Contacts of the helix formed by residues 201 - 217 (chain B) in PDB entry 5UFL
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 SER 201 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B GLU* 5.8 0.9 - - - -
160B MET* 3.3 26.2 - - - +
199B HIS* 3.3 19.6 + - - -
200B SER* 1.3 79.3 + - - +
202B LEU* 1.3 64.1 + - - +
203B THR* 3.5 11.8 + - - -
204B VAL* 3.3 16.7 + - - +
205B VAL* 3.3 14.6 + - - +
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Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B HIS 5.0 1.6 - - - +
200B SER 3.3 10.5 + - - +
201B SER* 1.3 69.2 + - - +
203B THR* 1.3 57.9 - - - +
204B VAL 3.3 0.2 - - - -
205B VAL* 3.6 14.7 - - + +
206B VAL* 2.9 30.8 + - - +
237B LEU* 5.3 3.8 - - + -
240B ASN* 4.1 24.2 - - - +
241B ILE* 4.1 29.6 - - + +
244B ASN* 4.2 7.2 - - + +
245B GLY* 3.6 36.1 - - - +
246B ASP 5.5 0.4 - - - +
250B THR* 4.2 4.6 - - + +
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Residues in contact with THR 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B MET* 3.8 19.1 - - - -
201B SER* 3.2 11.6 + - - -
202B LEU* 1.3 75.3 - - - +
204B VAL* 1.3 62.7 + - - +
206B VAL* 3.5 2.9 - - + +
207B PHE* 3.0 58.7 + - + -
246B ASP* 4.4 8.8 - - - +
249B LEU* 4.1 15.2 - - + +
250B THR* 3.2 24.7 - - + +
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B GLU* 5.0 1.3 - - - +
159B LYS* 6.0 2.0 - - + -
160B MET* 3.8 38.8 - - + +
163B LEU* 3.7 20.2 - - + +
196B LEU* 3.8 26.7 - - + +
199B HIS* 3.6 32.1 - - + +
201B SER* 3.3 10.4 + - - +
203B THR* 1.3 75.8 - - - +
205B VAL* 1.3 65.4 + - - +
207B PHE* 3.4 9.4 + - - +
208B ALA* 3.0 21.7 + - - +
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Residues in contact with VAL 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU 3.4 14.8 - - - +
197B LEU* 3.4 31.7 - - + +
199B HIS* 3.2 28.0 - - + +
201B SER 3.3 8.5 + - - +
202B LEU* 3.3 17.4 + - + +
204B VAL* 1.3 76.8 - - - +
206B VAL* 1.3 57.6 + - - +
208B ALA* 3.4 3.1 + - - +
209B LEU* 2.9 27.9 + - + +
237B LEU* 3.9 18.2 - - + -
241B ILE* 3.8 19.3 - - + -
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LEU 2.9 16.1 + - - +
203B THR* 3.5 17.0 - - - +
205B VAL* 1.3 73.8 - - - +
207B PHE* 1.3 65.8 + - + +
209B LEU* 3.9 3.4 - - - +
210B SER* 2.7 37.9 + - - -
241B ILE* 3.9 24.5 - - + -
250B THR* 4.3 13.0 - - + -
253B TYR* 4.0 20.4 - - + +
254B SER* 3.7 32.8 - - - +
257B LEU* 4.5 9.4 - - + +
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Residues in contact with PHE 207 (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 GLN* 3.4 17.7 - - - -
160B MET* 3.4 32.1 - - + -
163B LEU* 3.8 20.6 - - + +
164B GLY* 3.5 13.7 - - - -
167B ALA* 4.0 1.9 - - + +
203B THR* 3.0 42.1 + - + -
204B VAL* 3.4 6.3 + - - +
205B VAL 3.4 0.2 - - - -
206B VAL* 1.3 77.1 - - + +
208B ALA* 1.3 65.3 + - - +
210B SER* 3.3 6.3 + - - -
211B ILE* 3.2 30.6 + - - +
249B LEU* 3.9 12.8 - - + -
253B TYR* 3.6 46.7 - + - -
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Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 4.4 6.4 - - + +
193B LEU* 3.8 37.9 - - + +
196B LEU* 4.0 15.5 - - + -
197B LEU* 4.4 3.6 - - + -
204B VAL 3.0 18.1 + - - +
205B VAL* 3.5 6.5 - - - +
207B PHE* 1.3 75.7 - - - +
209B LEU* 1.3 60.6 + - - +
211B ILE* 3.4 4.5 + - - +
212B LEU* 3.1 28.5 + - - +
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU* 3.7 16.3 - - + +
205B VAL 2.9 17.6 + - - +
206B VAL* 4.0 4.7 - - - +
208B ALA* 1.3 73.8 - - - +
210B SER* 1.3 58.6 + - - +
212B LEU* 3.6 2.4 + - - -
213B SER* 2.8 29.5 + - - -
225B LEU* 3.7 36.6 - - + -
226B PHE* 5.0 4.7 - - + -
234B THR* 4.4 8.1 - - + -
237B LEU* 4.1 22.0 - - + -
238B ILE* 3.6 33.4 - - + -
241B ILE* 4.8 6.1 - - + -
257B LEU* 3.6 15.0 - - + -
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Residues in contact with SER 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ALA* 4.2 17.5 - - - -
171B ARG* 6.1 5.2 - - - -
206B VAL* 2.7 22.8 + - - +
207B PHE* 3.6 6.2 - - - -
208B ALA 3.3 0.2 - - - -
209B LEU* 1.3 74.5 - - - +
211B ILE* 1.3 60.7 + - - +
213B SER* 3.3 5.7 + - - -
214B SER* 2.9 32.8 + - - -
253B TYR* 4.2 14.9 + - - -
257B LEU* 4.2 20.9 - - - +
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Residues in contact with ILE 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 3.6 41.3 - - + +
166B LEU* 4.3 14.6 - - + +
167B ALA* 3.7 22.2 - - - +
170B CYS* 4.3 9.4 - - - -
189B PHE* 4.1 8.5 - - + -
193B LEU* 3.6 22.4 - - + -
207B PHE 3.2 17.1 + - - +
208B ALA 3.7 4.3 - - - +
210B SER* 1.3 75.4 - - - +
212B LEU* 1.3 61.9 + - - +
214B SER* 3.2 6.9 + - - -
215B LEU* 3.1 52.2 + - + +
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Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B TYR* 4.1 27.6 - - + +
193B LEU* 3.6 50.3 - - + +
194B ILE* 4.0 13.5 - - + -
197B LEU* 4.2 14.4 - - + -
208B ALA 3.1 17.5 + - - +
209B LEU* 3.8 4.7 - - - +
211B ILE* 1.3 79.4 - - - +
213B SER* 1.3 56.5 + - - +
215B LEU* 4.9 0.9 - - - -
216B THR* 2.6 45.8 + - + +
225B LEU* 3.8 27.4 - - + -
226B PHE* 4.7 1.8 - - - -
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Residues in contact with SER 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU 2.8 20.4 + - - -
210B SER 3.6 3.8 - - - -
211B ILE 3.3 0.2 - - - -
212B LEU* 1.3 79.4 - - - +
214B SER* 1.3 62.0 + - - +
215B LEU 3.3 0.7 + - - -
217B LEU* 3.2 30.8 + - - +
226B PHE* 3.9 18.3 - - - -
257B LEU* 3.3 20.1 - - - +
260B ASP* 5.3 4.5 - - - +
261B LEU* 3.1 26.2 - - - +
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Residues in contact with SER 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ALA 5.0 0.5 + - - -
170B CYS* 3.3 27.7 - - - +
171B ARG* 4.2 12.1 + - - -
177B GLN* 3.1 37.9 + - - +
181B LYS* 4.9 1.0 + - - -
210B SER 2.9 23.0 + - - -
211B ILE* 3.2 9.2 + - - -
213B SER* 1.3 73.9 + - - +
215B LEU* 1.3 59.3 + - - +
217B LEU* 5.0 2.1 - - - +
260B ASP* 6.1 0.7 - - - -
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Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B CYS* 4.4 10.3 - - - -
177B GLN* 3.9 42.2 - - + +
180B ILE* 3.9 27.6 - - + -
181B LYS* 2.9 34.8 + - + +
189B PHE* 4.8 3.8 - - + -
190B TYR* 4.1 19.5 - - + +
211B ILE* 3.1 37.7 + - + +
212B LEU* 5.4 0.2 - - - -
214B SER* 1.3 81.9 - - - +
216B THR* 1.3 67.4 + - + +
217B LEU 3.4 5.2 + - - -
218B ASN 5.2 0.2 + - - -
219B GLU* 4.0 6.1 + - - +
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Residues in contact with THR 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B TYR* 3.5 47.6 - - + +
212B LEU* 2.6 38.6 + - + +
215B LEU* 1.3 73.2 - - + +
217B LEU* 1.3 63.4 + - - +
218B ASN 3.9 0.4 - - - -
219B GLU* 3.7 14.5 - - + +
221B VAL* 4.7 3.6 - - + -
222B GLY* 3.4 39.7 + - - +
225B LEU* 4.4 2.9 - - - +
226B PHE* 3.8 9.3 - - - -
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B SER* 3.2 23.4 + - - +
214B SER* 5.3 1.8 - - - +
215B LEU 3.4 4.4 + - - -
216B THR* 1.3 80.5 - - - +
218B ASN* 1.3 76.2 + - - +
219B GLU 3.6 3.6 + - - +
222B GLY 5.1 1.0 - - - +
223B GLU* 5.0 5.5 - - - +
226B PHE* 4.2 21.0 - - + +
260B ASP* 4.9 11.7 - - + +
261B LEU* 4.8 8.5 - - + -
264B ASN* 4.0 22.8 + - + +
267B ILE* 3.3 33.9 - - + -
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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