Contacts of the helix formed by residues 211 - 223 (chain Z) in PDB entry 5V09
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 211 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208Z ASP 4.3 8.3 - - - +
210Z PHE* 1.3 97.7 - - + +
212Z GLU* 1.3 65.4 + - - +
213Z GLU* 4.1 4.2 + - - +
214Z LYS* 3.4 33.6 + - + +
215Z PHE* 2.9 24.5 + - - +
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Residues in contact with GLU 212 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160Z LYS* 4.0 17.5 + - - -
176Z ALA 5.5 3.1 - - - +
177Z PHE 4.0 2.8 - - - +
178Z GLY* 3.5 29.8 - - - +
180Z LYS* 6.0 1.9 - - - -
197Z GLN* 4.0 19.8 + - - +
210Z PHE 3.9 1.0 + - - -
211Z THR* 1.3 72.9 - - - +
213Z GLU* 1.3 59.0 + - - +
215Z PHE* 3.4 5.3 + - - +
216Z ARG* 2.9 43.7 + - - +
283Z LEU* 5.7 1.7 - - - +
299Z ASN* 5.1 2.1 + - - +
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Residues in contact with GLU 213 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211Z THR* 3.3 4.1 + - - +
212Z GLU* 1.3 79.1 - - - +
214Z LYS* 1.3 61.0 + - + +
216Z ARG* 3.2 32.6 + - - +
217Z TYR* 2.6 65.6 + - + +
248Z PRO 5.3 3.5 - - - +
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Residues in contact with LYS 214 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208Z ASP* 3.1 40.4 + - - +
209Z VAL* 3.7 22.4 - - + -
211Z THR* 3.4 22.9 + - - +
212Z GLU 3.5 0.4 - - - -
213Z GLU* 1.3 82.2 - - + +
215Z PHE* 1.3 58.7 + - - +
217Z TYR* 3.2 12.4 + - + -
218Z MET* 2.9 25.5 + - - +
242Z LEU* 3.1 25.0 + - + +
246Z ASN* 3.3 20.8 + - - +
248Z PRO* 5.9 6.7 - - - -
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Residues in contact with PHE 215 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Z LEU* 4.1 20.4 - - + -
10Z ILE* 4.4 16.2 - - + -
175Z LEU* 4.1 34.1 - - + -
176Z ALA* 4.6 2.0 - - - -
200Z LEU* 4.0 28.7 - - + -
206Z LEU* 4.1 14.1 - - + -
209Z VAL* 3.9 21.7 - - - +
210Z PHE 4.9 2.0 - - - +
211Z THR 2.9 21.1 + - - +
212Z GLU* 3.6 5.6 - - - +
214Z LYS* 1.3 76.4 - - - +
216Z ARG* 1.3 58.2 + - - +
218Z MET* 3.2 23.5 + - + +
219Z CYS* 2.9 48.4 + - - -
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Residues in contact with ARG 216 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176Z ALA* 4.0 22.4 + - + +
212Z GLU* 2.9 36.4 + - - +
213Z GLU* 3.2 41.5 + - - +
215Z PHE* 1.3 76.4 - - - +
217Z TYR* 1.3 70.8 + - - +
219Z CYS* 3.1 7.6 + - - +
220Z ILE* 2.9 35.8 + - + +
279Z ASN* 2.7 29.3 + - - +
282Z PHE* 3.6 27.8 - - + -
283Z LEU* 3.5 34.6 - - - +
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Residues in contact with TYR 217 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213Z GLU* 2.6 61.5 + - + +
214Z LYS* 3.2 13.7 + - + +
216Z ARG* 1.3 78.5 + - - +
218Z MET* 1.3 58.3 + - - +
220Z ILE* 3.4 3.6 + - + +
221Z LEU* 2.9 34.5 + - + +
242Z LEU* 3.8 12.8 - - + -
248Z PRO 5.4 3.8 - - - -
250Z ILE* 3.9 40.2 - - + +
275Z PHE* 3.7 26.9 - + + -
279Z ASN* 3.5 36.0 + - - -
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Residues in contact with MET 218 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Z LEU* 4.4 3.6 - - + -
9Z PHE* 4.4 5.4 - - + -
206Z LEU* 3.9 16.8 - - + -
209Z VAL* 4.4 5.2 - - + -
214Z LYS 2.9 12.7 + - - +
215Z PHE* 3.4 48.5 - - + +
217Z TYR* 1.3 74.3 - - - +
219Z CYS* 1.3 74.0 + - - +
221Z LEU* 3.2 2.4 + - - +
222Z SER* 2.9 23.7 + - - -
235Z LEU* 4.3 17.3 - - + +
238Z ALA* 3.8 8.1 - - + +
239Z CYS* 3.6 42.6 - - + +
242Z LEU* 3.4 14.1 - - + +
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Residues in contact with CYS 219 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Z ILE* 3.7 37.7 - - + +
6Z LEU* 4.3 10.1 - - - -
176Z ALA* 3.9 21.8 - - + -
215Z PHE* 2.9 41.8 + - - +
216Z ARG 3.1 7.2 + - - +
218Z MET* 1.3 84.0 - - - +
220Z ILE* 1.3 62.4 + - + +
222Z SER* 2.7 22.2 + - - -
223Z GLY 3.5 4.7 + - - -
235Z LEU* 4.9 0.4 - - - -
282Z PHE* 5.4 0.9 - - + -
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Residues in contact with ILE 220 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216Z ARG* 2.9 28.6 + - + +
217Z TYR* 3.7 3.6 - - - +
219Z CYS* 1.3 76.8 - - - +
221Z LEU* 1.3 62.7 + - - +
223Z GLY* 3.2 14.2 + - - -
224Z CYS* 4.1 13.6 + - - -
227Z LEU* 4.3 11.1 - - + +
229Z SER* 5.1 0.7 - - - -
271Z TYR* 4.4 3.8 + - - -
275Z PHE* 3.5 31.4 - - + -
278Z ALA* 3.9 16.8 - - + -
279Z ASN* 3.6 39.7 - - + +
282Z PHE* 3.8 27.6 - - + -
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Residues in contact with LEU 221 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217Z TYR 2.9 24.6 + - - +
218Z MET 3.2 0.2 + - - -
220Z ILE* 1.3 76.5 - - - +
222Z SER* 1.3 61.5 + - - +
229Z SER* 3.3 15.8 - - - -
230Z LEU* 4.9 1.1 + - + -
233Z ILE* 3.7 13.8 - - + +
238Z ALA* 3.6 25.6 - - + +
241Z VAL* 4.9 10.5 - - + -
242Z LEU* 4.6 20.6 - - + -
250Z ILE* 5.0 2.9 - - + -
254Z ILE* 4.1 23.6 - - + -
257Z ILE* 5.7 11.2 - - + -
271Z TYR* 3.7 25.0 + - + +
275Z PHE* 3.7 20.6 - - + -
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Residues in contact with SER 222 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Z ILE* 3.3 19.0 - - - +
218Z MET 2.9 12.1 + - - -
219Z CYS 2.7 22.5 + - - -
221Z LEU* 1.3 77.1 - - - +
223Z GLY* 1.3 55.0 + - - +
229Z SER* 3.2 2.2 + - - -
233Z ILE 3.4 0.7 - - - +
234Z GLY* 3.4 31.9 + - - -
235Z LEU* 3.6 18.1 - - - +
403Z NA 2.5 30.5 - - - -
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Residues in contact with GLY 223 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Z GLY 3.9 10.6 - - - +
3Z ILE* 4.4 5.9 - - - -
4Z GLN* 4.6 4.0 + - - +
219Z CYS 4.1 2.3 - - - +
220Z ILE 3.2 9.5 + - - -
221Z LEU 3.2 0.4 - - - -
222Z SER* 1.3 86.0 + - - +
224Z CYS* 1.3 62.0 + - - -
228Z SER* 4.5 1.3 - - - -
229Z SER* 3.7 22.2 - - - -
403Z NA 4.5 0.9 - - - -
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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