Contacts of the helix formed by residues 224 - 235 (chain B) in PDB entry 1R4N
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 LEU 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331A ASP* 3.7 32.8 - - + +
339A TYR* 4.6 12.8 - - + +
343A GLN* 5.2 5.4 - - - +
213B PHE* 5.7 2.7 - - + -
223B ARG* 1.3 86.4 - - + +
225B PRO* 1.3 76.5 - - + +
226B GLU* 3.8 21.8 - - + +
227B HIS* 2.8 49.3 + - + +
228B CYS 3.5 3.3 + - - -
273B ILE* 3.7 8.5 - - - +
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Residues in contact with PRO 225 (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 0.2 - - - +
224B LEU* 1.3 85.5 - - + +
226B GLU* 1.3 70.9 + - - +
228B CYS* 3.1 15.4 + - + +
229B ILE* 3.2 19.1 + - - +
273B ILE* 3.6 10.5 - - + -
274B ARG 3.1 26.7 - - - +
275B GLY* 3.3 30.5 - - - +
276B VAL* 3.8 12.4 - - + +
280B LEU* 3.7 11.0 - - + -
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Residues in contact with GLU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B PHE* 3.8 26.6 - - + -
224B LEU* 3.8 15.7 - - + +
225B PRO* 1.3 95.1 - - - +
227B HIS* 1.3 58.9 + - - +
228B CYS 3.1 0.3 + - - -
229B ILE* 3.2 2.1 + - - +
230B GLU* 2.9 31.7 + - - +
280B LEU* 3.9 16.7 - - + +
284B VAL* 4.2 25.3 - - + +
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Residues in contact with HIS 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ASP* 3.7 7.7 + - - -
213B PHE* 3.5 39.4 - + + +
214B PRO* 6.2 0.4 - - - +
217B THR* 4.7 9.8 + - - -
218B ILE* 3.7 16.4 - - + +
222B PRO* 4.0 18.0 - - + +
223B ARG* 3.1 45.3 + - - -
224B LEU* 2.8 41.6 + - + +
226B GLU* 1.3 75.6 - - - +
228B CYS* 1.3 62.5 + - - +
230B GLU* 4.2 4.7 - - - -
231B TYR* 3.5 18.0 + - - +
267B ARG* 3.9 3.4 + - - -
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Residues in contact with CYS 228 (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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222B PRO* 4.5 4.9 - - - -
224B LEU 4.2 2.9 - - - -
225B PRO* 3.1 9.6 + - - +
226B GLU 3.1 1.0 - - - -
227B HIS* 1.3 76.7 - - - +
229B ILE* 1.3 68.7 + - - +
231B TYR* 2.9 14.0 + - - +
232B VAL* 3.0 14.6 + - - +
264B SER* 3.8 20.2 - - - +
267B ARG* 3.9 18.5 + - + +
268B ALA* 3.4 35.4 - - + +
271B TYR* 5.8 0.4 - - - -
273B ILE* 4.1 24.9 - - - -
276B VAL* 4.8 0.7 - - + -
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Residues in contact with ILE 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B PRO 3.2 13.3 + - - +
226B GLU 3.7 4.0 - - - +
228B CYS* 1.3 74.7 - - - +
230B GLU* 1.3 56.7 + - - +
231B TYR 2.7 12.3 + - - -
232B VAL* 2.8 14.4 + - - +
233B ARG* 2.9 10.0 + - + +
260B ILE* 4.2 1.8 - - + -
264B SER* 3.0 27.1 - - - +
276B VAL* 4.5 8.1 - - + -
280B LEU* 3.6 14.6 - - + +
281B THR* 3.3 49.6 - - + +
284B VAL* 3.4 35.2 - - + -
285B VAL* 4.2 8.7 - - + -
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Residues in contact with GLU 230 (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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212B ASN* 5.4 1.9 + - - -
213B PHE* 3.8 24.3 + - + +
218B ILE* 3.8 26.1 - - + +
226B GLU 2.9 20.0 + - - +
227B HIS 4.3 3.6 - - - +
229B ILE* 1.3 72.2 - - - +
231B TYR* 1.3 56.9 + - - +
233B ARG* 2.9 34.3 + - - -
234B MET* 2.9 43.1 + - + +
284B VAL* 3.8 9.7 - - + +
287B ARG* 2.9 33.1 + - - -
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Residues in contact with TYR 231 (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 ILE* 3.3 24.2 - - - +
219B ALA* 4.4 8.3 - - + -
227B HIS 3.5 7.8 + - - +
228B CYS 2.9 4.8 + - - +
229B ILE 2.7 4.8 + - - -
230B GLU* 1.3 72.5 - - - +
232B VAL* 1.3 70.0 + - + +
233B ARG 2.6 15.8 + - - -
234B MET* 5.0 0.4 - - - -
235B LEU* 2.9 51.5 + - + +
236B GLN* 3.2 36.4 + - + +
267B ARG* 2.9 53.8 + - - +
448E TYR* 5.3 4.7 + - - -
449E GLN* 5.5 4.3 + - - -
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Residues in contact with VAL 232 (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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228B CYS 3.0 5.1 + - - +
229B ILE 2.8 6.0 + - - +
231B TYR* 1.3 79.7 - - + +
233B ARG* 1.3 57.4 + - - +
236B GLN* 3.6 22.0 - - - +
237B TRP* 3.6 19.2 + - - +
259B TRP* 4.0 8.0 - - + -
260B ILE* 3.5 27.9 - - + +
263B LYS* 3.3 34.8 - - + +
264B SER* 3.3 37.5 - - - +
267B ARG* 4.5 2.7 - - + -
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Residues in contact with ARG 233 (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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229B ILE 2.9 11.2 + - - +
230B GLU* 2.9 30.8 + - - +
231B TYR 2.6 6.1 + - - -
232B VAL* 1.3 75.5 - - - +
234B MET* 1.3 92.6 + - - +
235B LEU 3.1 2.7 + - - -
237B TRP* 3.9 3.9 - - - +
238B PRO* 3.3 19.1 - - - +
249B LEU* 3.7 27.1 - - + +
260B ILE* 4.7 2.7 - - + -
284B VAL* 4.6 1.1 - - - -
285B VAL* 3.9 45.5 + - + +
287B ARG* 4.3 17.7 - - - +
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Residues in contact with MET 234 (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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212B ASN* 5.5 7.9 - - - +
213B PHE* 5.6 3.6 - - + +
215B MET* 5.1 14.4 - - - +
218B ILE* 4.3 22.4 - - + -
230B GLU* 2.9 46.8 + - + +
231B TYR* 5.0 0.2 - - - -
233B ARG* 1.3 91.2 - - - +
235B LEU* 1.3 72.9 + - + +
238B PRO* 3.9 10.7 - - - +
287B ARG* 5.0 3.1 - - - +
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Residues in contact with LEU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B MET* 4.4 29.2 - - + -
218B ILE* 5.0 6.1 - - + -
219B ALA* 4.4 15.5 - - + -
231B TYR* 2.9 37.9 + - + +
233B ARG 3.1 0.8 - - - -
234B MET* 1.3 97.1 - - + +
236B GLN* 1.3 65.4 + - - +
237B TRP 3.2 2.2 - - - -
238B PRO* 3.0 15.1 - - + +
239B LYS* 3.0 16.9 + - - +
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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