Contacts of the helix formed by residues 215 - 234 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B THR* 4.1 5.0 + - - +
214B VAL* 1.3 74.3 - - - +
216B ALA* 1.3 55.6 + - - +
217B ALA* 2.7 26.1 + - - +
218B ARG* 2.7 45.6 + - - +
219B TYR* 3.1 8.4 + - - +
253B SER* 4.1 4.0 - - - -
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Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ASN* 1.3 71.5 + - - +
217B ALA* 1.3 60.6 + - - +
219B TYR* 4.0 1.8 - - - -
220B GLN* 3.2 12.5 + - - +
253B SER* 3.8 16.5 - - - +
256B ALA* 3.5 31.4 - - + -
258B ALA* 4.8 9.1 - - + +
259B VAL* 3.2 30.7 - - + +
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Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ASN* 2.7 20.9 + - - +
216B ALA* 1.3 73.9 - - - +
218B ARG* 1.3 65.5 + - - +
220B GLN* 3.4 13.2 + - - +
221B GLN* 3.1 24.5 + - - +
258B ALA* 5.6 0.9 - - - +
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Residues in contact with ARG 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B GLU* 2.9 25.0 + - - -
208B LEU* 3.9 25.6 - - - +
209B LYS* 4.2 20.4 - - - +
212B GLU* 5.2 6.7 - - - +
213B THR 4.0 16.1 + - - +
214B VAL* 4.3 8.3 - - + -
215B ASN* 2.7 30.7 + - - +
217B ALA* 1.3 74.6 - - - +
219B TYR* 1.3 56.9 + - - +
221B GLN* 3.4 9.7 + - - +
222B GLN* 3.1 37.0 + - - +
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Residues in contact with TYR 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B GLU* 4.6 4.0 - - - -
196B TRP* 3.9 24.6 + + - -
214B VAL* 3.8 22.0 - - + +
215B ASN 3.1 8.7 + - - +
216B ALA* 4.0 4.0 - - - +
218B ARG* 1.3 75.9 - - - +
220B GLN* 1.3 59.1 + - - +
222B GLN* 2.8 36.5 + - - +
223B LEU* 2.9 27.9 + - + +
246B PHE* 3.7 14.4 - - - -
248B HIS* 3.0 28.0 + + - +
253B SER* 3.4 24.5 - - - +
254B HIS* 3.4 29.7 + + - -
259B VAL* 3.6 27.6 - - + -
263B LEU* 6.2 0.4 - - + -
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Residues in contact with GLN 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ALA 3.2 16.1 + - - +
217B ALA* 3.4 10.4 - - - +
219B TYR* 1.3 79.0 - - - +
221B GLN* 1.3 61.4 + - - +
223B LEU* 3.4 20.9 + - - +
224B ILE* 3.3 25.9 + - + +
258B ALA* 3.2 38.2 + - - +
259B VAL* 3.9 6.2 - - + +
261B ASP* 5.3 4.2 + - - -
262B THR* 3.2 20.9 + - + +
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Residues in contact with GLN 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B ALA 3.1 11.3 + - - +
218B ARG* 3.4 16.4 - - - +
220B GLN* 1.3 80.0 - - - +
222B GLN* 1.3 55.9 + - - +
224B ILE* 3.8 9.6 + - + +
225B ASN* 2.5 45.9 + - - +
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Residues in contact with GLN 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B GLU* 5.6 0.3 - - - +
194B CYS* 3.9 11.7 - - - -
196B TRP* 3.6 32.2 - - + -
204B TYR* 4.4 2.3 - - + -
206B GLU* 2.7 41.3 + - - +
208B LEU* 3.8 19.0 - - - +
214B VAL* 4.2 8.6 - - - +
218B ARG* 3.1 23.7 + - - +
219B TYR* 2.8 27.9 + - - +
221B GLN* 1.3 75.1 - - - +
223B LEU* 1.3 55.8 + - - +
224B ILE 3.1 2.0 - - - -
225B ASN* 3.2 4.6 + - - +
226B LEU* 2.7 36.4 + - - +
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Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B TRP* 5.6 2.2 - - + +
219B TYR* 2.9 33.8 + - + +
220B GLN* 3.4 13.4 + - - +
222B GLN* 1.3 75.3 - - - +
224B ILE* 1.3 57.2 + - - +
226B LEU* 3.4 12.2 - - + +
227B ASN* 3.1 24.9 + - - +
246B PHE* 4.3 17.3 - - + -
259B VAL* 3.6 31.0 - - + -
262B THR* 4.5 16.2 - - + -
263B LEU* 3.6 28.3 - - + -
266B LEU* 4.2 4.9 - - + +
268B TRP* 3.8 23.3 - - + -
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Residues in contact with ILE 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B GLN* 3.3 27.3 + - + +
221B GLN* 4.0 8.5 - - + +
222B GLN 3.1 0.4 - - - -
223B LEU* 1.3 74.2 - - - +
225B ASN* 1.3 68.7 + - - +
226B LEU 3.0 1.6 - - - -
227B ASN* 3.0 7.7 + - + +
228B ARG* 2.9 24.9 + - + +
262B THR* 4.3 17.7 - - + -
266B LEU* 5.1 9.0 - - + -
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Residues in contact with ASN 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B TYR* 3.6 28.4 - - + +
206B GLU* 3.8 10.3 + - - +
221B GLN* 2.5 39.4 + - - +
222B GLN 3.2 4.4 + - - +
224B ILE* 1.3 78.9 - - - +
226B LEU* 1.3 63.6 + - - +
228B ARG* 3.6 15.3 - - - +
229B ALA* 3.2 19.8 + - - +
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B VAL* 5.4 2.7 - - + -
196B TRP* 4.1 40.6 - - + +
203B ILE* 3.7 29.4 - - + -
204B TYR* 3.8 22.1 - - + -
222B GLN 2.7 21.3 + - - +
223B LEU* 3.4 11.2 - - + +
225B ASN* 1.3 70.2 - - - +
227B ASN* 1.3 55.6 - - - +
229B ALA* 2.8 9.4 + - - +
230B LEU* 2.6 43.9 + - + +
246B PHE* 4.3 5.8 - - + -
268B TRP* 3.7 28.9 - - + -
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Residues in contact with ASN 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B LEU 3.1 7.0 + - - +
224B ILE* 3.0 8.3 + - + +
226B LEU* 1.3 80.5 - - - +
228B ARG* 1.3 56.4 + - - +
230B LEU* 3.8 6.5 - - - +
231B GLN* 2.9 35.1 + - - +
237B TYR* 2.6 37.2 + - - -
241B GLN* 3.8 15.6 - - - +
266B LEU* 3.3 35.1 - - + +
268B TRP* 3.4 9.5 - - + -
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Residues in contact with ARG 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B ILE* 2.9 13.2 + - + +
225B ASN* 3.6 18.8 - - - +
227B ASN* 1.3 75.0 - - - +
229B ALA* 1.3 66.6 + - - +
231B GLN* 3.1 25.8 + - - +
232B ARG* 3.3 22.4 + - - +
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Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B ILE* 4.6 6.5 - - - +
204B TYR* 4.0 26.7 - - + -
225B ASN 3.2 9.6 + - - +
226B LEU 2.8 9.8 + - - +
228B ARG* 1.3 79.1 - - + +
230B LEU* 1.3 57.5 + - - +
232B ARG* 3.4 30.1 - - - +
233B LYS* 3.0 36.9 + - + +
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Residues in contact with LEU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B VAL* 4.7 21.1 - - + -
203B ILE* 4.0 19.2 - - + +
226B LEU* 2.6 36.6 + - + +
227B ASN* 3.6 6.7 - - - +
229B ALA* 1.3 72.2 - - - +
231B GLN* 1.3 55.1 + - - +
233B LYS* 4.5 1.3 - - - -
234B ARG* 2.8 42.1 + - + +
237B TYR* 3.2 53.4 - - + -
244B VAL* 4.8 5.2 - - + -
268B TRP* 4.3 19.3 - - + -
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Residues in contact with GLN 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B ASN* 2.9 24.4 + - - +
228B ARG* 3.1 14.9 + - - +
230B LEU* 1.3 77.4 - - - +
232B ARG* 1.3 59.7 + - - +
234B ARG 3.4 14.8 - - - +
235B PRO* 4.1 4.5 - - - +
237B TYR* 3.6 25.3 - - + -
238B GLN* 4.3 35.0 - - + +
241B GLN* 3.5 23.8 - - - +
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Residues in contact with ARG 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B TYR* 5.8 1.6 - - - -
228B ARG* 3.3 18.1 + - - +
229B ALA* 3.4 34.3 - - - +
231B GLN* 1.3 78.0 - - + +
233B LYS* 1.3 83.7 + - - +
234B ARG 5.1 0.4 - - - -
235B PRO* 5.1 3.9 - - - +
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Residues in contact with LYS 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B VAL* 4.6 11.9 + - - +
203B ILE* 4.2 23.1 + - + +
229B ALA* 3.0 26.6 + - + +
230B LEU* 4.0 3.8 - - - +
232B ARG* 1.3 103.4 - - - +
234B ARG* 1.3 88.5 + - + +
235B PRO* 3.2 10.5 - - - +
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Residues in contact with ARG 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B ASP* 2.7 39.8 + - - +
200B SER* 3.8 16.5 + - - -
201B GLY* 3.7 18.2 - - - +
202B VAL 4.5 4.8 + - - -
203B ILE* 3.5 28.1 - - + +
230B LEU* 2.8 23.6 + - + +
231B GLN 3.4 9.7 - - - +
233B LYS* 1.3 105.6 + - + +
235B PRO* 1.3 66.8 - - - +
236B GLU* 3.3 26.0 - - - +
237B TYR* 3.2 24.8 - - + +
238B GLN 4.4 0.2 + - - -
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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
------------------------------------------------------------
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