Contacts of the helix formed by residues 227 - 243 (chain B) in PDB entry 3NA0
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 ASN 227 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B GLN* 4.5 14.9 + - - +
220B GLY 4.9 1.8 + - - -
221B MET* 4.0 9.6 - - - -
225B VAL 4.4 0.2 + - - -
226B VAL* 1.3 76.9 - - - +
228B PRO* 1.4 71.3 - - - +
229B GLU* 3.2 20.2 + - - +
230B ALA* 3.0 31.7 + - + +
231B GLN 3.1 9.5 + - - -
280B TYR* 5.5 3.8 + - - -
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Residues in contact with PRO 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B VAL* 3.1 13.8 - - + +
227B ASN* 1.4 92.2 - - - +
229B GLU* 1.3 66.3 + - + +
231B GLN* 3.4 10.4 + - + +
232B ARG* 3.1 26.9 + - - +
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Residues in contact with GLU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ASN* 3.2 11.4 + - - +
228B PRO* 1.3 84.1 - - + +
230B ALA* 1.3 63.2 + - - +
232B ARG* 3.1 26.4 + - - +
233B PHE* 3.3 18.2 + - - +
276B LYS* 2.6 45.8 + - + +
280B TYR* 5.1 1.6 - - - -
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Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B PHE* 4.0 12.7 - - + -
219B GLN* 5.5 3.1 - - + +
221B MET* 3.5 30.5 - - + -
227B ASN* 3.0 18.0 + - + +
229B GLU* 1.3 75.5 - - - +
231B GLN* 1.3 65.1 + - - +
233B PHE* 3.1 7.9 + - - +
234B ILE* 3.1 24.5 + - - +
280B TYR* 3.9 21.3 + - - +
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Residues in contact with GLN 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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200B ASP* 5.5 5.1 + - - +
204B ARG* 3.0 39.4 + - - +
221B MET* 3.7 9.2 - - + +
226B VAL* 4.2 8.5 - - + +
227B ASN 3.1 11.8 + - - +
228B PRO* 3.5 13.9 - - + +
230B ALA* 1.3 78.3 - - - +
232B ARG* 1.3 55.9 - - - +
234B ILE* 3.2 21.9 + - - +
235B ASP* 2.9 64.9 + - - +
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Residues in contact with ARG 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 PRO 3.1 13.0 + - - +
229B GLU* 3.1 39.1 + - - +
230B ALA 3.2 0.4 - - - -
231B GLN* 1.3 76.3 - - - +
233B PHE* 1.3 57.1 + - - +
235B ASP* 3.6 9.1 + - + +
236B ALA* 3.0 28.2 + - - +
272B VAL* 3.8 37.7 - - + +
275B SER* 6.3 0.6 - - - -
276B LYS* 3.8 15.8 - - - +
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Residues in contact with PHE 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B PHE* 3.4 33.2 - + + -
229B GLU 3.3 8.0 + - - +
230B ALA* 3.1 11.8 + - - +
232B ARG* 1.3 76.8 - - - +
234B ILE* 1.3 65.5 + - - +
236B ALA* 3.2 11.8 + - - +
237B ILE* 3.2 39.6 + - + +
272B VAL* 4.1 8.4 - - - +
273B ILE* 3.3 46.9 - - + -
276B LYS* 3.4 29.4 - - + -
277B ALA* 4.4 4.7 - - + -
280B TYR* 5.1 4.7 - + - +
321B THR 5.2 0.4 - - - -
324B LEU* 4.0 33.7 - - + -
325B ALA 4.6 0.2 - - - -
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Residues in contact with ILE 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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203B PHE* 3.8 28.7 - - + -
204B ARG* 4.0 26.9 - - + -
207B PHE* 3.8 39.9 - - + -
221B MET* 4.1 13.0 - - + -
230B ALA 3.1 18.3 + - - +
231B GLN* 3.5 21.3 - - - +
233B PHE* 1.3 74.1 - - - +
235B ASP* 1.3 64.1 + - - +
237B ILE* 3.2 26.0 + - - +
238B TYR* 3.5 6.8 + - - +
328B VAL* 4.2 10.3 - - + +
329B ASP* 4.7 1.4 - - - +
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Residues in contact with ASP 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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231B GLN* 2.9 46.5 + - - +
232B ARG* 3.8 8.4 - - + +
234B ILE* 1.3 74.2 - - - +
236B ALA* 1.3 65.5 + - - +
237B ILE 3.3 0.2 + - - -
238B TYR* 3.3 8.6 + - - +
239B GLN* 3.0 29.7 + - + +
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Residues in contact with ALA 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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232B ARG 3.0 18.5 + - - +
233B PHE 3.2 6.0 + - - +
235B ASP* 1.3 75.8 - - - +
237B ILE* 1.3 52.5 + - - +
239B GLN* 3.2 9.2 + - - +
240B MET* 2.8 35.7 + - - +
269B ALA* 3.6 25.5 - - - +
272B VAL* 3.6 21.3 - - + -
273B ILE* 4.1 7.2 - - + -
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Residues in contact with ILE 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 PHE* 3.2 47.2 + - + +
234B ILE* 3.5 7.6 - - - +
235B ASP 3.2 0.4 - - - -
236B ALA* 1.3 76.3 - - - +
238B TYR* 1.3 62.7 + - - +
240B MET* 3.3 6.0 + - + +
241B PHE* 3.2 31.6 + - + -
273B ILE* 3.9 22.2 - - + -
325B ALA* 3.7 29.8 - - + +
328B VAL* 3.5 25.4 - - + -
329B ASP* 3.6 24.2 - - - +
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Residues in contact with TYR 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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203B PHE* 5.1 9.9 - + + -
234B ILE 3.5 6.2 + - - +
235B ASP* 3.3 10.1 + - - +
237B ILE* 1.3 78.3 - - - +
239B GLN* 1.3 77.9 + - - +
241B PHE* 3.2 6.0 + - + +
242B HIS* 2.8 56.1 + + + +
329B ASP* 3.3 20.1 + - - +
498B ASN* 4.1 11.0 + - + -
500B ILE* 6.1 0.2 - - + -
502B MET* 3.6 39.8 - - + +
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Residues in contact with GLN 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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235B ASP* 3.0 20.2 + - + +
236B ALA* 3.4 9.9 - - - +
238B TYR* 1.3 99.0 - - - +
240B MET* 1.3 56.7 + - - +
242B HIS* 4.5 10.6 - - - -
243B THR* 2.9 52.5 + - + +
265B ASP* 5.5 2.0 - - - +
269B ALA* 3.8 13.2 - - + -
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Residues in contact with MET 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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126B TRP* 3.2 33.4 - - + -
236B ALA 2.8 19.2 + - - +
237B ILE* 3.4 6.1 - - + +
239B GLN* 1.3 73.3 - - - +
241B PHE* 1.3 73.0 + - + +
243B THR* 4.0 2.9 - - - -
244B SER* 2.6 27.7 + - - -
266B HIS* 3.2 13.2 + - + -
269B ALA* 3.6 10.4 - - + +
270B TRP* 3.3 51.8 - - + +
273B ILE* 4.0 15.9 - - + -
325B ALA* 5.3 0.9 - - + -
602B 2DC 3.7 27.1 - - + -
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Residues in contact with PHE 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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126B TRP* 3.6 29.4 - + - -
237B ILE* 3.2 34.2 + - + -
238B TYR* 3.2 9.2 + - + +
240B MET* 1.3 80.4 - - + +
242B HIS* 1.3 67.5 + - - +
244B SER* 3.0 22.2 + - - -
245B VAL* 3.8 2.1 + - - +
325B ALA 4.6 3.6 - - - -
326B GLY* 5.7 0.2 - - - -
329B ASP* 3.4 27.1 - - + -
330B THR* 5.7 2.2 - - + -
498B ASN* 3.4 16.4 - - + +
499B LEU* 3.6 27.5 - - + +
500B ILE* 4.0 21.8 - - + -
602B 2DC 3.8 37.5 - - + -
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Residues in contact with HIS 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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72B HIS* 4.5 14.9 + + - -
238B TYR* 2.8 48.6 + + + +
239B GLN* 4.0 14.6 - - - +
241B PHE* 1.3 73.1 - - - +
243B THR* 1.3 63.4 + - + +
244B SER 3.1 4.7 + - - -
245B VAL* 3.3 15.4 + - - +
246B PRO* 3.7 6.9 - - - +
498B ASN* 3.0 36.1 + - - +
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Residues in contact with THR 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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239B GLN* 2.9 44.6 + - + +
242B HIS* 1.3 75.1 - - + +
244B SER* 1.3 62.7 + - - +
245B VAL 3.3 0.7 - - - -
246B PRO* 3.5 3.9 - - - +
247B MET* 3.4 6.1 - - - +
262B THR* 3.0 39.8 - - + +
265B ASP* 4.0 26.0 - - + +
266B HIS* 2.9 32.8 + - - +
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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