Contacts of the helix formed by residues 232 - 241 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453F GLU* 2.8 27.7 + - - +
565F LYS* 6.0 0.7 - - + -
230G GLU* 3.1 35.0 + - + +
231G VAL* 1.3 77.1 - - - +
233G ASP* 1.3 65.2 + - - +
234G ALA* 3.5 2.8 + - - -
235G VAL* 3.1 18.7 + - + +
236G GLU* 3.1 24.2 + - - +
4032G SO4 3.5 28.9 - - - +
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Residues in contact with ASP 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530F ASP* 4.4 5.7 - - - +
565F LYS* 4.7 6.3 + - - +
232G THR* 1.3 73.1 - - - +
234G ALA* 1.3 58.6 + - - +
236G GLU* 3.2 9.4 + - - +
237G ALA* 2.9 27.3 + - - +
267G ALA* 3.3 28.3 + - + +
268G ARG* 3.6 6.8 + - - +
269G LEU* 2.8 34.5 + - + +
270G ALA* 3.0 26.9 + - - +
4032G SO4 3.3 21.1 + - - +
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Residues in contact with ALA 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451F ILE* 3.8 18.2 - - + -
453F GLU* 3.4 35.7 - - + +
567F THR* 4.6 7.0 - - + +
232G THR* 3.2 1.5 + - - +
233G ASP* 1.3 81.8 - - - +
235G VAL* 1.3 56.7 + - - +
237G ALA* 3.8 1.6 - - - +
238G ARG* 3.0 37.4 + - + +
269G LEU* 4.1 15.8 - - + +
4032G SO4 4.6 0.8 + - - -
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Residues in contact with VAL 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453F GLU* 3.8 15.7 - - - +
175G VAL* 3.8 22.5 - - + +
176G ASN* 4.3 7.2 - - - +
226G MET* 3.7 41.3 - - + +
230G GLU 3.9 13.7 - - - +
231G VAL* 4.6 5.8 - - + -
232G THR* 3.1 26.4 + - + +
234G ALA* 1.3 77.8 - - - +
236G GLU* 1.3 62.2 + - - +
238G ARG* 3.4 2.4 + - - +
239G SER* 2.8 28.9 + - - -
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Residues in contact with GLU 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226G MET* 4.2 9.0 - - + -
231G VAL* 3.6 22.6 - - + +
232G THR 3.1 16.4 + - - +
233G ASP* 3.7 7.7 - - - +
235G VAL* 1.3 74.8 - - - +
237G ALA* 1.3 59.1 + - - +
239G SER* 3.2 1.0 + - - -
240G LEU* 2.8 40.8 + - + +
254G TRP* 3.5 21.5 - - + -
266G PRO* 4.4 0.5 - - - +
267G ALA 4.9 0.9 + - - -
270G ALA* 3.7 16.4 - - + +
308G TYR* 2.4 29.4 + - - -
802Q ARG* 2.9 31.1 + - - +
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Residues in contact with ALA 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451F ILE* 3.7 19.6 - - + +
233G ASP 2.9 16.5 + - - +
234G ALA 3.8 2.2 - - - +
236G GLU* 1.3 76.8 - - - +
238G ARG* 1.3 56.4 + - - +
241G GLY* 3.1 24.6 + - - -
269G LEU* 3.5 36.6 - - + +
270G ALA* 4.3 1.9 - - - +
273G ALA* 3.8 17.5 - - + +
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Residues in contact with ARG 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451F ILE* 3.5 44.1 + - + +
452F VAL* 5.6 0.4 - - - +
453F GLU* 4.9 9.9 + - - -
474F CYS* 4.9 5.7 - - - -
477F GLU* 3.2 36.8 + - - -
173G PHE* 4.2 15.8 - - - -
175G VAL* 4.0 29.7 + - + +
178G GLN* 4.3 21.0 - - - +
234G ALA* 3.0 27.5 + - - +
235G VAL 3.9 3.4 - - - +
237G ALA* 1.3 76.3 - - - +
239G SER* 1.3 63.1 + - - +
241G GLY* 3.7 1.9 - - - -
242G LEU* 3.3 26.2 + - - +
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Residues in contact with SER 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152G LEU* 3.9 15.7 - - - +
175G VAL* 3.6 8.8 - - - +
224G VAL* 4.1 12.1 - - - -
226G MET* 3.2 43.0 - - - +
235G VAL 2.8 20.9 + - - -
236G GLU 3.2 3.3 + - - -
238G ARG* 1.3 76.4 - - - +
240G LEU* 1.3 65.6 - - - +
241G GLY 3.2 0.5 + - - -
242G LEU* 3.3 17.9 + - - +
250G TYR* 3.7 8.8 - - - -
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Residues in contact with LEU 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152G LEU* 3.6 23.3 - - + -
236G GLU* 2.8 32.2 + - + +
239G SER* 1.3 73.2 - - - +
241G GLY* 1.3 57.4 + - - +
250G TYR* 3.6 13.8 + - - -
254G TRP* 5.1 2.9 - - + -
270G ALA* 4.2 20.0 - - + +
273G ALA* 4.0 13.8 - - + +
274G PHE* 3.8 33.7 - - + -
277G GLY* 5.7 1.4 - - - -
287G SER* 5.2 0.7 + - - -
289G PHE* 3.6 33.4 - - + -
291G TRP* 3.9 28.5 - - + -
308G TYR* 5.4 2.2 - - + -
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Residues in contact with GLY 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479F ASN* 4.0 14.2 + - - -
237G ALA 3.1 17.8 + - - -
238G ARG* 3.7 4.7 - - - -
239G SER 3.1 0.2 - - - -
240G LEU* 1.3 78.7 - - - +
242G LEU* 1.3 59.7 + - - +
243G ASN 3.5 0.5 + - - -
244G PRO* 3.4 24.9 - - - +
273G ALA* 4.6 7.1 - - - +
276G ARG* 6.4 2.0 - - - -
277G GLY* 6.3 2.5 - - - -
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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