Contacts of the helix formed by residues 215 - 229 (chain G) in PDB entry 6CM9
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 LEU 215 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179G THR 5.5 4.3 - - - +
181G ASN 6.0 2.5 - - - +
183G LEU* 4.1 20.4 - - + -
198G LEU* 3.9 19.7 - - + -
211G HIS* 4.8 6.1 - - + +
212G PHE* 3.7 42.6 - - + +
213G ARG 3.4 0.2 - - - -
214G LYS* 1.3 76.2 - - - +
216G VAL* 1.3 63.6 + - - +
217G PRO* 3.6 1.8 - - - -
218G GLN* 3.8 23.2 + - - +
219G LEU* 3.5 35.1 + - + +
252G LEU* 5.2 1.8 - - + -
256G LEU* 5.5 0.2 - - + -
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Residues in contact with VAL 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213G ARG* 3.3 32.5 - - + +
214G LYS 3.2 1.8 - - - -
215G LEU* 1.3 77.1 - - - +
217G PRO* 1.4 63.1 - - + +
218G GLN 3.2 0.5 + - - -
219G LEU* 3.3 11.2 + - - +
220G VAL* 2.9 41.6 + - + +
253G LEU* 4.4 11.2 - - + -
256G LEU* 4.1 17.3 - - + -
263G SER* 4.2 13.7 - - - +
266G ALA* 4.1 21.8 - - + -
267G MET* 4.5 12.6 - - + -
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Residues in contact with PRO 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 ARG 5.1 0.7 - - - +
214G LYS 3.4 15.5 - - - +
216G VAL* 1.4 94.1 - - + +
218G GLN* 1.3 57.5 + - - +
220G VAL* 3.4 12.4 - - + +
221G ARG* 2.9 29.1 + - - +
266G ALA* 5.2 9.2 - - + -
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Residues in contact with GLN 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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181G ASN* 5.0 11.1 + - - +
183G LEU* 3.5 27.9 + - + +
184G ASN* 3.1 40.5 + - - +
215G LEU* 3.9 27.7 - - + +
216G VAL 3.2 0.6 - - - -
217G PRO* 1.3 79.3 - - + +
219G LEU* 1.3 57.5 + - - +
221G ARG* 3.3 9.4 + - - +
222G ILE* 3.0 32.1 + - + +
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Residues in contact with LEU 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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183G LEU* 5.0 11.2 - - + -
195G VAL* 5.7 1.3 - - + -
215G LEU* 3.5 33.3 + - + +
216G VAL* 3.3 11.2 + - - +
218G GLN* 1.3 76.4 - - - +
220G VAL* 1.3 62.9 + - - +
222G ILE* 3.5 18.4 - - + +
223G LEU* 2.9 29.5 + - - +
249G ILE* 3.7 32.2 - - + +
252G LEU* 3.7 25.1 - - + -
253G LEU* 3.7 30.7 - - + -
256G LEU* 5.2 3.6 - - + -
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Residues in contact with VAL 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 VAL* 2.9 35.1 + - + +
217G PRO* 3.4 12.8 - - + +
218G GLN 3.3 0.2 - - - -
219G LEU* 1.3 76.4 - - - +
221G ARG* 1.3 58.4 + - - +
223G LEU* 3.3 2.8 + - - +
224G LYS* 2.9 29.8 + - + +
253G LEU* 4.8 4.9 - - + -
266G ALA 4.3 18.2 - - - +
267G MET* 4.4 6.3 - - + -
269G ASP* 5.9 2.5 - - + -
270G ILE* 3.7 40.9 - - + +
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Residues in contact with ARG 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 PRO 2.9 13.4 + - - +
218G GLN* 3.5 10.1 - - - +
220G VAL* 1.3 77.8 - - - +
222G ILE* 1.3 58.3 + - + +
224G LYS* 3.5 13.9 + - - +
225G ASN* 2.8 53.0 + - - +
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Residues in contact with ILE 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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183G LEU* 3.3 35.0 - - + +
191G LEU* 3.8 35.9 - - + -
218G GLN* 3.0 25.0 + - + +
219G LEU* 3.5 18.4 - - + +
220G VAL 3.2 0.2 - - - -
221G ARG* 1.3 77.6 - - + +
223G LEU* 1.3 56.4 + - - +
225G ASN* 3.3 6.8 + - - +
226G LEU* 2.9 33.3 + - + +
249G ILE* 3.9 17.5 - - + -
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Residues in contact with LEU 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 LEU 2.9 16.9 + - - +
220G VAL 3.8 3.4 - - - +
222G ILE* 1.3 76.3 - - - +
224G LYS* 1.3 58.0 + - - +
226G LEU* 3.1 25.3 + - + +
227G ILE* 3.0 44.5 + - + +
246G GLN* 3.8 29.6 - - + +
249G ILE* 3.8 19.7 - - + -
250G LEU* 3.7 29.4 - - + -
253G LEU* 4.5 0.7 - - + -
270G ILE* 3.7 26.7 - - + +
274G VAL* 6.0 2.2 - - + -
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Residues in contact with LYS 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 VAL* 2.9 18.3 + - + +
221G ARG* 3.9 12.8 - - - +
223G LEU* 1.3 78.1 - - - +
225G ASN* 1.3 63.0 + - - +
227G ILE* 3.2 6.8 + - - +
228G MET* 2.9 61.2 + - + +
269G ASP* 4.7 9.5 + - - +
270G ILE* 3.8 16.7 - - + +
273G GLN* 4.0 15.3 - - - +
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Residues in contact with ASN 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 ARG* 2.8 47.6 + - - +
222G ILE* 3.6 6.6 - - - +
224G LYS* 1.3 81.6 - - - +
226G LEU* 1.3 62.4 + - - +
228G MET* 4.1 9.2 - - - +
229G SER* 3.2 28.9 + - - +
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Residues in contact with LEU 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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188G HIS* 3.7 33.7 - - + +
222G ILE* 2.9 20.3 + - + +
223G LEU* 3.1 28.7 + - + +
225G ASN* 1.3 77.0 - - - +
227G ILE* 1.3 63.5 + - - +
229G SER* 3.5 16.1 - - - +
241G SER* 3.9 14.7 - - - +
242G ASP* 4.0 14.8 - - + +
245G LEU* 3.7 28.9 - - + -
246G GLN* 4.0 20.5 + - + +
249G ILE* 4.1 6.5 - - + -
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Residues in contact with ILE 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 LEU* 3.0 30.7 + - + +
224G LYS* 3.2 8.3 + - - +
226G LEU* 1.3 80.4 - - - +
228G MET* 1.3 61.8 + - + +
229G SER 3.6 0.2 + - - -
230G GLY* 4.0 10.9 + - - -
241G SER* 5.5 1.1 + - - -
246G GLN* 4.2 17.9 - - - +
270G ILE* 4.7 9.2 - - + +
273G GLN* 4.1 27.4 - - + +
274G VAL* 4.0 35.7 - - + +
277G ASN* 4.8 16.6 - - + +
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Residues in contact with MET 228 (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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224G LYS* 2.9 48.2 + - + +
225G ASN* 4.8 7.0 - - - +
227G ILE* 1.3 74.3 - - - +
229G SER* 1.3 60.6 + - - +
230G GLY* 2.9 8.5 + - - -
273G GLN* 3.8 28.0 - - - +
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Residues in contact with SER 229 (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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225G ASN* 3.2 22.3 + - - +
226G LEU* 3.5 14.2 - - - +
227G ILE 3.4 0.8 - - - -
228G MET* 1.3 72.2 - - - +
230G GLY* 1.3 62.4 + - - +
231G TYR* 3.1 12.0 + - - +
232G SER* 4.7 6.3 + - - -
241G SER* 3.5 7.4 + - - -
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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