Contacts of the helix formed by residues 214 - 226 (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 TRP 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B TRP* 3.4 48.8 + + + +
207B ARG 4.7 1.2 - - - +
208B ASN* 4.7 5.8 - - + +
212B GLY 4.6 3.4 - - - -
213B SER* 1.3 72.6 - - - +
215B PHE* 1.3 61.7 + - - +
217B GLN* 3.9 5.9 - - - +
218B SER* 2.8 30.8 + - - -
243B VAL* 4.5 10.8 - - + -
247B PHE* 3.3 52.3 - + + -
248B GLU 3.7 10.1 - - - -
249B SER* 3.4 39.0 - - - -
259B LYS 3.5 11.9 - - - -
261B GLN* 3.5 36.1 - - + +
990D ASP* 3.6 19.3 + - - -
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Residues in contact with PHE 215 (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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159B ILE* 3.6 26.5 - - + -
160B ILE 4.3 2.9 - - - -
161B GLN* 3.7 7.8 + - + +
196B ALA* 3.9 28.9 - - + -
197B TYR 4.0 4.5 - - - -
198B SER* 3.3 44.9 - - - +
213B SER* 3.2 1.4 - - - -
214B TRP* 1.3 80.0 - - - +
216B ILE* 1.3 64.1 + - + +
218B SER* 3.3 1.4 + - - -
219B LEU* 2.7 46.1 + - + +
236B LEU* 5.2 4.9 - - + -
239B VAL* 3.9 17.9 - - + -
243B VAL* 4.3 7.6 - - + +
261B GLN* 4.3 5.4 - - - +
263B PRO* 3.8 28.9 - - + -
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Residues in contact with ILE 216 (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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70B ASP* 3.6 34.8 - - + +
73B ASN* 5.0 2.2 - - + -
74B LEU* 4.0 28.9 - - + -
117B VAL* 4.6 0.2 - - + -
119B LEU* 3.9 23.1 - - + -
159B ILE* 4.2 18.4 - - + -
161B GLN* 4.2 6.7 - - + -
213B SER* 3.2 23.1 + - - +
215B PHE* 1.3 88.5 - - + +
217B GLN* 1.3 65.2 + - - +
219B LEU* 3.8 4.9 - - + +
220B CYS* 3.0 28.3 + - - +
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Residues in contact with GLN 217 (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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70B ASP* 4.3 3.6 - - - +
73B ASN* 4.3 12.4 - - - +
208B ASN* 4.6 0.7 - - - +
211B ASP* 3.3 36.3 - - - +
212B GLY 2.7 28.2 - - - +
213B SER 2.9 21.9 + - - +
214B TRP* 3.7 9.7 + - - +
216B ILE* 1.3 76.2 - - - +
218B SER* 1.3 59.6 + - - +
220B CYS* 3.5 1.7 + - - +
221B ALA* 2.9 29.5 + - - +
242B LYS* 5.2 2.0 - - - -
247B PHE* 4.0 16.4 - - + -
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Residues in contact with SER 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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214B TRP 2.8 21.3 + - - -
215B PHE 3.6 2.9 - - - -
217B GLN* 1.3 75.4 - - - +
219B LEU* 1.3 63.4 + - - +
221B ALA* 3.3 1.6 + - - +
222B MET* 3.0 29.8 + - - +
239B VAL* 4.3 6.1 - - - -
242B LYS* 3.3 27.4 - - - +
243B VAL* 3.7 17.9 - - - +
247B PHE* 3.1 24.4 - - - -
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Residues in contact with LEU 219 (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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74B LEU* 5.1 5.6 - - + -
159B ILE* 3.8 42.6 - - + -
215B PHE* 2.7 33.2 + - + +
216B ILE* 3.8 10.8 - - + +
218B SER* 1.3 73.1 - - - +
220B CYS* 1.3 59.5 + - - +
222B MET* 3.4 1.0 + - - +
223B LEU* 2.9 55.8 + - + +
232B PHE* 5.1 4.5 - - + -
235B ILE* 5.0 2.9 - - + -
236B LEU* 3.9 25.8 - - + -
239B VAL* 4.0 18.1 - - + +
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Residues in contact with CYS 220 (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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73B ASN* 3.3 51.6 - - - +
74B LEU* 3.7 24.5 - - - -
77B THR* 3.4 22.2 + - - +
78B PHE* 5.6 0.4 - - - -
216B ILE* 3.0 17.7 + - - +
217B GLN 3.9 0.7 - - - +
219B LEU* 1.3 76.5 - - - +
221B ALA* 1.3 63.9 + - - +
223B LEU* 3.8 5.9 - - - +
224B LYS* 3.2 30.8 + - - +
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Residues in contact with ALA 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 GLN 2.9 18.6 + - - +
218B SER* 3.4 9.4 - - - +
220B CYS* 1.3 76.7 - - - +
222B MET* 1.3 59.0 + - + +
224B LYS* 3.3 12.8 + - - +
225B GLN* 3.0 30.2 + - - +
242B LYS* 4.4 15.9 - - + +
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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
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218B SER 3.0 16.6 + - - +
221B ALA* 1.3 74.2 - - - +
223B LEU* 1.3 61.2 + - - +
225B GLN* 4.8 5.8 - - - +
226B TYR* 2.8 60.0 + - + +
227B ALA 4.1 0.2 + - - -
235B ILE* 3.9 13.7 - - + +
238B ARG* 3.8 28.7 - - + +
239B VAL* 3.7 29.4 - - + +
242B LYS* 3.9 26.0 - - + +
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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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77B THR* 3.8 20.6 - - + -
78B PHE* 3.8 31.2 - - + -
81B LEU* 4.0 11.2 - - + +
219B LEU* 2.9 35.4 + - + +
220B CYS* 3.8 4.9 - - - +
222B MET* 1.3 79.0 - - - +
224B LYS* 1.3 57.8 + - - +
227B ALA* 2.9 35.3 + - + +
232B PHE* 4.3 7.6 - - + -
235B ILE* 4.0 24.4 - - + +
275B PHE* 3.9 28.7 - - + -
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Residues in contact with LYS 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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73B ASN* 3.3 27.5 + - - +
76B GLU* 6.1 3.3 - - - +
77B THR* 3.4 22.3 + - + +
80B ASN* 5.5 7.6 - - - +
81B LEU* 6.4 0.2 - - - -
220B CYS* 3.2 18.8 + - - +
221B ALA* 3.4 17.2 - - - +
223B LEU* 1.3 76.6 - - - +
225B GLN* 1.3 63.3 + - - +
227B ALA* 5.6 0.2 - - - +
228B ASP* 4.0 9.5 - - - +
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Residues in contact with GLN 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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221B ALA 3.0 18.0 + - - +
222B MET* 4.4 5.9 - - - +
224B LYS* 1.3 83.1 - - + +
226B TYR* 1.3 99.6 + - + +
228B ASP* 3.7 10.8 - - - +
229B LYS* 4.8 3.3 - - - +
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Residues in contact with TYR 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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222B MET* 2.8 52.6 + - + +
225B GLN* 1.3 111.4 + - + +
227B ALA* 1.3 54.4 + - - +
228B ASP 3.0 6.7 - - - +
229B LYS* 2.9 40.4 + - + -
230B LEU* 2.9 37.2 + - + -
235B ILE* 3.9 11.3 - - + +
238B ARG* 3.7 34.6 + - + -
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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