Contacts of the helix formed by residues 224 - 234 (chain E) 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 TYR 224 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223E CYS* 1.3 86.8 - - + +
225E MET* 1.3 65.3 + - - +
226E ASN 3.4 1.3 - - - -
227E SER* 3.4 5.7 + - - -
228E LEU* 3.2 23.0 + - - +
285E TRP* 3.2 16.7 - + - -
291E PHE* 2.8 34.4 + + + -
292E MET* 5.3 1.3 - - - -
294E HIS 3.1 26.4 - - - -
295E ASP* 3.3 12.8 + - - -
296E VAL* 3.4 30.1 - - + -
299E LEU* 3.3 28.3 - - + -
465E TYR* 3.6 24.4 - + + -
514E TYR* 3.0 24.3 + + + +
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Residues in contact with MET 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222E THR* 3.1 26.0 + - + +
223E CYS 3.2 0.6 - - - -
224E TYR* 1.3 79.0 - - - +
226E ASN* 1.3 62.1 + - - +
228E LEU* 3.4 2.8 + - + +
229E LEU* 3.0 39.0 + - + +
276E THR* 2.9 50.3 - - + +
279E LEU* 4.6 5.8 - - + -
280E THR* 4.7 2.7 - - + -
283E PHE* 4.1 15.5 - - - -
291E PHE* 3.3 39.3 - - + -
299E LEU* 3.7 21.3 - - + -
303E LEU* 6.1 0.2 - - + -
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Residues in contact with ASN 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216E LEU* 3.0 45.0 - - + +
217E LYS 3.1 22.7 + - - +
218E ASN* 5.7 1.1 - - - -
219E GLN 5.9 0.5 + - - -
222E THR* 3.4 17.5 + - - -
223E CYS 4.2 6.5 + - - +
224E TYR 3.4 0.2 - - - -
225E MET* 1.3 82.2 - - - +
227E SER* 1.3 66.6 + - - +
228E LEU 3.2 0.9 + - - -
229E LEU* 3.3 9.9 + - - +
230E GLN* 3.3 20.6 + - + +
276E THR* 4.6 3.3 + - - +
465E TYR 6.0 0.2 - - - +
482E ASP* 4.3 21.9 - - - +
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Residues in contact with SER 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223E CYS 4.9 0.2 + - - -
224E TYR* 3.4 8.6 + - - +
225E MET 3.4 0.4 - - - -
226E ASN* 1.3 79.2 - - - +
228E LEU* 1.3 51.9 + - - +
231E THR* 2.8 30.7 + - - -
454E LEU* 3.3 23.4 - - - +
465E TYR* 3.9 12.3 + - - +
466E VAL* 3.5 29.4 + - - -
467E VAL* 3.4 24.8 + - - +
514E TYR* 4.1 6.9 + - - -
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Residues in contact with LEU 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E TYR 3.2 16.0 + - - +
225E MET* 3.7 6.3 - - - +
226E ASN 3.1 0.2 - - - -
227E SER* 1.3 76.7 - - - +
229E LEU* 1.3 61.4 + - + +
230E GLN 3.2 1.6 - - - -
231E THR* 3.2 15.3 + - + +
232E LEU* 2.9 60.9 + - + +
296E VAL* 4.6 13.9 - - + +
299E LEU* 4.8 9.4 - - + -
300E CYS* 4.5 24.2 - - + +
303E LEU* 3.6 18.6 - - + -
403E HIS* 5.0 0.9 - - + -
454E LEU* 4.0 2.2 - - + +
515E MET* 4.7 18.4 - - + -
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Residues in contact with LEU 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216E LEU* 3.4 18.4 - - + -
225E MET* 3.0 31.5 + - + +
226E ASN 3.3 4.0 + - - +
228E LEU* 1.3 76.3 - - + +
230E GLN* 1.3 58.0 + - - +
232E LEU* 3.4 6.0 + - + +
233E PHE* 2.9 30.1 + - - +
260E LEU* 4.0 21.1 - - + -
263E VAL* 4.3 11.0 - - + -
264E PHE* 4.0 3.9 - - + -
267E LEU* 4.7 2.0 - - + +
276E THR* 3.3 32.5 - - + -
279E LEU* 3.5 26.7 - - + -
303E LEU* 4.6 15.5 - - + -
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Residues in contact with GLN 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E VAL 3.8 2.9 + - - +
215E GLY* 3.3 19.2 - - - -
216E LEU* 3.0 29.6 + - + +
226E ASN* 3.3 16.1 + - + +
227E SER 4.1 4.5 - - - +
228E LEU 3.2 0.4 - - - -
229E LEU* 1.3 75.3 - - - +
231E THR* 1.3 65.9 + - - +
233E PHE* 3.1 1.8 + - - -
234E PHE* 2.9 54.2 + - - -
267E LEU* 4.1 16.6 - - - +
467E VAL* 4.4 9.4 - - + -
469E LEU* 3.9 15.9 - - + -
480E PHE* 3.9 20.5 - - + +
482E ASP 5.0 0.7 - - - +
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Residues in contact with THR 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E SER 2.8 19.1 + - - -
228E LEU* 3.2 19.9 + - + -
230E GLN* 1.3 79.8 - - - +
232E LEU* 1.3 54.8 + - + +
234E PHE* 3.7 2.8 + - - +
235E THR* 2.6 33.7 + - - +
403E HIS* 4.4 12.1 - - - +
451E HIS* 5.2 3.0 + - + -
452E ALA* 3.8 14.9 - - + +
454E LEU* 3.7 12.0 - - + +
467E VAL* 4.0 3.5 - - - +
469E LEU* 4.2 10.7 - - + +
515E MET* 5.5 0.2 - - + -
517E VAL* 3.7 31.6 - - + -
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Residues in contact with LEU 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E LEU* 2.9 48.8 + - + +
229E LEU* 3.6 10.1 - - + +
231E THR* 1.3 77.4 - - + +
233E PHE* 1.3 65.0 + - - +
235E THR* 3.1 23.1 + - - +
238E LEU* 4.4 22.9 - - + +
239E ARG* 4.8 3.3 + - - +
260E LEU* 5.0 4.9 - - + -
264E PHE* 3.9 22.3 - - + -
300E CYS* 4.4 14.8 - - - -
303E LEU* 3.6 24.7 - - + -
304E LEU* 4.6 7.9 - - + -
324E PHE* 5.3 3.8 - - + -
403E HIS* 4.9 8.1 - - + -
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Residues in contact with PHE 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E LEU 2.9 18.3 + - - +
230E GLN* 3.1 5.4 + - - +
232E LEU* 1.3 78.0 - - - +
234E PHE* 1.3 79.9 + + - +
235E THR 3.1 3.6 + - - -
236E ASN 3.7 2.8 + - - -
239E ARG* 3.0 63.8 + - - +
264E PHE* 2.9 52.2 - + + -
267E LEU* 3.3 34.1 - - + -
268E GLN* 3.3 32.1 - - + -
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Residues in contact with PHE 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213E TYR* 3.7 24.9 - + - -
214E VAL 5.5 2.5 - - - -
230E GLN* 2.9 53.1 + - - +
231E THR 3.7 2.2 + - - +
232E LEU 3.3 0.2 - - - -
233E PHE* 1.3 89.8 - + - +
235E THR* 1.3 56.0 + - - +
236E ASN* 2.6 23.1 - - - +
239E ARG* 4.5 3.4 - - - +
451E HIS* 3.5 26.4 + - - +
469E LEU* 3.8 13.5 - - + -
471E PRO* 3.3 41.1 - - + +
480E PHE* 3.7 23.3 - + - -
528E LEU* 3.7 8.8 - - - +
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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