Contacts of the helix formed by residues 230 - 243 (chain G) in PDB entry 6BAA
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 TYR 230 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219G GLN* 3.1 39.7 - - - -
226G SER 2.5 19.9 + - - -
227G LYS 4.8 2.9 + - - -
228G GLY 3.7 8.5 - - - -
229G THR* 1.3 75.7 - - - +
231G TRP* 1.3 65.3 + - - +
232G TRP* 3.1 13.7 - + + +
233G MET* 2.9 31.0 + - + +
234G ASN* 3.7 4.7 + - - -
374G GLN* 3.9 10.9 + - - +
375G ALA* 5.2 0.5 - - - -
378G TYR* 3.3 33.3 - + - +
1243G ALA* 4.7 7.9 - - + +
1246G ARG* 3.3 29.9 - - + +
1247G TRP* 3.6 26.8 - - + -
1250G VAL* 3.5 20.9 - - + -
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Residues in contact with TRP 231 (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 ASN* 5.8 3.4 - - - +
225G LEU* 5.1 2.5 - - + -
226G SER* 3.3 22.0 - - - +
229G THR* 3.2 23.2 + - + +
230G TYR* 1.3 75.7 - - - +
232G TRP* 1.3 63.3 + - - +
234G ASN* 2.9 47.7 + - + +
235G ALA* 4.1 2.1 + - - +
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Residues in contact with TRP 232 (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 ARG 4.3 12.1 - - - -
217G PHE* 4.2 11.4 - + - -
218G LEU* 3.6 31.6 - - + -
219G GLN* 2.7 47.6 + - + +
222G VAL* 3.9 26.7 - - + -
226G SER* 3.9 11.9 + - - -
230G TYR* 4.2 7.9 - + - +
231G TRP* 1.3 80.7 - - - +
233G MET* 1.3 112.4 - - + +
234G ASN 3.3 0.3 + - - -
235G ALA* 3.4 16.0 + - - +
236G PHE* 3.7 13.7 + - + +
1240G PHE* 3.9 24.5 - + - -
1243G ALA* 4.1 11.9 - - + -
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Residues in contact with MET 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230G TYR* 2.9 21.7 + - + +
232G TRP* 1.3 104.6 - - + +
234G ASN* 1.3 65.6 - - - +
236G PHE* 3.0 35.9 + - - +
237G ILE* 3.0 20.3 + - + +
1189G LEU* 6.1 0.4 - - - -
1240G PHE* 4.7 6.7 - - + +
1243G ALA* 3.4 45.1 - - + +
1244G ALA* 3.8 9.9 - - - +
1247G TRP* 3.8 28.3 - - + -
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Residues in contact with ASN 234 (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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229G THR 5.0 0.4 + - - -
230G TYR 3.9 2.2 + - - -
231G TRP* 2.9 62.3 + - + +
232G TRP 3.2 0.2 - - - -
233G MET* 1.3 76.7 - - - +
235G ALA* 1.3 65.4 + - - +
237G ILE* 3.1 31.9 + - + +
238G LYS* 3.7 10.3 + - - +
1247G TRP* 2.6 38.2 + - - +
1251G CYS* 5.0 0.5 - - - -
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Residues in contact with ALA 235 (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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231G TRP 4.1 1.9 + - - +
232G TRP* 3.4 11.0 + - - +
233G MET 3.3 0.6 - - - -
234G ASN* 1.3 79.6 - - - +
236G PHE* 1.3 63.1 + - - +
238G LYS* 3.8 18.4 + - - +
239G THR* 3.9 10.0 + - - -
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Residues in contact with PHE 236 (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 VAL* 6.0 5.6 - - + -
216G ARG 5.5 3.4 - - - -
232G TRP* 3.7 11.0 + - + +
233G MET* 3.0 28.3 + - - +
235G ALA* 1.3 80.2 - - - +
237G ILE* 1.3 80.5 + - + +
239G THR* 3.4 21.4 + - - -
240G ALA* 3.6 9.6 + - + -
245G ILE* 4.8 13.4 - - + +
249G ALA 5.7 3.6 - - - -
250G ILE* 4.6 22.2 - - + -
1185G ALA* 5.3 3.1 - - + -
1189G LEU* 4.9 17.0 - - + -
1240G PHE* 4.5 29.8 - + - -
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Residues in contact with ILE 237 (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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233G MET* 3.0 23.7 + - + +
234G ASN* 3.1 27.4 - - - +
236G PHE* 1.3 85.2 - - + +
238G LYS* 1.3 76.0 + - + +
239G THR 3.0 2.2 - - - -
240G ALA* 2.7 26.8 + - - +
241G HIS* 2.9 12.2 + - - +
1181G TYR* 4.2 25.6 - - + +
1185G ALA* 3.9 24.9 - - + -
1244G ALA* 6.0 2.0 - - + -
1247G TRP* 4.0 34.5 - - + -
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Residues in contact with LYS 238 (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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234G ASN* 3.7 14.3 + - - +
235G ALA* 4.0 11.4 - - - +
236G PHE 3.5 0.6 - - - -
237G ILE* 1.3 85.5 - - + +
239G THR* 1.3 56.7 + - - +
241G HIS* 3.4 10.7 + - - +
242G LYS* 2.9 27.4 + - - +
1181G TYR* 5.0 16.6 - - + +
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Residues in contact with THR 239 (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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235G ALA 3.9 8.1 + - - -
236G PHE* 3.4 14.4 + - - -
237G ILE 3.0 0.4 - - - -
238G LYS* 1.3 78.4 - - - +
240G ALA* 1.3 53.4 + - - +
242G LYS* 3.0 6.6 + - + +
243G LYS* 2.7 59.6 + - + +
245G ILE* 5.6 4.0 - - + -
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Residues in contact with ALA 240 (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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236G PHE* 3.6 7.3 + - + +
237G ILE* 2.7 22.4 + - - +
239G THR* 1.3 75.2 - - - +
241G HIS* 1.3 58.4 + - - +
243G LYS 2.9 20.8 - - - +
244G PRO* 4.9 0.3 - - - +
245G ILE* 3.5 28.6 - - + +
1184G VAL* 3.5 14.1 - - + +
1185G ALA* 4.5 20.0 - - + -
1188G ASP* 4.4 6.2 - - - +
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Residues in contact with HIS 241 (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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237G ILE 2.9 10.4 + - - +
238G LYS* 3.6 10.1 - - - +
240G ALA* 1.3 78.4 - - - +
242G LYS* 1.3 66.7 + - + +
1180G LYS* 4.9 19.7 + - + -
1181G TYR* 3.4 47.2 + + + -
1184G VAL* 4.2 24.2 - - + +
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Residues in contact with LYS 242 (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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238G LYS 2.9 13.5 + - - +
239G THR* 3.0 10.7 + - + +
241G HIS* 1.3 83.5 - - + +
243G LYS* 1.3 66.8 + - + +
244G PRO* 4.6 1.2 - - - +
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Residues in contact with LYS 243 (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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323D ASP* 5.4 7.4 - - - -
239G THR* 2.7 40.4 + - + +
240G ALA* 2.9 22.4 - - - +
242G LYS* 1.3 82.2 - - + +
244G PRO* 1.3 100.2 + - + +
245G ILE* 4.3 4.8 - - + +
246G ASP* 5.1 3.4 - - - +
249G ALA* 4.9 13.1 - - - +
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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