Contacts of the helix formed by residues 232 - 241 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230E GLU* 3.1 41.0 + - + +
231E VAL* 1.3 77.4 - - - +
233E ASP* 1.3 64.6 + - - +
234E ALA* 3.4 2.6 + - - -
235E VAL* 3.0 18.4 + - + +
236E GLU* 3.1 23.6 + - - +
4060E SO4 2.9 24.0 - - - +
453H GLU* 3.0 26.7 + - - +
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Residues in contact with ASP 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E THR* 1.3 71.1 - - - +
234E ALA* 1.3 59.2 + - - +
236E GLU* 3.2 8.8 + - - +
237E ALA* 2.9 27.4 + - - +
267E ALA* 3.4 28.9 + - + +
268E ARG* 3.5 7.8 + - - +
269E LEU* 2.7 34.2 + - + +
270E ALA* 2.9 27.4 + - - +
4060E SO4 2.8 25.4 + - - +
530H ASP* 4.4 5.4 - - - +
565H LYS* 6.0 2.7 - - - -
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Residues in contact with ALA 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E THR* 3.2 2.5 + - - +
233E ASP* 1.3 80.4 - - - +
235E VAL* 1.3 56.1 + - - +
237E ALA* 3.4 2.3 + - - +
238E ARG* 2.9 37.1 + - + +
269E LEU* 4.2 14.5 - - + +
4060E SO4 4.2 1.4 + - - +
451H ILE* 4.0 17.0 - - + -
453H GLU* 3.5 35.4 - - + +
567H THR* 4.6 7.0 - - + +
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Residues in contact with VAL 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E VAL* 4.0 21.8 - - + +
176E ASN* 4.4 7.9 - - - +
226E MET* 3.6 42.4 - - + +
230E GLU 3.9 13.7 - - - +
231E VAL* 4.4 6.5 - - + -
232E THR* 3.0 30.6 + - + +
234E ALA* 1.3 76.2 - - - +
236E GLU* 1.3 61.1 + - - +
238E ARG* 3.4 2.6 + - - +
239E SER* 2.9 28.2 + - - -
453H GLU* 3.9 14.4 - - - +
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Residues in contact with GLU 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E MET* 4.1 9.2 - - + -
231E VAL* 3.7 17.1 - - + +
232E THR 3.1 15.3 + - - +
233E ASP* 3.7 8.5 - - - +
235E VAL* 1.3 75.4 - - - +
237E ALA* 1.3 58.7 + - - +
239E SER* 3.2 1.6 + - - -
240E LEU* 2.8 43.6 + - + +
254E TRP* 3.6 13.0 - - + -
266E PRO* 4.4 0.9 - - - +
267E ALA 4.8 0.9 + - - -
270E ALA* 3.7 16.0 - - + +
308E TYR* 2.4 31.6 + - - -
802N ARG* 2.9 38.3 + - - +
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Residues in contact with ALA 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E ASP 2.9 17.0 + - - +
234E ALA 3.8 4.3 - - - +
236E GLU* 1.3 78.2 - - - +
238E ARG* 1.3 60.8 + - - +
241E GLY* 3.1 20.6 + - - -
269E LEU* 3.5 37.0 - - + +
270E ALA* 4.3 2.1 - - - +
273E ALA* 3.7 16.2 - - + +
451H ILE* 3.8 16.9 - - + +
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Residues in contact with ARG 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E PHE* 4.3 9.3 - - - -
175E VAL* 3.8 31.1 + - + +
178E GLN* 2.6 49.2 + - - +
234E ALA 2.9 26.2 + - - +
235E VAL 3.9 3.1 - - - +
237E ALA* 1.3 76.3 - - - +
239E SER* 1.3 62.8 + - - +
241E GLY* 3.7 2.6 - - - -
242E LEU* 3.3 25.3 + - - +
451H ILE* 3.6 43.1 + - + +
452H VAL* 5.7 0.2 - - - +
453H GLU* 4.6 8.5 - - - +
474H CYS* 5.2 4.4 - - - -
477H GLU* 3.5 31.5 + - - -
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Residues in contact with SER 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E LEU* 3.9 16.2 - - - +
175E VAL* 3.7 5.4 - - - +
224E VAL* 3.6 15.6 - - - +
226E MET* 3.1 44.3 - - - +
235E VAL 2.9 21.3 + - - -
236E GLU 3.2 3.6 + - - -
238E ARG* 1.3 75.1 - - - +
240E LEU* 1.3 66.2 + - - +
241E GLY 3.2 0.7 + - - -
242E LEU* 3.2 17.1 + - - +
250E TYR* 3.8 7.6 - - - -
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Residues in contact with LEU 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E LEU* 3.3 27.8 - - + -
236E GLU* 2.8 41.0 + - + +
237E ALA 4.6 0.2 - - - +
239E SER* 1.3 73.1 - - - +
241E GLY* 1.3 58.1 + - - +
250E TYR* 3.5 20.3 + - - -
254E TRP* 4.9 3.4 - - + -
270E ALA* 4.5 13.7 - - + +
273E ALA* 4.1 14.4 - - + +
274E PHE* 3.9 32.3 - - + -
277E GLY* 5.7 1.2 - - - -
287E SER* 5.2 0.5 + - - -
289E PHE* 3.5 27.4 - - + -
291E TRP* 4.0 26.0 - - + -
308E TYR* 5.2 3.1 - - + -
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Residues in contact with GLY 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E ALA 3.1 16.7 + - - -
238E ARG* 3.7 4.9 - - - -
239E SER 3.1 1.0 - - - -
240E LEU* 1.3 78.3 - - - +
242E LEU* 1.3 59.3 + - - +
243E ASN 3.4 0.5 + - - -
244E PRO* 3.3 25.8 - - - +
273E ALA* 4.6 7.2 - - - +
276E ARG* 6.5 1.6 - - - -
277E GLY* 6.3 2.0 - - - -
479H ASN* 4.1 13.2 + - - -
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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