Contacts of the helix formed by residues 222 - 234 (chain B) in PDB entry 1NBF
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 222 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B LYS 3.9 5.0 + - - -
218B ASN* 2.8 14.0 + - - +
219B GLN* 2.7 55.2 + - + +
221B ALA* 1.3 79.6 - - - +
223B CYS* 1.3 65.9 + - - +
224B TYR* 3.1 10.8 - - + +
225B MET* 3.0 24.6 + - + +
226B ASN* 3.0 22.6 + - - -
280B THR* 4.9 3.1 - - - +
285B TRP* 4.9 5.4 - - + -
290B SER* 4.1 13.5 - - - +
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Residues in contact with CYS 223 (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 ASN* 3.6 1.6 - - - +
221B ALA 3.4 0.2 - - - -
222B THR* 1.3 72.7 - - - +
224B TYR* 1.3 61.8 + - - +
226B ASN* 3.8 1.1 - - - +
227B SER* 3.0 28.4 + - - -
464B HIS* 3.7 10.1 - - + -
465B TYR* 3.3 35.8 - - - +
482B ASP* 3.4 21.7 - - - +
375C GLY 3.7 0.7 - - - -
376C GLZ 1.9 75.5 + - - +
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Residues in contact with TYR 224 (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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221B ALA 2.9 30.1 - - - -
222B THR* 3.9 7.2 - - + +
223B CYS* 1.3 81.4 - - - +
225B MET* 1.3 81.3 + - + +
227B SER* 3.6 0.7 + - - -
228B LEU* 3.3 16.8 + - - +
285B TRP* 2.9 35.3 - + - -
289B ASP 4.8 0.9 + - - -
290B SER* 5.9 0.2 - - - -
292B MET 3.9 10.2 + - - -
294B HIS* 3.4 45.6 - + + +
295B ASP 4.7 0.9 - - - -
296B VAL* 3.4 18.7 - - + +
299B LEU* 3.9 28.9 - - + +
465B TYR* 3.5 32.8 - - + -
375C GLY 3.5 11.0 - - - -
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Residues in contact with MET 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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222B THR* 3.0 22.5 + - + +
224B TYR* 1.3 93.5 - - + +
226B ASN* 1.3 63.4 + - - +
228B LEU* 3.3 1.9 + - - +
229B LEU* 2.8 45.3 + - + +
276B THR* 3.2 42.0 - - + +
279B LEU* 4.3 9.9 - - + -
280B THR* 4.2 16.8 - - - +
283B PHE* 4.0 26.7 - - + -
285B TRP* 4.7 7.9 - - - -
299B LEU* 3.7 19.9 - - + +
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Residues in contact with ASN 226 (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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216B LEU* 3.4 41.2 + - + +
217B LYS 3.5 21.8 + - - +
218B ASN* 4.0 0.2 - - - +
222B THR* 3.0 26.1 + - - +
223B CYS 3.8 4.0 - - - +
225B MET* 1.3 80.7 - - - +
227B SER* 1.3 61.7 + - - +
229B LEU* 3.3 0.6 + - - -
230B GLN* 3.0 31.2 + - + +
276B THR* 3.9 12.1 - - - +
482B ASP* 2.9 34.4 + - - +
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Residues in contact with SER 227 (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 CYS 3.0 18.3 + - - -
224B TYR* 3.8 5.4 - - - -
225B MET 3.2 0.2 - - - -
226B ASN* 1.3 79.1 - - - +
228B LEU* 1.3 59.0 + - - +
230B GLN 3.6 0.2 + - - -
231B THR* 2.9 26.6 + - - -
296B VAL* 4.7 1.6 - - - -
454B LEU* 4.0 15.5 - - - -
465B TYR* 3.4 7.6 + - - -
466B VAL* 3.4 36.3 + - - -
467B VAL* 3.6 16.8 + - - +
480B PHE 4.8 0.7 + - - -
482B ASP 5.9 0.5 + - - -
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Residues in contact with LEU 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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224B TYR 3.3 8.9 + - - +
225B MET 3.9 3.4 - - - +
227B SER* 1.3 76.5 - - - +
229B LEU* 1.3 63.3 + - + +
231B THR* 3.2 12.4 + - + -
232B LEU* 2.9 54.5 + - + +
296B VAL* 3.8 18.5 - - + +
299B LEU* 3.5 24.0 - - + +
300B CYS* 3.4 48.2 - - + +
303B LEU* 4.4 7.4 - - + -
454B LEU* 4.5 1.1 - - + -
515B MET* 4.4 12.1 - - + -
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Residues in contact with LEU 229 (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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216B LEU* 3.7 15.9 - - + -
225B MET* 2.8 39.9 + - + +
226B ASN* 3.3 5.1 + - - +
228B LEU* 1.3 78.1 - - + +
230B GLN* 1.3 57.7 - - - +
232B LEU* 3.2 6.3 + - + +
233B PHE* 2.8 33.1 + - - +
260B LEU* 4.0 18.2 - - + -
263B VAL* 4.3 12.6 - - + -
264B PHE* 4.1 11.3 - - + -
267B LEU* 5.0 1.3 - - + -
276B THR* 3.8 28.7 - - + -
279B LEU* 4.0 22.9 - - + -
299B LEU* 6.2 0.4 - - + -
303B LEU* 5.2 9.2 - - + -
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Residues in contact with GLN 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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214B VAL 3.1 21.5 + - - +
215B GLY* 3.9 4.3 - - - -
216B LEU* 3.7 15.9 + - + +
226B ASN* 3.0 17.7 + - + +
227B SER* 3.9 4.7 - - - +
229B LEU* 1.3 75.2 - - - +
231B THR* 1.3 63.6 + - - +
233B PHE* 4.3 2.3 - - - -
234B PHE* 3.0 57.5 + - - +
267B LEU* 3.6 22.2 - - - +
467B VAL* 4.1 4.0 - - + -
469B LEU* 4.0 16.2 - - + -
480B PHE* 3.6 25.1 - - + -
482B ASP 5.0 1.2 - - - +
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Residues in contact with THR 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B SER 2.9 16.3 + - - -
228B LEU* 3.2 22.6 + - + -
230B GLN* 1.3 81.0 - - - +
232B LEU* 1.3 61.2 + - + +
234B PHE* 3.7 3.1 + - - +
235B THR* 2.9 23.3 + - - +
403B HIS* 4.8 9.0 - - + +
451B HIS* 4.9 3.0 - - - +
452B ALA* 4.6 4.2 - - + +
454B LEU* 3.4 17.5 - - + +
467B VAL* 3.7 11.4 - - - +
469B LEU* 4.3 10.7 - - - +
515B MET* 5.2 1.1 - - + -
517B VAL* 3.9 30.1 - - + -
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Residues in contact with LEU 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 LEU* 2.9 45.1 + - + +
229B LEU* 3.8 7.0 - - + +
231B THR* 1.3 79.0 - - + +
233B PHE* 1.3 60.7 + - - +
235B THR* 2.9 30.5 + - - +
238B LEU* 3.7 29.7 - - + +
239B ARG 4.6 1.7 + - - -
260B LEU* 6.1 2.5 - - + -
264B PHE* 4.1 14.2 - - + -
303B LEU* 3.9 24.5 - - + -
304B LEU* 4.3 20.6 - - + -
324B PHE* 4.4 9.6 - - + -
403B HIS* 4.7 11.7 - - + -
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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
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213B TYR* 5.7 1.6 - + - -
229B LEU 2.8 21.3 + - - +
230B GLN* 3.8 4.3 - - - +
232B LEU* 1.3 73.1 - - - +
234B PHE* 1.3 97.2 + + - +
235B THR 3.3 3.1 + - - -
236B ASN* 3.9 0.9 - - - +
239B ARG* 2.8 73.7 + - - +
264B PHE* 3.2 55.8 - + + -
267B LEU* 3.6 29.2 - - + -
268B GLN* 3.7 19.7 - - + -
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Residues in contact with PHE 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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213B TYR* 3.7 39.5 - + + -
230B GLN* 3.0 48.6 + - - +
231B THR 3.7 0.6 + - - +
232B LEU 3.2 0.4 - - - -
233B PHE* 1.3 101.6 - + - +
235B THR* 1.3 56.0 + - - +
236B ASN* 3.0 19.9 + - - +
239B ARG* 4.1 6.7 - - - -
451B HIS* 3.3 29.4 + - + +
469B LEU* 3.9 17.9 - - + -
471B PRO* 3.6 23.1 - - + +
480B PHE* 3.5 22.0 - + - -
528B LEU* 3.5 8.7 - - - +
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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