Contacts of the helix formed by residues 234 - 247 (chain B) in PDB entry 1O4X
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 HIS 234 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B LYS 4.0 11.8 + - - -
233B MET* 1.3 79.1 - - - +
235B ASN* 1.3 66.9 + - - +
236B SER* 2.9 14.8 + - - +
237B GLU* 3.0 35.6 + - + +
238B ILE* 3.0 10.4 + - - +
336D A 3.3 27.9 + - - +
337D C 3.4 37.2 - - - -
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Residues in contact with ASN 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ARG* 3.8 15.1 - - - +
227B ALA* 6.1 0.2 - - - +
233B MET 4.6 1.9 - - - +
234B HIS* 1.3 73.1 - - - +
236B SER* 1.3 55.1 + - - +
238B ILE* 4.2 16.5 - - - +
239B SER* 2.4 41.7 + - - +
305C T 4.7 0.4 - - - -
334D A 3.4 24.3 + - + -
335D G 2.3 75.8 + - + +
336D A 4.3 4.8 + - - +
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Residues in contact with SER 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B HIS* 2.9 10.6 + - - +
235B ASN* 1.3 79.4 - - - +
237B GLU* 1.3 65.4 + - - +
239B SER* 3.9 0.5 + - - -
240B LYS* 3.3 28.4 + - - +
304C C 3.2 23.4 + - - -
305C T 3.4 33.7 - - - +
335D G 3.6 5.4 + - - +
336D A 5.3 2.3 - - - -
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Residues in contact with GLU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B MET* 2.8 39.2 - - + +
234B HIS* 3.0 24.9 + - + +
236B SER* 1.3 80.6 - - - +
238B ILE* 1.3 67.3 + - - +
240B LYS* 2.9 26.1 + - + +
241B ARG* 3.0 22.6 + - - +
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Residues in contact with ILE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ARG* 4.6 11.0 - - + +
226B MET* 3.8 30.1 - - + -
227B ALA* 4.6 13.2 - - + +
230B ASN 4.0 9.6 - - - +
233B MET* 3.4 46.0 - - + +
234B HIS 3.0 9.6 + - - +
235B ASN* 4.0 14.1 - - - +
237B GLU* 1.3 75.7 - - - +
239B SER* 1.3 65.1 + - - +
241B ARG* 3.0 9.1 + - - +
242B LEU* 2.8 48.5 + - + +
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Residues in contact with SER 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B PHE* 5.2 0.6 - - - -
223B ARG* 3.9 15.5 + - - +
235B ASN* 2.4 32.1 + - - +
236B SER 3.9 0.2 - - - -
238B ILE* 1.3 72.8 - - - +
240B LYS* 1.3 61.3 + - - +
242B LEU* 4.0 9.1 - - - +
243B GLY 3.2 13.3 + - - -
305C T 2.7 32.6 + - - -
306C T 3.1 39.0 + - - +
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Residues in contact with LYS 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B SER* 3.3 21.5 + - - +
237B GLU* 2.9 17.4 + - + +
239B SER* 1.3 76.2 - - - +
241B ARG* 1.3 67.6 + - + +
243B GLY* 3.4 2.3 + - - -
244B ALA* 3.1 20.3 + - - +
305C T 3.7 41.1 + - - +
306C T 3.8 15.9 - - - +
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Residues in contact with ARG 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B MET* 4.4 19.7 - - + +
230B ASN* 4.1 15.0 - - - +
233B MET* 2.3 42.8 - - - +
237B GLU* 3.0 16.4 + - - +
238B ILE* 3.0 7.6 + - - +
240B LYS* 1.3 74.4 - - + +
242B LEU* 1.3 62.5 + - - +
244B ALA* 3.0 8.5 + - - +
245B GLU* 2.7 31.0 + - - +
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Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B PHE* 4.5 5.8 - - + -
218B TRP* 3.7 18.8 - - + -
219B SER* 5.0 4.7 - - - -
222B GLN* 3.8 26.2 - - + -
223B ARG* 4.0 35.9 - - + +
226B MET* 4.3 20.6 - - + -
238B ILE* 2.8 38.6 + - + +
239B SER* 4.0 4.7 - - - +
241B ARG* 1.3 76.6 - - - +
243B GLY* 1.3 53.7 + - - +
245B GLU* 3.7 10.9 - - - +
246B TRP* 2.6 39.5 + - - +
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Residues in contact with GLY 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B PHE* 4.4 4.0 - - - -
239B SER 3.2 12.7 + - - -
240B LYS 3.4 3.3 + - - -
241B ARG 3.2 0.2 - - - -
242B LEU* 1.3 78.3 - - - +
244B ALA* 1.3 62.1 + - - +
246B TRP* 3.7 4.1 - - - +
247B LYS* 3.0 34.6 + - - +
306C T 4.0 16.6 - - - -
307C T 4.1 12.7 - - - +
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Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B LYS 3.1 13.1 + - - +
241B ARG* 3.0 12.2 + - - +
243B GLY* 1.3 78.4 - - - +
245B GLU* 1.3 63.1 + - - +
247B LYS* 3.4 11.1 + - - +
248B LEU* 3.1 24.4 + - + +
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Residues in contact with GLU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B TRP* 4.6 12.4 - - + -
222B GLN* 4.5 15.0 + - - -
226B MET* 4.8 8.3 - - - +
241B ARG 2.7 19.0 + - - +
242B LEU* 3.7 19.6 - - - +
244B ALA* 1.3 70.7 - - - +
246B TRP* 1.3 65.7 + - - +
248B LEU* 2.9 27.6 + - + +
249B LEU* 3.5 17.9 + - + +
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Residues in contact with TRP 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B ALA* 4.0 21.8 - - + -
215B PHE* 3.5 36.2 - + + +
218B TRP* 3.3 53.5 - + + -
242B LEU 2.6 23.0 + - - +
243B GLY 3.7 3.1 - - - +
245B GLU* 1.3 72.7 - - - +
247B LYS* 1.3 66.8 + - + +
248B LEU 3.1 1.0 + - - -
249B LEU* 3.3 31.2 + - + +
254B LYS* 3.3 56.5 - - + +
257B PHE* 4.3 14.1 - + + -
258B ILE* 5.7 2.5 - - + -
307C T 3.4 32.6 + - - -
308C G 3.7 8.1 + - - -
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Residues in contact with LYS 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B GLY 3.0 18.0 + - - +
244B ALA* 3.8 8.1 - - - +
245B GLU 3.2 0.4 - - - -
246B TRP* 1.3 83.9 - - + +
248B LEU* 1.3 67.1 + - + +
249B LEU 3.4 4.5 + - - +
254B LYS* 4.6 6.4 + - - +
307C T 2.9 37.0 + - - -
308C G 6.0 0.4 - - - -
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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