Contacts of the helix formed by residues 181 - 200 (chain B) in PDB entry 1CF5
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 181 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B GLU* 5.6 12.6 - - + +
179B PRO 3.7 1.6 + - - -
180B ASN* 1.3 85.4 + - - +
182B ALA* 1.3 59.3 + - - +
183B ILE 4.0 2.2 - - - +
184B ILE* 4.1 20.8 - - + +
185B SER* 3.4 14.4 + - - -
214B ILE* 3.4 31.0 - - + +
215B LYS 3.5 20.0 - - - +
216B PRO 4.2 3.6 - - - +
218B GLY* 3.6 22.7 - - - +
220B ARG* 6.1 0.4 - - - +
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Residues in contact with ALA 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B TYR* 4.1 14.6 - - + -
180B ASN* 2.8 11.8 + - - +
181B LEU* 1.3 78.1 - - - +
183B ILE* 1.3 58.2 + - - +
184B ILE 3.3 0.9 - - - -
185B SER* 3.7 1.2 - - - -
186B LEU* 3.0 41.8 + - + +
214B ILE 3.3 18.4 - - - +
215B LYS* 4.4 1.6 - - - -
216B PRO* 4.1 18.4 - - + -
221B PHE* 6.5 0.2 - - + -
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Residues in contact with ILE 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 5.2 3.1 - - + -
164B TYR* 3.8 22.3 - - + -
165B ILE* 4.1 25.5 - - + +
168B HIS* 3.8 20.4 - - + +
177B PHE* 3.6 31.4 - - + -
179B PRO* 4.2 14.8 - - + -
180B ASN* 3.2 25.4 + - + +
182B ALA* 1.3 75.7 - - - +
184B ILE* 1.3 65.6 + - - +
186B LEU* 3.5 5.4 - - - +
187B GLU* 3.1 42.1 + - - +
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Residues in contact with ILE 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ARG* 3.9 30.7 - - + +
121B GLU* 4.0 30.7 - - + +
154B GLN* 4.3 1.8 - - - +
179B PRO* 3.7 28.3 - - + +
181B LEU* 4.1 21.0 - - + +
182B ALA 3.3 0.6 - - - -
183B ILE* 1.3 71.2 - - - +
185B SER* 1.3 58.5 + - - +
187B GLU* 2.5 49.6 + - - +
188B ASN* 3.0 27.0 + - - +
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Residues in contact with SER 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU 3.4 20.0 + - - -
182B ALA* 3.7 7.4 - - - -
184B ILE* 1.3 78.8 - - - +
186B LEU* 1.3 62.0 + - - -
188B ASN* 3.9 6.7 - - - +
189B GLN* 3.1 31.5 + - - +
212B ASP 4.3 1.6 + - - -
213B LEU* 3.3 16.5 - - - +
214B ILE* 3.1 34.7 + - - +
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B PHE* 3.4 39.8 - - + -
164B TYR* 3.9 26.5 - - + -
165B ILE* 4.2 8.7 - - + -
182B ALA* 3.0 23.4 + - + +
183B ILE 3.5 5.4 - - - +
184B ILE 2.9 2.2 + - - -
185B SER* 1.3 76.5 - - - +
187B GLU* 1.3 65.5 + - - +
189B GLN* 3.1 10.8 + - - -
190B TRP 3.3 8.8 + - - -
193B LEU* 4.8 5.2 - - + -
213B LEU* 3.9 30.3 - - + -
230B VAL* 4.9 2.7 - - + -
234B ASN* 3.6 23.6 - - - +
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Residues in contact with GLU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR* 4.0 12.9 - - + -
120B ARG* 2.9 32.3 + - - +
154B GLN* 2.7 36.7 - - - +
158B GLU* 3.6 38.8 - - + +
161B ARG* 5.6 0.7 + - - -
162B PHE* 4.5 0.9 - - - -
165B ILE* 4.3 7.2 - - + +
183B ILE* 3.1 28.4 + - - +
184B ILE* 2.5 20.3 + - - +
186B LEU* 1.3 76.6 - - - +
188B ASN* 1.3 60.0 + - - +
189B GLN 3.4 0.2 + - - -
190B TRP* 3.6 13.2 + - - +
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Residues in contact with ASN 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR* 4.8 1.8 - - - -
120B ARG* 2.4 31.7 + - - +
184B ILE* 3.0 27.4 + - - +
185B SER* 3.9 9.2 - - - +
187B GLU* 1.3 77.9 - - - +
189B GLN* 1.3 75.3 + - + +
190B TRP 3.5 0.4 - - - -
191B SER* 3.5 9.4 + - - -
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Residues in contact with GLN 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B SER* 3.1 21.2 + - - +
186B LEU 3.1 3.7 + - - +
188B ASN* 1.3 91.5 + - + +
190B TRP* 1.3 53.7 + - - +
191B SER* 3.4 11.1 + - - -
192B ALA* 3.1 16.2 + - - +
193B LEU* 2.7 39.4 + - + +
211B VAL* 4.0 15.9 - - + +
212B ASP* 3.7 26.8 + - - +
213B LEU* 4.1 7.0 - - + -
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Residues in contact with TRP 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.5 2.9 - - + -
68B ASN* 3.5 10.3 - - - -
69B VAL* 4.4 7.6 - - + -
70B TYR* 4.4 9.0 - + - -
158B GLU* 5.5 0.7 - - - +
161B ARG* 3.1 66.1 - - + +
162B PHE* 3.5 31.6 - + + -
186B LEU 3.3 4.7 + - - -
187B GLU 3.8 13.0 - - - +
188B ASN 3.5 1.0 - - - -
189B GLN* 1.3 74.9 - - - +
191B SER* 1.3 73.3 + - - +
193B LEU* 4.4 2.9 - - + -
194B SER* 2.8 41.1 + - - -
235B ILE* 4.7 3.1 - - + -
237B LEU 3.4 19.1 + - - -
238B LEU 4.4 2.5 - - - -
239B LEU* 3.0 55.6 - - + -
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Residues in contact with SER 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ASN 3.5 18.8 + - - -
189B GLN* 3.7 7.1 + - - -
190B TRP* 1.3 80.9 - - - +
192B ALA* 1.3 64.6 + - - +
194B SER* 3.8 1.6 - - - -
195B LYS* 2.9 27.4 + - - +
239B LEU* 4.6 16.8 - - - -
244B SER* 4.1 7.6 - - - +
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Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLN* 3.1 29.2 + - - +
191B SER* 1.3 78.3 + - - +
193B LEU* 1.3 68.1 + - - +
195B LYS* 3.2 9.7 + - - +
196B GLN* 2.9 27.6 + - + +
209B ASN* 6.1 0.9 - - - +
211B VAL* 3.8 19.5 - - + -
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Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B PHE* 3.9 22.2 - - + -
186B LEU* 4.8 11.9 - - + -
189B GLN 2.7 16.2 + - - +
190B TRP* 4.0 3.1 - - - +
192B ALA* 1.3 74.9 - - - +
194B SER* 1.3 64.4 + - - +
196B GLN* 2.9 4.7 + - - -
197B ILE* 2.9 34.3 + - + +
207B PHE* 4.7 3.4 - - + -
211B VAL* 3.2 36.8 - - + -
213B LEU* 4.9 5.2 - - + -
223B VAL* 4.3 20.4 - - + -
230B VAL* 4.9 7.2 - - + -
231B VAL* 5.8 0.2 - - + -
235B ILE* 3.7 35.2 - - + -
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Residues in contact with SER 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 5.7 0.2 - - - +
190B TRP* 2.8 39.3 + - - -
191B SER 3.8 1.3 - - - -
193B LEU* 1.3 72.7 - - - +
195B LYS* 1.3 65.8 + - - +
197B ILE* 3.9 2.0 + - - +
198B PHE* 3.5 17.5 + - - +
235B ILE* 5.4 1.1 - - - +
237B LEU 4.1 1.2 + - - -
238B LEU* 3.7 22.0 - - - +
239B LEU* 3.0 47.3 + - - +
244B SER* 4.1 4.1 + - - -
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Residues in contact with LYS 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B SER 2.9 17.4 + - - +
192B ALA* 3.3 12.8 - - - +
194B SER* 1.3 74.7 - - - +
196B GLN* 1.3 72.8 + - + +
198B PHE* 3.0 25.6 + - - +
199B LEU* 3.3 32.6 + - + +
244B SER* 3.4 31.6 - - - +
245B THR* 3.9 26.9 + - - +
246B ALA* 5.5 3.1 - - + +
249B ASN* 4.8 10.1 + - - -
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Residues in contact with GLN 196 (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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192B ALA* 2.9 21.4 + - + +
193B LEU 2.9 1.0 + - - +
195B LYS* 1.3 82.9 - - + +
197B ILE* 1.3 67.7 + - - +
198B PHE 2.9 1.5 + - - -
199B LEU* 3.2 18.3 + - - +
200B ALA* 2.8 24.4 + - - +
207B PHE* 3.3 30.7 - - + -
208B ARG* 2.7 32.6 + - - +
209B ASN* 3.4 43.2 + - + +
211B VAL* 4.2 4.7 - - + -
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Residues in contact with ILE 197 (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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31B VAL* 3.7 23.4 - - + +
32B TYR* 4.0 8.9 - - + -
34B ILE* 4.3 12.8 - - + -
193B LEU* 2.9 21.4 + - + +
194B SER 4.2 3.4 - - - +
196B GLN* 1.3 73.6 - - - +
198B PHE* 1.3 59.2 + - - +
200B ALA* 3.0 26.1 + - - +
201B GLN 3.5 2.8 + - - -
207B PHE* 4.1 18.6 - - + -
226B VAL* 5.1 1.1 - - + -
231B VAL* 3.4 29.6 - - + -
235B ILE* 3.7 23.6 - - + -
238B LEU* 3.9 24.9 - - + -
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Residues in contact with PHE 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B HIS* 5.0 3.8 - + - -
31B VAL* 4.2 15.3 - - + -
36B LEU* 3.9 26.2 - - + -
194B SER 3.5 10.2 + - - +
195B LYS* 3.0 14.6 - - - +
196B GLN 2.9 0.8 - - - -
197B ILE* 1.3 76.2 - - - +
199B LEU* 1.3 78.2 + - + -
200B ALA 3.0 2.7 - - - -
201B GLN* 2.9 51.1 + - - +
238B LEU* 5.6 1.3 - - + -
241B SER* 3.5 37.9 - - - -
244B SER* 5.1 3.8 - - - +
245B THR* 5.9 5.2 - - - -
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Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LYS* 3.5 40.2 - - + +
196B GLN* 3.2 28.1 + - - +
198B PHE* 1.3 94.5 - - + +
200B ALA* 1.3 57.8 + - - +
202B ASN* 2.9 30.8 + - + +
203B GLN* 3.4 12.5 + - - +
208B ARG* 4.2 33.7 - - + +
245B THR* 5.1 5.6 - - - +
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Residues in contact with ALA 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 3.3 24.4 + - + -
196B GLN 2.8 13.5 + - - +
197B ILE* 3.0 20.0 - - - +
198B PHE 2.9 0.4 + - - -
199B LEU* 1.3 73.4 - - - +
201B GLN* 1.3 65.2 + - - +
202B ASN 3.3 0.3 + - - -
203B GLN* 3.4 4.7 + - - +
205B GLY* 3.4 23.1 + - - +
206B LYS 3.4 24.0 + - - +
207B PHE* 4.4 6.7 - - + -
226B VAL* 4.7 1.6 - - + -
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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
------------------------------------------------------------
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