Contacts of the helix formed by residues 215 - 234 (chain G) in PDB entry 4U7B
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 ASN 215 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213G THR 4.0 3.6 + - - -
214G VAL* 1.3 74.6 - - - +
216G ALA* 1.3 67.0 + - - +
217G ALA* 2.8 29.5 + - - +
218G ARG* 2.9 29.2 + - - +
219G TYR* 3.1 9.4 + - - +
253G SER* 4.3 6.5 - - - -
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Residues in contact with ALA 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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215G ASN* 1.3 73.7 + - - +
217G ALA* 1.3 62.0 + - - +
219G TYR* 4.2 1.6 - - - -
220G GLN* 3.6 9.2 + - - +
253G SER* 3.9 23.3 - - - +
256G ALA* 3.8 28.3 - - + -
258G ALA* 5.2 6.8 - - + +
259G VAL* 3.4 20.9 - - + +
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Residues in contact with ALA 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215G ASN* 2.8 22.2 + - - +
216G ALA* 1.3 71.9 - - - +
218G ARG* 1.3 64.3 + - - +
220G GLN* 3.1 25.5 + - - +
221G GLN* 3.5 4.9 + - - +
258G ALA* 6.4 0.9 - - - -
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Residues in contact with ARG 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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206G GLU* 3.2 23.1 + - - +
208G LEU* 3.7 22.7 - - - +
209G LYS* 5.1 4.0 - - - +
212G GLU* 3.1 30.9 + - - +
213G THR 4.3 8.4 + - - +
214G VAL* 4.0 24.7 - - + -
215G ASN* 2.9 20.9 + - - +
217G ALA* 1.3 78.5 - - - +
219G TYR* 1.3 63.1 + - - +
221G GLN* 3.1 22.5 + - - +
222G GLN* 3.1 19.2 + - - +
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Residues in contact with TYR 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G GLU* 4.7 5.8 - - - -
196G TRP* 3.8 24.1 + + - -
214G VAL* 3.7 17.9 - - + -
215G ASN 3.1 10.6 + - - +
216G ALA* 4.2 6.5 - - - +
217G ALA 3.3 0.2 - - - -
218G ARG* 1.3 77.0 - - - +
220G GLN* 1.3 57.1 + - - +
222G GLN* 3.3 21.1 + - - +
223G LEU* 3.0 60.2 + - + +
246G PHE* 3.7 27.4 - + - -
248G HIS* 3.9 10.3 - + - +
253G SER* 4.5 4.0 - - - +
254G HIS* 3.3 43.1 + + + -
259G VAL* 3.8 20.4 - - + -
263G LEU* 6.1 0.7 - - + -
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Residues in contact with GLN 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216G ALA 3.6 8.3 + - - +
217G ALA* 3.1 14.5 + - - +
219G TYR* 1.3 77.0 - - - +
221G GLN* 1.3 64.9 - - - +
223G LEU* 3.4 11.7 + - - +
224G ILE* 3.2 31.4 + - + +
258G ALA* 2.8 41.0 - - - +
259G VAL* 3.3 5.5 + - + -
262G THR* 2.7 34.8 + - + +
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Residues in contact with GLN 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 ALA 3.5 4.7 + - - +
218G ARG* 3.1 17.2 + - - +
220G GLN* 1.3 77.2 - - - +
222G GLN* 1.3 61.9 + - + +
224G ILE* 3.1 19.7 + - - +
225G ASN* 2.8 45.0 + - - +
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Residues in contact with GLN 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G GLU* 5.0 0.2 - - - +
194G CYS* 3.5 22.8 - - - +
196G TRP* 3.5 30.9 - - + -
204G TYR* 4.4 2.8 - - - -
206G GLU* 2.9 43.2 + - - +
208G LEU* 3.8 6.9 - - - +
214G VAL* 3.8 17.8 - - - +
218G ARG* 3.1 18.9 + - - +
219G TYR* 3.3 30.8 + - + +
221G GLN* 1.3 77.3 - - - +
223G LEU* 1.3 58.2 + - - +
225G ASN* 3.4 1.8 + - - +
226G LEU* 2.9 31.2 + - - +
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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
----------------------------------------------------------
196G TRP* 5.3 2.7 - - + +
219G TYR* 3.0 49.2 + - + +
220G GLN* 3.6 11.4 - - - +
221G GLN 3.3 0.2 - - - -
222G GLN* 1.3 76.0 - - - +
224G ILE* 1.3 57.9 + - - +
226G LEU* 3.5 10.8 - - + +
227G ASN* 3.2 25.1 + - - +
246G PHE* 4.0 18.8 - - + -
259G VAL* 3.7 18.8 - - + +
262G THR* 4.8 6.5 - - + -
263G LEU* 3.8 27.8 - - + -
266G LEU* 4.1 14.2 - - + +
268G TRP* 3.9 18.6 - - + -
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Residues in contact with ILE 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 GLN* 3.2 22.3 + - + +
221G GLN* 3.1 23.7 + - - +
223G LEU* 1.3 74.5 - - - +
225G ASN* 1.3 66.8 + - - +
227G ASN* 3.2 8.3 + - + +
228G ARG* 2.9 42.2 + - - +
262G THR* 4.2 20.4 - - + -
266G LEU* 5.5 3.4 - - + -
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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
----------------------------------------------------------
204G TYR* 3.7 27.0 + - + +
206G GLU* 4.0 11.1 + - - -
221G GLN* 2.8 44.4 + - - +
222G GLN 3.8 2.2 - - - +
224G ILE* 1.3 76.1 - - - +
226G LEU* 1.3 53.2 + - - +
228G ARG* 3.3 20.9 + - - +
229G ALA* 2.8 37.9 + - - +
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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
----------------------------------------------------------
153G VAL* 5.0 3.6 - - + -
196G TRP* 3.9 45.5 - - + +
203G ILE* 4.0 17.3 - - + -
204G TYR* 4.3 18.5 - - + -
222G GLN 2.9 18.8 + - - +
223G LEU* 3.5 10.3 - - + +
225G ASN* 1.3 72.2 - - - +
227G ASN* 1.3 58.5 + - - +
229G ALA 2.9 3.1 + - - -
230G LEU* 2.5 55.2 + - + +
246G PHE* 4.3 5.2 - - + -
268G TRP* 3.8 28.9 - - + -
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Residues in contact with ASN 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 3.2 8.9 + - - +
224G ILE* 3.2 11.1 + - + +
226G LEU* 1.3 80.4 - - - +
228G ARG* 1.3 61.0 + - - +
230G LEU* 3.6 6.5 - - - +
231G GLN* 3.1 28.1 + - - +
237G TYR* 2.6 38.0 + - - -
241G GLN* 4.2 12.2 + - - +
266G LEU* 3.3 33.1 - - + +
268G TRP* 3.9 7.1 - - + -
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Residues in contact with ARG 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 ILE* 2.9 32.8 + - + +
225G ASN* 3.5 23.0 + - - +
227G ASN* 1.3 77.0 + - - +
229G ALA* 1.3 56.6 + - - +
231G GLN* 2.8 38.7 + - + +
232G ARG* 3.4 14.1 + - + +
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Residues in contact with ALA 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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203G ILE* 4.4 6.3 - - - +
204G TYR* 3.9 31.0 - - + -
225G ASN 2.8 20.0 + - - +
226G LEU 3.6 2.2 - - - +
228G ARG* 1.3 74.4 - - - +
230G LEU* 1.3 61.5 + - - +
232G ARG* 3.6 28.9 + - - +
233G LYS* 3.4 30.0 + - + +
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Residues in contact with LEU 230 (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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153G VAL* 4.4 18.2 - - + -
203G ILE* 3.8 32.6 - - + +
226G LEU* 2.5 41.7 + - + +
227G ASN* 3.6 6.7 - - - +
229G ALA* 1.3 74.3 - - - +
231G GLN* 1.3 61.1 + - - +
233G LYS* 4.8 0.2 - - - -
234G ARG* 3.2 29.0 + - + +
237G TYR* 3.2 51.1 - - + -
244G VAL* 4.5 4.5 - - + -
268G TRP* 4.5 13.5 - - + -
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Residues in contact with GLN 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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227G ASN* 3.1 19.8 + - - +
228G ARG* 2.8 19.3 + - + +
230G LEU* 1.3 78.7 - - - +
232G ARG* 1.3 57.5 + - + +
233G LYS 3.7 0.3 + - - -
234G ARG 4.0 12.5 - - - +
235G PRO* 4.7 3.6 - - - +
237G TYR* 3.8 17.2 - - + +
238G GLN* 3.4 43.4 + - + +
241G GLN* 3.6 28.0 + - - +
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Residues in contact with ARG 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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204G TYR* 5.8 1.8 - - - -
228G ARG* 3.8 15.3 - - + +
229G ALA* 3.6 31.7 - - - +
231G GLN* 1.3 77.5 - - - +
233G LYS* 1.3 91.5 + - - +
234G ARG 3.7 0.7 - - - -
235G PRO* 5.2 3.9 - - - +
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Residues in contact with LYS 233 (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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202G VAL 4.5 7.3 + - - +
203G ILE* 3.3 35.7 - - + +
229G ALA* 3.4 15.7 + - - +
230G LEU* 4.4 3.1 - - - +
231G GLN 3.4 0.2 - - - -
232G ARG* 1.3 108.1 - - - +
234G ARG* 1.3 88.2 + - + +
235G PRO* 3.5 10.4 - - - +
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Residues in contact with ARG 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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198G ASP* 2.8 41.8 + - - +
200G SER* 3.7 18.7 + - - -
201G GLY* 3.7 24.0 + - - +
202G VAL 4.7 3.4 + - - -
203G ILE* 4.0 20.9 - - + +
230G LEU* 3.2 18.1 + - + +
231G GLN 4.0 7.0 - - - +
233G LYS* 1.3 109.8 + - + +
235G PRO* 1.3 67.0 - - - +
236G GLU* 3.2 17.9 - - + +
237G TYR* 2.9 27.1 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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