Contacts of the helix formed by residues 203 - 223 (chain B) in PDB entry 1NUA
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 SER 203 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B ALA 3.0 14.4 + - - +
202B SER* 1.3 84.8 + - - +
204B GLU* 1.3 53.0 + - - +
205B GLU* 3.4 18.2 + - - +
206B GLU* 2.8 40.5 + - - +
207B PHE* 2.7 32.2 + - - +
372B GLY* 3.8 0.6 - - - -
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Residues in contact with GLU 204 (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 SER* 1.3 71.6 - - - +
205B GLU* 1.3 59.5 + - + +
207B PHE* 3.6 1.8 - - - +
208B THR* 2.6 42.3 + - - -
315B ARG* 2.6 30.3 + - - +
371B ILE* 3.1 42.8 - - + +
372B GLY* 3.7 6.8 - - - -
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Residues in contact with GLU 205 (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 SER* 3.4 12.4 + - - +
204B GLU* 1.3 82.6 + - + +
206B GLU* 1.3 62.3 + - - +
208B THR* 3.2 21.1 + - - -
209B ALA* 3.4 6.6 + - - +
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Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B VAL* 6.1 0.2 - - - +
199B ALA* 3.8 17.9 - - + -
202B SER* 6.1 0.2 - - - +
203B SER* 2.8 31.3 + - - +
205B GLU* 1.3 69.2 - - - +
207B PHE* 1.3 66.1 + - - +
209B ALA* 3.1 13.5 + - - +
210B LEU* 3.3 14.0 + - - +
242B ARG* 2.7 45.7 + - - +
245B ALA* 3.4 30.1 - - + +
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Residues in contact with PHE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ILE* 4.0 20.4 - - + -
199B ALA* 3.9 12.1 - - + +
200B ALA* 3.6 36.1 - - + -
203B SER 2.7 18.6 + - - +
204B GLU 3.6 5.6 - - - +
206B GLU* 1.3 72.1 - - - +
208B THR* 1.3 63.9 + - - +
210B LEU* 3.2 16.3 + - + +
211B GLU* 3.2 44.9 + - + -
315B ARG* 3.7 18.8 - - - -
316B ILE* 4.1 15.0 - - + -
319B CYS* 3.6 21.8 - - + -
371B ILE* 3.6 26.9 - - + -
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Residues in contact with THR 208 (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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204B GLU* 2.6 34.7 + - - -
205B GLU* 3.4 8.8 + - - -
206B GLU 3.1 0.2 - - - -
207B PHE* 1.3 78.4 - - - +
209B ALA* 1.3 60.3 + - - +
211B GLU* 3.1 21.4 + - + +
212B GLU* 2.9 45.1 + - + +
315B ARG* 4.0 6.7 + - - +
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Residues in contact with ALA 209 (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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205B GLU 3.4 5.7 + - - +
206B GLU* 3.1 13.9 + - - +
208B THR* 1.3 77.8 - - - +
210B LEU* 1.3 58.1 + - - +
212B GLU* 3.2 16.1 + - - +
213B ASN* 2.9 38.0 + - - +
242B ARG* 3.4 35.7 - - - +
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Residues in contact with LEU 210 (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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192B MET* 3.9 20.4 - - + -
195B VAL* 4.0 14.1 - - + +
196B ILE* 3.8 26.9 - - + -
199B ALA* 3.4 32.1 - - + -
206B GLU* 3.3 9.1 + - - +
207B PHE* 3.2 13.8 + - + +
209B ALA* 1.3 78.8 - - - +
211B GLU* 1.3 58.7 + - - +
214B ALA 3.0 13.7 + - - -
242B ARG* 3.8 22.9 - - + +
319B CYS* 4.3 4.0 - - - -
323B TYR* 2.6 43.3 + - + +
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Residues in contact with GLU 211 (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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207B PHE* 3.2 28.5 + - + +
208B THR* 3.1 21.6 + - + +
210B LEU* 1.3 81.0 - - - +
212B GLU* 1.3 60.3 + - + +
214B ALA* 3.0 22.7 - - - +
215B GLU 4.7 0.2 + - - -
315B ARG* 2.6 51.1 + - - +
318B LYS* 5.7 1.4 - - - +
319B CYS* 3.9 18.8 + - + +
322B ALA* 5.4 0.6 - - - +
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Residues in contact with GLU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B THR* 2.9 31.3 + - + +
209B ALA* 3.6 16.0 + - - +
211B GLU* 1.3 75.4 - - + +
213B ASN* 1.3 67.4 + - - +
214B ALA 3.0 5.3 + - - -
215B GLU* 4.0 8.5 + - - +
216B THR* 4.6 4.3 + - - -
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Residues in contact with ASN 213 (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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209B ALA* 2.9 22.5 + - - +
210B LEU 3.9 0.2 - - - -
212B GLU* 1.3 75.2 + - - +
214B ALA* 1.3 65.4 + - - +
215B GLU 3.4 0.7 - - - -
216B THR* 3.2 11.7 + - - -
217B ILE* 2.8 43.8 + - + +
238B ILE* 3.3 30.4 - - + +
242B ARG* 2.8 40.8 - - - +
323B TYR* 4.0 3.1 - - - +
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Residues in contact with ALA 214 (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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210B LEU 3.0 15.7 + - - +
211B GLU* 3.0 21.3 - - - +
212B GLU 3.0 0.8 - - - -
213B ASN* 1.3 74.7 - - - +
215B GLU* 1.3 64.8 + - - +
217B ILE* 4.0 1.0 - - - +
218B LEU* 3.0 26.3 + - - +
322B ALA* 3.7 32.7 - - + +
323B TYR* 3.6 17.3 + - + -
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Residues in contact with GLU 215 (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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211B GLU 4.7 0.2 + - - -
212B GLU 4.0 6.3 + - - +
213B ASN 3.4 0.8 - - - -
214B ALA* 1.3 78.5 - - - +
216B THR* 1.3 54.4 + - - +
218B LEU* 3.5 3.8 - - - +
219B LYS* 2.7 44.5 + - + +
322B ALA* 4.9 2.2 + - - +
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Residues in contact with THR 216 (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 GLU 4.6 2.8 + - - -
213B ASN* 3.2 16.5 + - - -
215B GLU* 1.3 78.6 - - - +
217B ILE* 1.3 65.6 + - - +
219B LYS* 2.8 20.5 + - + +
220B ALA* 2.9 13.3 + - + +
235B THR* 3.4 32.1 - - + -
238B ILE* 5.2 6.8 - - + +
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Residues in contact with ILE 217 (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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188B PHE* 4.0 31.4 - - + -
192B MET* 5.3 3.6 - - + -
213B ASN* 2.8 34.1 + - + +
214B ALA 4.0 2.5 - - - +
216B THR* 1.3 74.5 - - + +
218B LEU* 1.3 63.7 + - - +
220B ALA* 3.1 9.1 + - - +
221B VAL* 3.0 26.3 + - + +
232B PHE* 4.7 2.2 - - + -
235B THR* 5.8 5.8 - - - -
238B ILE* 4.5 10.3 - - + -
239B LEU* 4.7 19.5 - - + +
242B ARG* 4.2 19.5 - - + -
243B ILE* 6.3 0.9 - - + -
323B TYR* 3.6 33.0 - - + +
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Residues in contact with LEU 218 (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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188B PHE* 5.6 3.1 - - + -
189B ILE* 4.3 15.7 - - + -
192B MET* 6.5 0.2 - - + -
214B ALA 3.0 19.9 + - - +
215B GLU* 3.7 4.3 - - - +
217B ILE* 1.3 78.3 - - + +
219B LYS* 1.3 60.9 + - - +
221B VAL* 3.6 12.1 + - + +
222B ARG* 3.2 66.8 + - - +
321B ALA 5.0 0.4 - - - +
322B ALA 3.2 22.4 - - - +
323B TYR* 4.1 23.8 - - + +
324B GLY 3.7 9.4 - - - +
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Residues in contact with LYS 219 (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 GLU* 2.7 24.5 + - + +
216B THR* 2.8 15.6 + - + +
218B LEU* 1.3 70.6 - - - +
220B ALA* 1.3 60.3 + - - +
222B ARG* 3.3 6.2 + - - +
223B ARG* 2.9 34.2 + - + +
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Residues in contact with ALA 220 (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 THR* 2.9 10.5 + - + +
217B ILE* 3.4 10.1 - - - +
219B LYS* 1.3 74.4 - - - +
221B VAL* 1.3 66.4 + - - +
223B ARG* 2.7 34.8 + - - +
231B ARG* 3.2 20.3 + - - +
232B PHE* 3.6 28.0 - - + -
235B THR* 4.9 6.7 - - + +
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Residues in contact with VAL 221 (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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183B LEU 5.7 1.3 - - - +
185B VAL* 3.8 37.6 - - + +
188B PHE* 3.7 56.5 - - + -
189B ILE* 4.5 4.5 - - + -
217B ILE* 3.0 18.0 + - + +
218B LEU* 3.8 11.9 - - + +
220B ALA* 1.3 75.9 - - - +
222B ARG* 1.3 57.6 + - + +
231B ARG* 3.0 26.7 + - - +
232B PHE* 4.1 7.4 - - + -
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Residues in contact with ARG 222 (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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185B VAL* 4.5 22.5 - - + +
189B ILE* 5.1 3.2 - - - +
218B LEU* 3.2 54.3 + - + +
219B LYS* 3.9 4.5 - - - +
220B ALA 3.1 0.8 - - - -
221B VAL* 1.3 80.5 - - + +
223B ARG* 1.3 69.7 + - - +
224B GLU* 3.5 6.2 + - - +
231B ARG* 4.6 0.2 + - - -
324B GLY* 4.2 13.1 - - - -
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Residues in contact with ARG 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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219B LYS* 2.9 18.4 + - + +
220B ALA* 2.7 34.8 - - - +
222B ARG* 1.3 78.2 - - - +
224B GLU* 1.3 66.4 + - - +
225B VAL* 4.1 18.6 - - + +
226B THR* 4.5 0.4 + - - +
229B GLU* 3.2 27.1 + - - -
230B HIS 3.8 6.9 + - - -
231B ARG* 2.6 63.6 + - - +
233B GLU* 4.0 16.6 + - - +
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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
------------------------------------------------------------
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