Contacts of the helix formed by residues 213 - 233 (chain E) in PDB entry 4U0Z
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 213 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211E GLY 3.4 2.4 + - - -
212E ASN* 1.4 85.6 - - - +
214E ALA* 1.4 60.4 + - - +
215E LEU 3.6 0.6 - - - +
216E ARG* 4.1 10.9 - - - +
217E ARG* 3.6 20.3 + - - +
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Residues in contact with ALA 214 (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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212E ASN* 3.1 13.0 - - - +
213E SER* 1.4 74.8 - - - +
215E LEU* 1.4 63.1 + - - +
216E ARG 3.4 0.2 - - - -
217E ARG* 3.7 7.1 + - - +
218E VAL* 3.3 24.7 + - - +
432E ALA* 4.2 20.0 - - + +
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Residues in contact with LEU 215 (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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209E PRO* 5.8 4.0 - - + +
211E GLY 6.0 0.4 - - - -
212E ASN* 4.0 22.8 - - + +
214E ALA* 1.4 75.2 - - - +
216E ARG* 1.4 58.8 + - - +
217E ARG 3.3 0.4 - - - -
218E VAL* 3.2 10.4 + - - +
219E MET* 2.9 28.6 + - - +
429E LEU* 5.8 3.0 - - - +
432E ALA* 5.0 6.2 - - + +
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Residues in contact with ARG 216 (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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211E GLY 3.5 23.0 + - - +
213E SER* 4.1 13.7 - - - +
214E ALA 3.4 0.4 - - - -
215E LEU* 1.4 77.4 - - - +
217E ARG* 1.4 54.6 + - - +
219E MET* 3.5 6.4 + - - +
220E GLU* 3.2 44.2 + - - +
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Residues in contact with ARG 217 (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 SER 3.6 17.0 + - - +
214E ALA* 3.8 8.3 - - - +
215E LEU 3.3 0.4 - - - -
216E ARG* 1.4 76.5 - - - +
218E VAL* 1.4 59.7 + - + +
220E GLU* 4.3 4.0 - - - +
221E GLU* 3.3 28.0 + - - +
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Residues in contact with VAL 218 (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 ALA 3.3 16.6 - - - +
215E LEU* 3.2 11.3 + - - +
217E ARG* 1.4 76.3 - - + +
219E MET* 1.4 53.2 + - - +
221E GLU* 3.2 14.9 - - + +
222E THR* 2.7 48.5 + - + +
428E THR* 4.9 16.4 - - + +
429E LEU* 3.9 30.3 - - + +
432E ALA* 5.2 9.2 - - + -
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Residues in contact with MET 219 (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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215E LEU 2.9 16.5 + - - +
216E ARG* 3.5 9.1 + - - +
218E VAL* 1.4 75.3 - - - +
220E GLU* 1.3 63.2 + - - +
222E THR* 3.1 16.6 + - - -
223E TYR* 3.3 13.5 + - - +
429E LEU* 5.7 3.8 - - + +
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Residues in contact with GLU 220 (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 ARG* 3.2 30.0 + - - +
217E ARG* 4.6 4.4 - - - +
218E VAL 3.4 0.2 - - - -
219E MET* 1.3 76.8 - - - +
221E GLU* 1.3 60.5 + - - +
223E TYR* 3.4 13.3 - - + +
224E TYR* 3.2 29.7 - - + -
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Residues in contact with GLU 221 (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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217E ARG 3.3 18.0 + - - +
218E VAL* 3.2 22.4 - - - +
220E GLU* 1.3 76.8 - - - +
222E THR* 1.4 64.9 + - + +
223E TYR 3.2 0.8 + - - -
224E TYR* 3.4 9.7 + - - +
225E HIS* 2.9 28.4 + - - +
240E LEU* 5.4 3.9 - - + +
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Residues in contact with THR 222 (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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218E VAL* 2.7 39.6 + - + +
219E MET* 3.1 16.3 + - - -
221E GLU* 1.4 80.8 - - + +
223E TYR* 1.4 58.9 + - - +
225E HIS* 3.7 21.0 - - + +
226E HIS* 2.9 28.9 + - - +
390E THR* 4.8 1.6 + - - -
428E THR* 5.5 8.7 - - + -
429E LEU* 5.5 5.6 - - + +
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Residues in contact with TYR 223 (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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219E MET 3.3 12.1 + - - +
220E GLU* 3.4 13.7 - - + +
221E GLU 3.2 0.4 - - - -
222E THR* 1.4 76.5 - - - +
224E TYR* 1.4 77.8 + + - +
226E HIS* 3.4 15.1 + - - +
227E ILE* 3.4 30.5 + - + +
247E LEU* 5.0 3.1 - - + -
268E HIS* 2.7 42.1 + + - -
271E MET* 3.3 45.8 - - + +
272E LYS* 3.6 26.9 + - - +
275E ASN* 5.1 7.2 - - - -
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Residues in contact with TYR 224 (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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220E GLU* 3.2 31.0 - - + -
221E GLU* 3.4 9.5 + - - +
223E TYR* 1.4 85.8 - + - +
225E HIS* 1.3 56.4 + - - +
227E ILE* 3.6 9.2 + - - +
228E TYR 3.2 20.6 + - - -
240E LEU* 3.3 24.4 - - + +
243E ILE* 4.1 4.2 - - + +
244E ARG* 3.9 34.1 - - + -
247E LEU* 3.7 43.3 + - + +
248E GLU* 3.6 27.5 - - - +
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Residues in contact with HIS 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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221E GLU* 2.9 19.2 + - - +
222E THR* 3.7 22.2 - - + +
224E TYR* 1.3 74.1 - - - +
226E HIS* 1.4 66.9 + - - +
228E TYR* 3.0 15.6 + - - +
229E HIS* 3.1 49.3 + + - -
240E LEU* 3.9 14.4 - - + +
390E THR* 3.7 25.0 - - + +
392E ARG* 4.2 22.0 + - - +
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Residues in contact with HIS 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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222E THR 2.9 22.0 + - - +
223E TYR* 3.4 7.1 + - - +
225E HIS* 1.4 71.2 - - - +
227E ILE* 1.4 56.2 + - - +
229E HIS* 3.6 1.4 + - - +
230E THR* 3.0 47.8 + - + +
267E MET* 4.4 0.7 - - + -
271E MET* 3.5 23.1 - - + +
374E ARG* 4.8 10.8 + - + +
375E LEU* 4.1 22.9 - - + -
378E ASN* 3.3 24.1 + - - -
388E PRO* 5.5 2.7 - - + -
389E ILE 3.2 23.2 + - - -
390E THR* 3.3 26.3 - - + +
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Residues in contact with ILE 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 TYR* 3.4 43.6 + - + +
224E TYR* 3.7 6.7 - - - +
225E HIS 3.2 0.6 - - - -
226E HIS* 1.4 72.6 - - - +
228E TYR* 1.4 66.1 + - - +
229E HIS 3.2 0.2 + - - -
230E THR* 3.2 7.7 + - - +
231E VAL* 3.0 29.8 + - + +
243E ILE* 4.1 16.2 - - + -
247E LEU* 3.8 18.6 - - + -
264E VAL* 4.3 22.9 - - + +
267E MET* 4.1 22.7 - - + -
268E HIS* 4.8 6.1 - - - +
271E MET* 3.8 23.3 - - - -
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Residues in contact with TYR 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 5.7 + - - -
225E HIS* 3.0 10.3 + - - +
227E ILE* 1.4 74.5 - - - +
229E HIS* 1.3 89.5 + + - +
231E VAL* 3.5 2.8 - - - +
232E ALA* 3.0 37.9 + - + +
236E ASN 5.5 0.2 - - - -
238E LEU 3.3 26.7 - - - -
239E THR* 4.2 2.5 - - - -
240E LEU* 3.7 44.6 - - + -
243E ILE* 3.6 19.2 - - + +
393E LYS* 3.6 22.3 - - + +
394E GLU* 5.5 0.4 - - - -
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Residues in contact with HIS 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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225E HIS* 3.1 57.2 + + - -
228E TYR* 1.3 95.3 - + - +
230E THR* 1.4 60.3 + - - +
232E ALA* 4.4 1.6 - - - -
233E ILE* 2.9 34.1 + - - +
390E THR* 3.8 11.0 - - + +
391E ILE 3.5 19.0 - - - +
392E ARG* 3.7 19.1 + - + -
393E LYS* 3.1 34.6 + - + -
394E GLU* 3.5 14.1 + - - -
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Residues in contact with THR 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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226E HIS* 3.0 32.9 + - + +
227E ILE* 3.4 13.0 - - - +
229E HIS* 1.4 74.1 - - - +
231E VAL* 1.3 58.6 + - - +
233E ILE* 3.3 10.8 - - - +
234E GLU* 4.3 1.6 + - - -
267E MET* 3.6 37.1 - - + +
371E ARG* 3.7 13.7 + - - +
374E ARG* 2.8 54.3 + - - +
390E THR* 5.4 0.2 - - - +
391E ILE 4.8 1.5 + - - -
501E APC 4.8 0.2 + - - -
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Residues in contact with VAL 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 ILE* 3.0 26.4 + - + +
228E TYR* 3.5 7.6 - - - +
230E THR* 1.3 76.9 - - - +
232E ALA* 1.4 60.4 + - + +
233E ILE 3.3 0.2 - - - -
234E GLU* 3.1 18.9 + - - -
235E GLY 3.4 1.0 + - - -
236E ASN* 3.3 39.7 + - + +
238E LEU 6.1 0.2 - - - +
243E ILE* 4.4 5.6 - - + -
263E GLU* 4.1 31.0 - - + +
264E VAL* 4.3 11.7 - - + +
267E MET* 3.8 28.7 - - + -
371E ARG* 4.6 7.2 - - - +
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Residues in contact with ALA 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 TYR* 3.0 30.1 + - + +
229E HIS 4.0 2.2 - - - +
231E VAL* 1.4 70.8 - - + +
233E ILE* 1.4 55.5 + - - +
234E GLU 3.1 5.4 - - - -
235E GLY* 2.8 22.9 + - - -
236E ASN 3.7 21.9 + - - +
393E LYS* 3.7 36.5 - - + +
396E ARG* 5.6 0.5 - - - -
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Residues in contact with ILE 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 HIS 2.9 15.7 + - - +
230E THR* 3.3 22.7 - - - +
232E ALA* 1.4 74.8 - - - +
234E GLU* 1.3 54.8 + - - +
235E GLY 3.4 0.4 + - - -
374E ARG* 3.4 25.8 - - - +
391E ILE* 3.7 25.1 - - + +
392E ARG 3.3 27.4 - - - +
393E LYS* 4.6 7.9 - - - +
396E ARG* 3.4 54.9 + - + +
399E TYR* 3.9 13.0 - - + -
400E TYR* 4.2 7.2 + - + -
501E APC 4.9 2.8 + - - +
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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