Contacts of the helix formed by residues 232 - 246 (chain B) in PDB entry 1CP3
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 PHE 232 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B PHE* 6.3 2.0 - + - -
157B LEU* 4.0 15.7 - - + -
159B ILE* 5.4 12.1 - - + -
194B LEU* 3.7 36.8 - - + -
196B ALA* 5.6 1.3 - - + -
219B LEU* 5.1 5.2 - - + -
223B LEU* 4.3 13.9 - - + -
230B LEU 3.9 0.8 + - - -
231B GLU* 1.3 70.2 - - - +
233B MET* 1.3 58.5 + - + +
235B ILE* 2.8 33.0 + - + +
236B LEU* 3.0 38.2 + - + +
269B LEU* 5.0 1.6 - - + -
273B LEU* 3.0 47.3 + - + +
275B PHE* 3.3 33.1 - + + -
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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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233A MET* 3.2 52.0 - - + -
234A HIS* 4.8 2.0 - - + +
237A THR* 4.8 11.0 - - - +
194B LEU* 3.8 26.2 - - - -
231B GLU* 2.8 24.9 + - - +
232B PHE* 1.3 74.2 - - - +
234B HIS* 1.3 55.2 + - + +
236B LEU* 3.4 7.1 + - - +
237B THR* 2.8 37.0 + - - +
265B ILE* 3.3 36.7 - - + +
267B SER* 3.9 14.4 - - - +
269B LEU* 5.1 5.2 - - + -
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Residues in contact with HIS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLU* 2.9 43.6 + - + -
233A MET* 5.0 0.7 - - + -
234A HIS* 3.3 38.6 + + - -
272A GLU* 3.6 28.5 + - + +
274A TYR* 4.6 3.4 - - - -
230B LEU* 4.3 22.2 - - + +
231B GLU* 2.8 15.2 + - - +
233B MET* 1.3 80.4 - - + +
235B ILE* 1.3 64.5 + - - +
237B THR* 3.5 8.5 + - - -
238B ARG* 3.4 26.7 + - - +
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Residues in contact with ILE 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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219B LEU* 5.0 4.0 - - + -
222B MET* 3.9 25.1 - - + +
223B LEU* 4.0 26.9 - - + +
226B TYR* 3.9 8.1 - - + +
227B ALA* 3.8 27.6 - - + +
230B LEU* 3.7 33.4 - - + +
231B GLU 3.0 12.0 + - - +
232B PHE* 2.8 24.6 + - + +
234B HIS* 1.3 72.6 - - - +
236B LEU* 1.3 58.3 + - - +
238B ARG* 3.2 10.0 + - - +
239B VAL* 3.1 27.6 + - + +
275B PHE* 4.6 4.0 - - + -
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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
----------------------------------------------------------
194B LEU* 4.1 9.4 - - + -
196B ALA* 4.3 16.6 - - + -
215B PHE* 5.2 3.6 - - + -
219B LEU* 3.9 28.0 - - + -
232B PHE* 3.0 47.3 + - + +
233B MET* 3.8 9.0 - - - +
234B HIS 3.3 0.2 - - - -
235B ILE* 1.3 76.3 - - + +
237B THR* 1.3 57.6 + - - +
238B ARG 3.2 0.2 - - - -
239B VAL* 3.3 11.7 - - + +
240B ASN* 2.8 32.1 + - - +
265B ILE* 3.2 43.5 - - + -
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Residues in contact with THR 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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233A MET* 5.0 10.0 - - - +
267A SER* 5.1 3.1 + - - -
269A LEU* 3.9 10.2 + - + +
270A THR 3.6 7.9 - - - +
271A LYS* 3.5 42.4 - - - +
272A GLU* 4.3 7.4 - - + +
233B MET* 2.8 23.0 + - - +
234B HIS* 3.8 10.6 - - - -
235B ILE 3.3 0.2 - - - -
236B LEU* 1.3 76.5 - - - +
238B ARG* 1.3 59.2 + - + +
240B ASN* 3.2 11.0 - - - +
241B ARG* 2.9 23.7 + - - +
265B ILE* 4.3 5.9 - - - +
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Residues in contact with ARG 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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35A ASN* 3.9 25.8 - - - +
272A GLU* 3.7 21.0 + - - +
222B MET* 3.8 20.8 - - + +
226B TYR* 3.7 32.0 + - - -
230B LEU* 3.0 40.8 - - - +
234B HIS 3.4 7.2 + - - +
235B ILE* 3.2 10.5 + - - +
237B THR* 1.3 77.8 - - - +
239B VAL* 1.4 52.4 + - - +
241B ARG* 3.0 32.5 + - - +
242B LYS* 2.7 34.5 + - - +
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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
----------------------------------------------------------
215B PHE* 3.9 33.7 - - + -
218B SER* 4.3 0.9 - - - -
219B LEU* 4.0 35.0 - - + +
222B MET* 3.7 25.3 - - + +
235B ILE* 3.1 16.4 + - + +
236B LEU* 3.3 16.2 - - + +
238B ARG* 1.4 73.5 - - - +
240B ASN* 1.3 65.7 + - - +
242B LYS* 2.9 5.8 + - - +
243B VAL* 2.9 36.2 + - + +
263B PRO* 4.6 1.8 - - + -
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Residues in contact with ASN 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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267A SER* 3.6 22.6 + - - -
268A MET* 3.9 4.9 - - - +
269A LEU 2.9 30.1 + - - +
270A THR* 4.3 0.4 - - - -
215B PHE* 5.6 0.2 - - - -
236B LEU* 2.8 18.1 + - - +
237B THR* 3.2 6.8 - - - +
239B VAL* 1.3 77.2 - - - +
241B ARG* 1.3 58.3 + - - +
243B VAL 3.7 0.2 + - - -
244B ALA* 3.0 28.2 + - - +
262B ILE* 3.5 11.4 - - + +
263B PRO* 3.3 36.8 + - - +
265B ILE* 3.6 17.8 - - - +
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Residues in contact with ARG 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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35A ASN* 3.6 36.4 + - - +
270A THR* 2.7 54.0 + - - +
271A LYS* 3.6 27.1 - - - +
237B THR* 2.9 9.6 + - - +
238B ARG* 3.5 40.1 - - - +
240B ASN* 1.3 72.7 - - - +
242B LYS* 1.3 60.9 + - - +
244B ALA* 4.1 0.4 - - - -
245B THR* 2.6 52.1 + - + +
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Residues in contact with LYS 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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217B GLN* 5.1 1.1 - - - -
218B SER* 3.3 39.0 - - - +
221B ALA* 4.4 13.5 - - + +
222B MET* 3.9 24.1 - - + +
238B ARG 2.7 17.3 + - - +
239B VAL* 2.9 9.0 + - - +
241B ARG* 1.3 73.0 - - - +
243B VAL* 1.3 57.6 + - - +
245B THR* 4.2 2.9 - - - -
246B GLU* 2.8 74.9 + - - +
247B PHE* 3.5 7.8 - - + -
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Residues in contact with VAL 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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214B TRP* 4.6 9.9 - - + -
215B PHE* 4.3 9.2 - - - -
218B SER* 3.7 23.3 - - - +
239B VAL* 2.9 21.1 + - + +
242B LYS* 1.3 72.5 - - - +
244B ALA* 1.3 61.2 + - - +
247B PHE* 3.5 35.1 + - + +
261B GLN* 3.4 40.4 + - + +
263B PRO* 3.5 30.7 - - + -
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Residues in contact with ALA 244 (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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186A LYS 3.8 1.9 - - - +
187A ILE* 5.0 1.8 - - + -
188A PRO* 3.6 17.9 - - + +
191A ALA* 5.2 0.2 - - + -
270A THR* 4.2 8.5 - - + -
240B ASN 3.0 21.6 + - - +
241B ARG* 3.6 6.7 - - - +
242B LYS 3.1 0.4 - - - -
243B VAL* 1.3 79.7 - - - +
245B THR* 1.3 64.7 + - + +
260B LYS* 2.9 28.6 + - - -
261B GLN 3.6 10.1 - - - -
262B ILE* 4.0 15.3 - - + -
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Residues in contact with THR 245 (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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185A HIS* 3.1 40.1 + - + -
186A LYS 4.6 1.1 - - - -
187A ILE* 4.2 18.4 - - + -
270A THR* 6.2 0.9 - - + -
241B ARG* 2.6 37.4 + - + +
242B LYS* 3.8 1.4 + - - -
244B ALA* 1.3 82.5 - - + +
246B GLU* 1.3 69.1 + - - +
247B PHE 3.6 0.6 - - - +
260B LYS* 3.8 8.3 + - - +
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Residues in contact with GLU 246 (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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185A HIS* 5.2 2.0 - - + -
242B LYS* 2.8 59.4 + - - +
245B THR* 1.3 86.5 + - - +
247B PHE* 1.3 69.6 + - + +
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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