Contacts of the helix formed by residues 235 - 243 (chain C) in PDB entry 1JPW
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 GLY 235 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199C VAL* 3.5 12.8 - - - +
203C GLN* 5.3 1.4 - - - +
232C PHE 3.0 3.9 + - - -
233C LYS 3.6 1.4 - - - -
234C SER* 1.3 82.1 - - - +
236C GLY* 1.3 61.7 + - - +
237C ILE 3.4 2.5 - - - -
238C PRO* 3.2 23.1 - - - +
239C ALA* 3.5 8.1 + - - +
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Residues in contact with GLY 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C VAL* 3.9 16.1 - - - +
218C LEU* 5.0 1.5 - - - +
231C ILE* 3.0 29.6 + - - -
232C PHE 3.4 1.0 + - - -
234C SER 3.3 1.8 - - - -
235C GLY* 1.3 78.6 - - - +
237C ILE* 1.3 52.1 + - - +
239C ALA* 3.6 3.5 + - - +
240C LEU* 2.7 42.6 + - - +
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Residues in contact with ILE 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C ILE 4.3 1.2 + - - -
232C PHE* 3.9 26.8 + - + -
236C GLY* 1.3 71.6 - - - +
238C PRO* 1.3 75.8 - - + +
239C ALA 3.0 1.6 - - - -
240C LEU* 2.8 16.0 + - + +
241C VAL* 2.9 19.3 + - + +
259C LEU* 4.7 2.2 - - + -
262C LEU* 3.4 31.2 - - + -
269C ALA* 3.9 17.0 - - + +
272C ALA* 3.7 29.2 - - + +
273C VAL* 3.9 36.8 - - + +
276C ALA* 4.3 0.2 - - + -
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Residues in contact with PRO 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C GLN* 4.2 11.6 + - - +
235C GLY* 3.2 24.0 - - - +
237C ILE* 1.3 95.7 - - + +
239C ALA* 1.3 58.8 + - - +
241C VAL* 3.4 4.7 + - - +
242C LYS* 3.4 18.2 + - - +
272C ALA* 5.6 2.5 - - + +
276C ALA* 3.9 21.2 - - + +
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Residues in contact with ALA 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C VAL* 3.7 19.5 - - + +
202C MET* 4.7 7.6 - - - -
203C GLN* 3.7 32.3 - - + +
218C LEU* 6.1 0.4 - - + -
235C GLY 3.5 11.5 + - - +
236C GLY 3.6 9.0 - - - +
238C PRO* 1.3 81.0 - - - +
240C LEU* 1.3 60.9 + - + +
242C LYS* 3.4 5.9 + - - +
243C MET* 3.3 27.7 + - - +
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Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C MET* 3.9 13.2 - - + -
215C ALA* 6.2 0.2 - - + -
218C LEU* 3.6 27.4 - - + -
231C ILE* 4.3 5.4 - - + -
236C GLY 2.7 28.6 + - - +
237C ILE* 2.8 6.7 + - - +
239C ALA* 1.3 74.9 - - - +
241C VAL* 1.3 64.1 + - - +
242C LYS 3.1 2.5 + - - -
243C MET* 3.3 17.0 + - - +
244C LEU* 3.7 11.3 + - - +
255C ALA* 3.9 13.2 - - + +
258C THR* 3.1 35.9 - - + -
259C LEU* 3.2 22.7 - - + +
262C LEU* 3.6 22.4 - - + -
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Residues in contact with VAL 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C ILE* 2.9 20.2 + - + +
238C PRO 3.4 6.0 + - - +
240C LEU* 1.3 77.2 - - - +
242C LYS* 1.3 60.5 + - - +
244C LEU* 3.3 19.0 - - + +
259C LEU* 3.9 21.8 - - + -
273C VAL* 4.6 2.2 - - + -
276C ALA* 3.6 34.8 - - + +
277C GLY 3.9 0.2 - - - +
278C GLY* 3.7 20.6 - - - -
281C LYS* 2.8 43.7 + - + +
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Residues in contact with LYS 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C GLN* 4.2 28.7 - - + +
238C PRO 3.4 10.0 + - - +
239C ALA* 3.4 12.1 - - - +
241C VAL* 1.3 77.0 - - - +
243C MET* 1.3 82.0 + - + +
244C LEU 2.8 11.6 + - - -
245C GLY* 3.0 14.5 + - - -
246C SER 4.4 0.5 + - - -
281C LYS* 3.6 11.2 + - - +
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Residues in contact with MET 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C MET* 3.0 64.8 - - - +
203C GLN* 3.9 1.6 - - - -
205C THR* 5.9 0.2 - - - -
211C ALA* 5.0 6.7 - - - -
215C ALA* 5.8 1.1 - - + -
239C ALA 3.3 10.5 - - - +
240C LEU* 3.3 10.5 + - + +
242C LYS* 1.3 111.9 - - + +
244C LEU* 1.3 55.4 + - - +
245C GLY 3.2 2.2 - - - -
246C SER* 3.0 27.0 - - - -
251C VAL* 4.1 25.3 - - + +
252C LEU* 3.9 5.5 - - - +
255C ALA* 4.0 14.3 - - + +
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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