Contacts of the helix formed by residues 222 - 243 (chain B) in PDB entry 4P9U
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 222 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B TYR 3.9 3.5 - - - +
220B PHE 3.1 0.4 - - - -
221B SER* 1.3 78.9 + - - +
223B PRO* 1.3 72.5 - - - +
224B GLN* 3.0 29.0 + - - +
225B ALA* 3.1 15.6 + - + +
226B ARG* 3.3 15.5 + - - +
262B ILE* 4.4 7.5 - - - +
266B MET* 3.7 41.1 - - + +
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Residues in contact with PRO 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 5.7 1.5 - - + +
171B LYS* 6.2 0.4 - - - +
221B SER 3.9 7.0 - - - +
222B ASN* 1.3 90.3 - - - +
224B GLN* 1.3 55.1 + - - +
226B ARG* 3.0 36.1 + - - +
227B GLU* 2.9 38.6 + - + +
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Residues in contact with GLN 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ASN* 3.0 20.9 + - - +
223B PRO* 1.3 79.0 - - - +
225B ALA* 1.3 59.8 + - - +
227B GLU* 3.7 9.9 + - + +
228B LEU* 3.5 19.6 + - - +
262B ILE* 3.9 20.3 - - + +
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Residues in contact with ALA 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B TYR* 3.5 47.6 + - + +
220B PHE* 4.3 3.5 - - + -
222B ASN* 3.1 13.2 + - + +
223B PRO 3.1 0.6 - - - -
224B GLN* 1.3 78.9 - - - +
226B ARG* 1.3 60.4 + - - +
228B LEU* 3.3 4.5 + - - +
229B ALA* 2.9 27.5 + - - +
255B TYR* 5.2 0.5 + - - -
262B ILE* 3.7 21.9 - - + +
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Residues in contact with ARG 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 4.3 23.1 - - + +
174B GLU* 5.2 7.1 + - - -
177B ILE* 3.5 30.9 - - - +
181B PHE* 3.3 50.9 - - + -
220B PHE* 2.8 51.1 + - + +
221B SER* 3.9 13.5 + - - +
222B ASN 3.5 8.3 - - - +
223B PRO* 3.0 38.2 + - - +
225B ALA* 1.3 78.5 - - - +
227B GLU* 1.3 56.4 + - - +
229B ALA 3.2 0.3 + - - -
230B MET* 2.9 28.9 + - - +
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Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 4.6 13.9 - - + +
223B PRO* 2.9 26.6 + - + +
224B GLN* 4.0 9.2 - - + +
226B ARG* 1.3 74.1 - - + +
228B LEU* 1.3 61.3 + - - +
230B MET* 3.5 21.5 + - - +
231B GLU* 3.0 29.7 + - - +
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B TYR* 5.3 0.7 - - - +
224B GLN 3.5 10.7 + - - +
225B ALA 3.3 7.6 + - - +
226B ARG 3.3 0.2 - - - -
227B GLU* 1.3 76.8 - - - +
229B ALA* 1.3 61.3 + - - +
231B GLU* 4.3 11.4 - - + -
232B PHE* 2.9 30.0 + - + +
235B GLN* 6.4 0.4 - - - +
255B TYR* 3.8 20.9 - - + -
258B ALA* 3.4 35.7 - - + -
259B SER* 4.0 11.0 - - - +
262B ILE* 4.1 14.4 - - + -
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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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181B PHE* 3.5 22.2 - - + -
220B PHE* 3.9 5.2 - - + -
225B ALA 2.9 15.8 + - - +
226B ARG 3.2 8.9 + - - +
228B LEU* 1.3 77.8 - - - +
230B MET* 1.3 56.6 + - - +
232B PHE* 3.2 2.6 - - - +
233B TYR* 2.9 46.4 + - - +
255B TYR* 3.8 24.4 - - - +
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Residues in contact with MET 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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132B ILE* 4.8 3.8 - - + +
135B CYS* 3.4 34.1 - - + +
136B GLU* 4.0 10.8 - - - +
138B LEU* 3.6 33.7 - - + -
181B PHE* 3.6 14.8 - - + -
226B ARG 2.9 17.4 + - - +
227B GLU* 3.9 18.6 - - - +
229B ALA* 1.3 73.3 - - - +
231B GLU* 1.3 65.2 + - - +
233B TYR* 3.1 13.0 + - + +
234B ARG* 3.0 52.5 + - - +
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Residues in contact with GLU 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 GLU 3.0 19.0 + - - +
228B LEU* 3.8 13.9 - - + +
229B ALA 3.3 0.2 - - - -
230B MET* 1.3 74.8 - - - +
232B PHE* 1.3 57.8 + - - +
234B ARG* 3.4 13.9 + - - +
235B GLN* 3.0 53.3 + - - +
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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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113B MET* 4.9 2.2 - - + -
189B PHE* 3.9 23.8 - + - -
228B LEU* 2.9 21.0 + - + +
229B ALA 3.2 3.4 - - - +
231B GLU* 1.3 74.3 - - - +
233B TYR* 1.3 78.9 + + - +
235B GLN* 3.2 10.0 + - - +
236B LEU* 2.9 54.7 + - + +
251B VAL* 3.8 26.5 - - + -
252B ILE* 4.0 18.8 - - + -
255B TYR* 3.4 57.2 - + + -
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Residues in contact with TYR 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B MET* 3.2 11.7 - - - +
131B VAL* 4.2 20.6 - - + -
132B ILE* 3.7 23.3 - - + -
135B CYS* 4.3 8.1 - - - -
181B PHE* 3.8 21.8 - + - -
185B ASP* 2.6 45.3 + - - +
188B LEU* 3.7 31.6 - - + -
189B PHE* 4.9 1.8 - + - -
229B ALA* 2.9 36.6 + - + +
230B MET* 3.1 15.7 + - + +
232B PHE* 1.3 90.3 - + - +
234B ARG* 1.3 58.5 + - - +
236B LEU* 3.3 6.3 + - - -
237B LEU* 2.9 24.4 + - - +
255B TYR* 5.4 0.2 - - - -
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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
----------------------------------------------------------
132B ILE* 3.8 30.0 - - + +
136B GLU* 4.0 22.8 + - - -
230B MET* 3.0 39.9 + - - +
231B GLU* 3.8 12.6 - - - +
233B TYR* 1.3 73.2 - - - +
235B GLN* 1.3 61.3 + - - +
237B LEU* 3.3 10.6 + - + +
238B ALA* 2.9 27.9 + - - +
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Residues in contact with GLN 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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228B LEU* 6.4 0.4 - - - +
231B GLU* 3.0 41.7 + - + +
232B PHE* 3.5 11.9 - - - +
234B ARG* 1.3 77.2 - - - +
236B LEU* 1.3 56.9 + - - +
238B ALA* 3.2 9.1 + - - +
239B VAL* 2.9 32.0 + - - +
251B VAL* 3.4 34.7 - - + +
254B GLN* 4.8 9.1 + - - +
255B TYR* 6.0 0.2 - - - +
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Residues in contact with LEU 236 (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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113B MET* 3.9 26.9 - - + -
117B PHE* 3.7 7.4 - - + -
128B MET* 3.4 19.7 - - + -
188B LEU* 4.4 10.5 - - + -
192B LEU* 4.9 1.6 - - + -
232B PHE* 2.9 60.4 + - + +
233B TYR* 3.5 4.5 - - - +
235B GLN* 1.3 75.2 - - - +
237B LEU* 1.3 57.7 + - - +
239B VAL* 3.1 7.9 + - - +
240B CYS* 2.9 28.8 + - - +
248B LEU* 3.6 28.7 - - + -
251B VAL* 4.2 6.5 - - + -
252B ILE* 4.3 2.0 - - + -
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Residues in contact with LEU 237 (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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125B GLU* 3.7 42.8 - - + +
128B MET* 3.3 15.4 - - + +
129B ILE* 3.7 20.0 - - + -
132B ILE* 3.9 16.4 - - + -
233B TYR 2.9 17.6 + - - +
234B ARG* 3.5 8.5 - - + +
236B LEU* 1.3 75.6 - - - +
238B ALA* 1.3 58.0 + - - +
240B CYS* 3.3 1.4 + - + -
241B GLN* 2.9 57.6 + - - +
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Residues in contact with ALA 238 (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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234B ARG 2.9 14.0 + - - +
235B GLN* 3.3 12.1 - - - +
237B LEU* 1.3 76.7 - - - +
239B VAL* 1.3 56.3 + - + +
241B GLN* 4.0 10.4 - - - +
242B SER* 2.9 32.4 + - - -
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Residues in contact with VAL 239 (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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117B PHE* 4.0 17.9 - - + -
235B GLN 2.9 21.4 + - - +
236B LEU* 3.1 10.7 + - - +
238B ALA* 1.3 76.8 - - + +
240B CYS* 1.3 58.3 + - - +
242B SER* 3.3 6.7 + - - -
243B GLY* 2.9 28.6 + - - -
244B GLU 3.7 18.0 + - - +
245B ARG* 4.2 11.9 - - - -
246B GLU* 5.4 2.5 - - - +
247B HIS 5.4 0.2 - - - -
248B LEU* 4.0 22.2 - - + +
251B VAL* 4.4 20.6 - - + -
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Residues in contact with CYS 240 (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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117B PHE* 3.6 47.6 - - + +
121B LYS* 3.4 53.3 - - - +
124B ALA* 4.1 0.2 - - - -
125B GLU* 4.1 15.0 - - + -
128B MET* 4.8 2.7 - - - -
236B LEU 2.9 14.3 + - - +
237B LEU* 3.8 6.3 - - - +
239B VAL* 1.3 77.1 - - - +
241B GLN* 1.3 62.3 + - - +
243B GLY* 3.6 7.3 + - - -
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Residues in contact with GLN 241 (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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121B LYS* 3.9 12.5 - - - +
125B GLU* 3.2 24.3 + - - +
129B ILE* 4.4 11.3 - - - +
237B LEU* 2.9 51.8 + - + +
238B ALA* 4.0 6.9 - - - +
240B CYS* 1.3 76.7 - - - +
242B SER* 1.3 64.4 + - - +
243B GLY 3.5 0.3 + - - -
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Residues in contact with SER 242 (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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238B ALA 2.9 17.1 + - - -
239B VAL* 3.3 6.6 + - - -
241B GLN* 1.3 77.0 - - - +
243B GLY* 1.3 63.2 + - - +
244B GLU* 3.1 21.0 + - - +
246B GLU* 5.6 0.3 + - - -
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Residues in contact with GLY 243 (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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117B PHE 6.2 0.2 - - - -
121B LYS* 5.8 3.1 - - - -
239B VAL 2.9 9.9 + - - -
240B CYS* 4.0 8.5 - - - -
241B GLN 3.3 2.7 - - - -
242B SER* 1.3 80.1 + - - +
244B GLU* 1.3 59.3 + - - +
245B ARG* 3.8 15.4 + - - +
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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
------------------------------------------------------------
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