Contacts of the helix formed by residues 232 - 241 (chain H) in PDB entry 1P8J
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 THR 232 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453E GLU* 3.1 21.2 + - - +
456E VAL* 4.7 8.3 - - + -
565E LYS* 6.3 0.2 - - - -
230H GLU* 3.1 35.6 + - + +
231H VAL* 1.3 76.1 - - - +
233H ASP* 1.3 65.5 + - - +
234H ALA* 3.5 4.4 + - - -
235H VAL* 3.1 29.0 + - + +
236H GLU* 3.1 15.9 + - - +
4045H SO4 3.3 28.9 - - - +
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Residues in contact with ASP 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530E ASP* 4.3 6.9 - - - +
565E LYS* 6.2 1.1 - - - -
232H THR* 1.3 72.5 - - - +
234H ALA* 1.3 57.5 + - - +
236H GLU* 3.1 9.6 + - - +
237H ALA* 2.9 26.6 + - - +
267H ALA* 3.3 27.6 - - + +
268H ARG* 3.5 6.8 + - - +
269H LEU* 2.7 33.9 + - + +
270H ALA* 2.9 27.7 + - - +
4045H SO4 3.0 21.2 + - - +
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Residues in contact with ALA 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451E ILE* 4.2 14.1 - - + -
453E GLU* 3.4 35.0 - - + +
565E LYS* 6.5 0.4 - - + -
567E THR* 4.7 8.1 - - + +
232H THR* 3.9 1.9 - - - +
233H ASP* 1.3 81.0 - - - +
235H VAL* 1.3 57.8 + - - +
237H ALA* 3.5 2.2 + - - +
238H ARG* 3.0 36.9 + - + +
269H LEU* 4.2 16.0 - - + +
4045H SO4 5.3 0.8 + - - -
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Residues in contact with VAL 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453E GLU* 3.9 16.2 - - - +
175H VAL* 3.7 23.0 - - + +
176H ASN* 4.2 7.6 - - - +
226H MET* 3.6 41.7 - - + +
230H GLU 4.0 12.8 - - - +
231H VAL* 4.6 4.5 - - + -
232H THR* 3.1 27.7 + - + +
234H ALA* 1.3 73.5 - - - +
236H GLU* 1.3 64.4 + - - +
238H ARG* 3.4 1.9 + - - +
239H SER* 2.8 29.6 + - - -
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Residues in contact with GLU 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226H MET* 4.2 9.2 - - + -
231H VAL* 3.5 24.2 - - + +
232H THR 3.1 15.7 + - - +
233H ASP* 3.7 7.5 - - - +
235H VAL* 1.3 75.5 - - - +
237H ALA* 1.3 59.5 + - - +
239H SER* 3.1 1.7 + - - -
240H LEU* 2.8 40.2 + - + +
254H TRP* 3.5 21.0 - - + -
266H PRO* 4.5 0.5 - - - +
267H ALA 4.9 0.9 + - - -
270H ALA* 3.8 15.9 - - + +
308H TYR* 2.4 31.0 + - - -
802R ARG* 3.0 27.7 + - - +
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Residues in contact with ALA 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451E ILE* 3.7 20.5 - - + +
233H ASP 2.9 16.8 + - - +
234H ALA* 3.7 2.7 - - - +
236H GLU* 1.3 78.7 - - - +
238H ARG* 1.3 56.2 + - - +
241H GLY* 3.1 25.1 + - - -
269H LEU* 3.6 36.1 - - + +
270H ALA* 4.3 2.4 - - - +
273H ALA* 3.7 17.3 - - + +
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Residues in contact with ARG 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451E ILE* 3.7 42.6 + - + +
452E VAL* 5.7 0.2 - - - +
453E GLU* 4.5 14.4 + - - -
474E CYS* 5.4 4.0 - - - -
477E GLU* 3.7 25.7 + - - -
173H PHE* 4.2 8.8 - - - -
175H VAL* 3.7 37.4 + - + +
178H GLN* 3.0 40.9 + - - +
234H ALA 3.0 26.9 + - - +
235H VAL 3.9 3.6 - - - +
237H ALA* 1.3 76.9 - - - +
239H SER* 1.3 63.2 + - - +
241H GLY* 3.7 2.1 - - - -
242H LEU* 3.2 25.1 + - - +
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Residues in contact with SER 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152H LEU* 3.8 15.7 - - - +
175H VAL* 3.7 4.9 - - - +
224H VAL* 3.7 16.5 - - - +
226H MET* 3.1 43.3 - - - +
235H VAL 2.8 20.8 + - - -
236H GLU 3.6 3.6 - - - -
238H ARG* 1.3 75.8 - - - +
240H LEU* 1.3 65.0 + - - +
241H GLY 3.2 0.9 + - - -
242H LEU* 3.2 16.9 + - - +
250H TYR* 3.7 9.4 - - - -
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Residues in contact with LEU 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152H LEU* 3.4 27.1 - - + -
236H GLU* 2.8 30.1 + - + +
239H SER* 1.3 73.1 - - - +
241H GLY* 1.3 56.8 + - - +
242H LEU 3.5 0.2 - - - -
250H TYR* 3.5 14.0 + - - -
254H TRP* 5.0 4.7 - - + -
270H ALA* 4.2 18.6 - - + +
273H ALA* 4.0 14.0 - - + +
274H PHE* 3.8 36.8 - - + -
277H GLY* 5.7 1.0 - - - -
287H SER* 5.1 0.7 + - - -
289H PHE* 3.5 34.0 - - + -
291H TRP* 4.0 24.9 - - + -
308H TYR* 5.3 2.2 - - + -
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Residues in contact with GLY 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479E ASN* 4.2 12.1 + - - -
237H ALA 3.1 17.3 + - - -
238H ARG* 3.7 4.9 - - - -
239H SER 3.1 0.2 - - - -
240H LEU* 1.3 78.5 - - - +
242H LEU* 1.3 61.3 + - - +
243H ASN 3.4 0.7 + - - -
244H PRO* 3.4 25.1 - - - +
250H TYR* 4.3 0.2 - - - -
273H ALA* 4.6 6.9 - - - +
276H ARG* 6.6 0.4 - - - -
277H GLY* 6.3 2.0 - - - -
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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
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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