Contacts of the helix formed by residues 211 - 227 (chain G) in PDB entry 6MZL
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 PRO 211 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210G ASP* 1.3 92.5 - - - +
212G THR* 1.3 63.0 + - + +
214G TYR* 3.2 16.0 + - + +
215G GLU* 2.8 30.0 + - - +
247G MET* 5.1 1.4 - - + +
250G GLU* 5.4 1.8 - - + +
251G LEU* 3.8 25.4 - - + +
254G ASN* 3.9 24.2 - - - +
256G HIS* 4.4 23.3 - - + +
259G GLU* 6.2 1.1 - - + -
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Residues in contact with THR 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210G ASP* 2.8 26.4 + - - +
211G PRO* 1.3 80.2 - - + +
213G MET* 1.3 63.0 + - - +
215G GLU* 3.0 36.8 + - - +
216G GLU* 2.7 31.3 + - - +
259G GLU* 4.4 20.2 - - + -
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Residues in contact with MET 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210G ASP* 3.3 33.4 + - + +
212G THR* 1.3 81.1 + - - +
214G TYR* 1.3 57.6 + - + +
216G GLU* 3.3 15.1 + - + +
217G TYR* 2.9 73.1 + - + +
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Residues in contact with TYR 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210G ASP 3.3 26.6 + - - -
211G PRO* 3.2 16.8 + - + +
212G THR 3.2 0.4 - - - -
213G MET* 1.3 74.2 - - + +
215G GLU* 1.3 57.5 + - - +
217G TYR* 3.4 29.9 - + + +
218G TYR* 2.9 28.4 + - - +
247G MET* 3.7 21.6 - - + +
250G GLU* 3.7 21.5 - - - -
325G GLN 5.6 0.4 - - - -
326G ASN* 3.0 30.9 + - + +
327G ASN* 5.2 0.4 - - - -
328G GLN* 3.6 35.2 + - + +
329G ILE* 5.4 4.5 - - + +
331G ASN* 5.5 0.2 + - - -
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Residues in contact with GLU 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211G PRO 2.8 15.6 + - - +
212G THR* 3.0 29.7 + - - +
214G TYR* 1.3 76.4 - - - +
216G GLU* 1.3 64.5 + - + +
218G TYR* 3.2 5.7 + - - +
219G SER* 2.9 29.1 + - - -
247G MET* 5.8 1.8 - - + -
251G LEU* 3.9 16.2 - - + +
259G GLU* 3.5 30.3 - - - +
263G PHE* 3.5 47.2 - - + +
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Residues in contact with GLU 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212G THR* 2.7 39.7 + - - +
213G MET* 3.3 17.3 + - + +
215G GLU* 1.3 81.5 - - + +
217G TYR* 1.3 65.0 + - + +
219G SER* 3.4 11.5 - - - +
220G GLY* 2.9 25.5 + - - -
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Residues in contact with TYR 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213G MET* 2.9 54.0 + - + +
214G TYR* 3.4 39.7 - + - +
215G GLU 3.2 0.2 - - - -
216G GLU* 1.3 77.3 - - + +
218G TYR* 1.3 59.8 + - - +
220G GLY* 3.5 0.6 + - - -
221G LEU* 2.9 31.7 + - - +
324G LYS* 3.8 23.4 + - + +
325G GLN 5.0 11.3 + - - -
327G ASN* 5.2 8.3 - - - -
329G ILE* 4.0 18.2 - - + -
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Residues in contact with TYR 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214G TYR 2.9 13.5 + - - +
215G GLU 3.3 7.9 - - - +
217G TYR* 1.3 75.5 - - - +
219G SER* 1.3 58.8 + - - +
221G LEU* 3.8 4.2 - - - +
222G LYS* 2.8 50.1 + - + +
240G PHE* 3.3 24.5 + + - -
243G LEU* 3.8 33.4 - - + -
244G PHE* 3.5 35.2 - + + +
247G MET* 5.1 9.4 - - + -
263G PHE* 3.4 24.9 - + + -
267G PHE* 3.8 31.8 + + + -
270G ASP* 5.1 0.2 + - - -
271G GLN* 3.9 9.2 + - - -
329G ILE* 4.6 5.7 - - + +
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Residues in contact with SER 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215G GLU 2.9 15.2 + - - -
216G GLU* 3.4 17.4 - - - +
217G TYR 3.2 0.2 - - - -
218G TYR* 1.3 76.8 - - - +
220G GLY* 1.3 57.2 + - - +
222G LYS* 3.3 5.9 + - - +
223G HIS* 3.0 28.2 + - - +
263G PHE* 4.3 0.5 - - - -
266G LYS* 5.4 2.3 + - - -
267G PHE* 3.2 36.8 - - - -
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Residues in contact with GLY 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216G GLU 2.9 15.7 + - - -
217G TYR* 3.9 1.1 - - - -
219G SER* 1.3 76.0 - - - +
221G LEU* 1.3 57.3 + - - +
223G HIS* 3.4 6.8 + - - +
224G PHE* 2.8 29.1 + - - +
320G HIS* 5.3 3.3 - - - -
324G LYS* 6.1 0.2 - - - -
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Residues in contact with LEU 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217G TYR 2.9 19.0 + - - +
218G TYR* 4.0 2.9 - - - +
220G GLY* 1.3 73.0 - - - +
222G LYS* 1.3 60.6 + - - +
224G PHE* 3.2 13.6 + - + +
225G ILE* 2.9 50.0 + - + +
243G LEU* 4.3 17.9 - - + -
317G LEU* 5.4 9.0 - - + -
320G HIS* 3.5 29.6 - - + +
321G LEU* 4.4 4.5 - - + -
324G LYS* 3.4 16.9 - - - +
329G ILE* 3.7 31.2 - - + -
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Residues in contact with LYS 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218G TYR* 2.8 35.7 + - + +
219G SER 3.4 4.7 - - - +
220G GLY 3.3 0.2 - - - -
221G LEU* 1.3 76.5 - - - +
223G HIS* 1.3 57.7 + - - +
225G ILE* 3.3 2.9 + - - -
226G GLU* 2.5 61.3 + - - +
240G PHE* 3.6 30.9 - - + -
267G PHE* 3.6 27.1 - - + -
270G ASP* 3.3 37.8 + - - +
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Residues in contact with HIS 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219G SER 3.0 16.2 + - - +
220G GLY* 3.8 6.7 - - - +
222G LYS* 1.3 76.4 - - - +
224G PHE* 1.3 51.9 + - - +
226G GLU* 3.1 22.2 + - + +
227G CYS* 2.7 58.9 + - - -
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Residues in contact with PHE 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220G GLY 2.8 17.3 + - - +
221G LEU* 3.2 18.1 + - + +
223G HIS* 1.3 80.0 - - - +
225G ILE* 1.3 61.8 + - + +
227G CYS* 3.0 28.8 + - + +
228G SER* 3.3 14.9 + - - -
316G LEU* 4.6 22.7 - - + -
319G ARG* 6.5 0.4 - - + -
320G HIS* 3.5 53.2 - + + -
323G GLU* 5.5 2.0 - - - -
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Residues in contact with ILE 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221G LEU* 2.9 39.4 + - + +
222G LYS* 4.9 0.7 - - - -
224G PHE* 1.3 77.9 - - + +
226G GLU* 1.3 59.9 + - - +
228G SER* 3.1 33.2 + - - +
233G ARG* 4.3 14.3 - - - +
236G LEU* 4.2 25.8 - - + +
239G LEU* 4.3 26.0 - - + -
240G PHE* 3.6 36.1 - - + -
243G LEU* 5.7 5.6 - - + -
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Residues in contact with GLU 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222G LYS* 2.5 54.1 + - - +
223G HIS* 3.1 30.1 + - + +
225G ILE* 1.3 78.0 - - - +
227G CYS* 1.3 56.4 + - - +
228G SER 3.2 7.1 + - - +
233G ARG* 4.4 33.0 + - - +
240G PHE* 4.3 11.6 - - + -
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Residues in contact with CYS 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223G HIS* 2.7 54.9 + - - +
224G PHE* 3.0 22.5 + - + +
226G GLU* 1.3 74.0 - - - +
228G SER* 1.3 58.9 + - - -
229G LEU* 5.5 1.4 - - - +
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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