Contacts of the helix formed by residues 218 - 235 (chain B) in PDB entry 5HQ0
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 218 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ILE* 5.7 4.0 - - + -
212B GLN* 3.5 5.0 + - - -
216B ARG 3.9 1.5 + - - +
217B LEU* 1.3 75.9 - - - +
219B GLN* 1.3 64.0 - - - +
220B GLU* 4.1 22.2 - - + +
221B THR* 3.2 21.4 + - - +
222B MET 3.5 1.6 + - - -
258B GLU* 4.3 18.4 - - + +
259B GLU* 2.8 29.3 + - - +
260B MET 5.9 0.2 - - - +
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Residues in contact with GLN 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLN* 3.0 14.7 + - - +
217B LEU 3.6 1.2 + - - -
218B LEU* 1.3 70.4 - - - +
220B GLU* 1.3 68.8 + - - +
222B MET* 3.0 17.8 + - - +
223B TYR* 3.0 31.4 + - + -
302B LEU* 3.9 15.3 - - + -
323B LYS* 6.4 1.3 - - + -
327B GLU* 3.1 26.9 + - - +
330B MET* 3.1 34.2 - - - +
402B LYS* 2.8 27.9 + - - -
403B TYR* 5.3 1.1 - - - +
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Residues in contact with GLU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LEU* 4.1 20.2 - - + +
219B GLN* 1.3 82.2 + - - +
221B THR* 1.3 56.2 + - - +
223B TYR* 3.2 2.7 + - - +
224B MET* 2.8 31.2 + - - +
258B GLU* 4.0 12.3 - - + +
299B PRO* 3.6 31.5 - - + +
302B LEU* 3.7 21.8 - - + +
303B HIS* 5.5 7.1 - - + +
306B ARG* 2.8 35.0 + - - -
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Residues in contact with THR 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LEU* 4.2 13.0 - - + -
218B LEU* 3.2 13.5 + - - +
220B GLU* 1.3 77.7 - - - +
222B MET* 1.3 52.0 + - - +
224B MET* 3.4 1.8 + - - -
225B THR* 2.8 38.5 + - - +
251B MET* 4.4 1.8 - - + +
254B ALA* 3.5 7.5 - - + +
255B SER* 3.6 40.2 - - - +
258B GLU* 3.3 23.6 - - - +
259B GLU* 2.6 25.0 + - - +
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Residues in contact with MET 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ILE* 5.0 1.3 - - - +
208B LEU* 3.1 27.6 - - - +
209B VAL* 3.6 13.2 - - + -
212B GLN* 3.0 53.1 - - + +
218B LEU 3.5 1.6 + - - -
219B GLN* 3.0 20.4 + - - +
221B THR* 1.3 76.2 - - - +
223B TYR* 1.3 66.2 + - - +
225B THR* 3.3 8.7 + - - -
226B VAL* 3.2 28.7 + - - +
251B MET* 3.3 17.3 - - + -
330B MET* 3.6 24.9 - - + +
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Residues in contact with TYR 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B GLN* 3.0 43.6 + - + -
220B GLU* 3.7 6.1 - - - +
222B MET* 1.3 73.0 - - - +
224B MET* 1.3 66.5 + - - +
226B VAL* 3.4 6.0 + - + +
227B SER* 3.0 23.0 + - - -
299B PRO* 4.1 13.9 - - + -
301B PRO* 3.4 35.7 - - + -
302B LEU* 3.9 26.6 - - + +
323B LYS 4.4 1.4 + - - -
326B MET* 3.3 31.0 - - + +
327B GLU* 3.4 14.7 + - - +
329B THR* 5.2 2.5 - - - -
330B MET* 3.0 36.6 - - + -
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Residues in contact with MET 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 GLU 2.8 17.2 + - - +
221B THR* 3.7 6.3 - - - +
223B TYR* 1.3 76.3 - - - +
225B THR* 1.3 62.6 + - - +
227B SER* 3.2 6.2 + - - +
228B ILE* 2.8 39.8 + - + +
231B ARG* 3.9 11.4 - - - +
254B ALA* 3.9 20.0 - - + -
257B TYR* 3.8 18.2 - - + -
258B GLU* 3.8 9.4 - - + +
296B LEU* 3.6 22.9 - - - +
298B ARG* 3.3 15.0 - - - +
299B PRO* 3.2 42.9 - - + +
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Residues in contact with THR 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B LEU* 4.0 12.8 - - + -
221B THR 2.8 24.1 + - - -
222B MET* 3.4 15.8 - - - -
223B TYR 3.2 0.2 - - - -
224B MET* 1.3 76.5 - - - +
226B VAL* 1.3 57.9 + - + +
228B ILE* 3.3 0.8 + - - -
229B ILE* 3.0 43.6 + - + +
250B ALA* 3.7 6.3 - - + +
251B MET* 3.4 50.5 - - + +
254B ALA* 3.5 8.0 - - - +
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Residues in contact with VAL 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ARG* 3.8 14.6 - - - +
205B ILE* 4.2 32.5 - - + -
208B LEU* 6.1 0.7 - - + -
222B MET* 3.2 17.6 + - - +
223B TYR* 3.8 10.3 - - + +
225B THR* 1.3 75.8 - - + +
227B SER* 1.3 67.7 + - - +
229B ILE* 3.2 6.9 + - + +
230B ASP* 2.9 40.8 + - - +
330B MET* 4.2 22.9 - - + +
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Residues in contact with SER 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLN* 4.7 9.7 + - - +
186B VAL* 5.8 2.0 - - - -
223B TYR 3.0 14.0 + - - -
224B MET* 3.5 13.7 - - - -
226B VAL* 1.3 77.3 - - - +
228B ILE* 1.3 57.4 + - - +
230B ASP* 4.0 3.7 - - - +
231B ARG* 2.7 65.9 + - - +
298B ARG 6.1 0.4 - - - -
299B PRO* 6.3 2.0 - - - -
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Residues in contact with ILE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B MET* 2.8 44.9 + - + +
225B THR 3.8 3.4 - - - +
227B SER* 1.3 73.0 - - - +
229B ILE* 1.3 68.3 + - - +
231B ARG* 4.2 4.9 - - - +
232B PHE* 3.0 23.8 + - + +
250B ALA* 3.9 32.3 - - + +
253B ILE* 4.1 20.4 - - + -
254B ALA* 4.3 1.6 - - + +
288B ILE* 3.7 31.2 - - + -
292B LEU* 4.0 11.8 - - + +
296B LEU* 4.1 16.4 - - + -
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Residues in contact with ILE 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B TYR* 4.8 1.3 - - - +
201B ARG* 5.6 7.4 - - + -
204B LEU* 4.4 14.6 - - + -
205B ILE* 4.9 9.9 - - + -
208B LEU* 3.6 31.6 - - + -
225B THR* 3.0 30.2 + - + +
226B VAL* 3.2 7.6 + - + +
228B ILE* 1.3 76.9 - - - +
230B ASP* 1.3 65.6 + - - +
232B PHE* 3.9 2.8 - - - +
233B MET* 3.0 42.9 + - - +
243B LEU* 5.5 0.9 - - + -
246B VAL* 4.4 16.4 - - + +
247B GLY* 3.8 12.3 - - - -
250B ALA* 3.5 13.0 - - + -
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Residues in contact with ASP 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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186B VAL* 3.7 25.6 - - + +
190B TYR* 2.3 38.5 + - - +
201B ARG* 2.8 36.0 + - - -
205B ILE* 5.4 0.2 - - - +
226B VAL* 2.9 24.6 + - - +
227B SER* 4.0 2.4 - - - +
229B ILE* 1.3 81.7 - - - +
231B ARG* 1.3 62.1 + - - +
234B GLN* 3.0 28.6 + - - +
336B VAL* 3.9 7.3 - - - +
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Residues in contact with ARG 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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183B GLU 5.2 2.0 + - - -
184B GLN* 3.7 47.7 - - - +
186B VAL* 4.3 4.7 - - + -
224B MET* 3.9 11.5 - - - +
227B SER* 2.7 43.1 + - - +
228B ILE* 4.2 9.7 - - - +
230B ASP* 1.3 73.3 - - - +
232B PHE* 1.3 63.3 + - - +
234B GLN* 3.4 31.7 + - - +
235B ASN* 3.9 9.7 - - - +
292B LEU* 4.3 24.1 - - + +
295B GLY 3.2 24.2 + - - -
296B LEU* 2.7 28.0 + - - +
297B GLY 4.7 0.2 - - - +
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Residues in contact with PHE 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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228B ILE* 3.0 19.0 + - + +
229B ILE* 3.9 1.6 - - - +
231B ARG* 1.3 79.0 - - - +
233B MET* 1.3 61.6 + - - +
235B ASN 3.1 3.5 + - - -
236B ASN* 3.1 61.8 + - + +
237B SER 5.7 0.2 - - - -
238B VAL* 3.8 23.8 - - + -
246B VAL* 4.1 23.1 - - + -
284B MET* 4.7 1.1 - - - -
287B LYS* 4.1 27.4 - - + -
288B ILE* 4.0 37.9 - - + -
291B ALA* 3.6 26.5 - - + -
292B LEU* 3.7 13.3 - - + +
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Residues in contact with MET 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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190B TYR* 3.9 11.2 - - + -
191B LEU* 3.7 17.3 - - + -
194B ARG* 2.6 43.6 + - + +
196B VAL* 3.3 49.1 - - + -
201B ARG* 6.3 2.9 - - - -
229B ILE* 3.0 28.9 + - + +
232B PHE* 1.3 78.6 - - + +
234B GLN* 1.3 59.7 + - - +
236B ASN 3.1 14.7 - - - +
238B VAL* 3.8 26.5 - - + +
243B LEU* 3.9 17.3 - - + -
246B VAL* 5.6 1.1 - - - -
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Residues in contact with GLN 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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185B ALA 3.2 20.8 + - - -
186B VAL* 3.4 5.5 - - - +
187B ARG* 2.8 65.2 + - - +
190B TYR* 3.4 29.0 - - + -
194B ARG* 3.2 9.9 + - - +
230B ASP 3.0 15.6 + - - +
231B ARG* 3.4 31.7 + - - +
233B MET* 1.3 76.4 - - - +
235B ASN* 1.3 71.2 + - - +
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Residues in contact with ASN 235 (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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187B ARG* 3.0 26.7 - - - +
194B ARG* 4.8 1.6 - - - +
231B ARG 3.9 6.9 - - - +
232B PHE 3.1 4.1 + - - +
233B MET 3.1 0.2 - - - -
234B GLN* 1.3 93.1 + - - +
236B ASN* 1.3 74.8 + - - +
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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