.7 - - - +
1601A IMO 3.5 57.2 - - + +
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Residues in contact with ASP 237 (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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233A ALA 3.3 2.2 + - - -
234A ALA 3.0 17.7 + - - +
235A MET 3.4 0.2 - - - -
236A LEU* 1.3 78.7 - - - +
238A ILE* 1.3 64.3 - - - +
239A ASP* 2.8 15.1 + - - +
240A PHE* 2.7 47.6 + - + +
241A GLY* 2.8 25.3 + - - -
246A VAL* 3.6 3.6 - - - +
249A SER 4.1 2.7 - - - -
250A CYS* 3.3 9.6 - - - -
251A THR* 2.9 35.2 + - - +
252A THR* 3.1 15.1 + - + -
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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