Contacts of the helix formed by residues 198 - 218 (chain B) in PDB entry 1FBA
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 198 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B ASP* 1.3 73.1 - - - +
199B ASP* 1.3 55.5 + - - +
201B ALA* 3.6 2.5 - - - +
202B GLN* 2.8 35.1 + - + +
233B VAL* 3.3 39.5 - - + +
234B THR* 3.6 6.7 - - - -
235B ALA* 3.7 9.3 - - - +
243B ASN* 3.6 38.8 - - - +
247B GLU* 4.1 28.3 - - + +
248B ILE* 4.9 2.5 - - - -
251B ALA* 4.0 12.1 - - + -
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Residues in contact with ASP 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ASP* 3.2 14.5 + - - +
198B LEU* 1.3 78.5 - - - +
200B ARG* 1.3 58.6 + - - +
202B GLN* 3.2 7.6 + - - +
203B LYS* 2.9 65.8 + - - +
6C TYR* 3.6 15.2 - - - -
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Residues in contact with ARG 200 (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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153B ILE* 3.5 17.8 - - + +
154B GLY 3.2 12.5 + - - -
157B THR 3.0 29.7 + - - +
196B HIS* 3.9 19.5 - - + -
197B ASP* 3.0 20.3 + - - +
199B ASP* 1.3 74.6 + - - +
201B ALA* 1.3 62.9 + - - +
203B LYS* 3.3 6.9 + - - +
204B VAL* 2.9 46.2 + - + +
2C THR* 2.9 39.8 + - - -
3C TYR* 3.3 46.3 + - - -
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Residues in contact with ALA 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ILE* 4.2 12.9 - - + +
196B HIS* 4.0 10.5 - - + +
197B ASP 3.1 10.5 + - - +
198B LEU 3.6 7.6 - - - +
200B ARG* 1.3 80.5 - - - +
202B GLN* 1.3 55.2 + - - +
204B VAL* 3.9 1.0 - - - +
205B THR* 3.0 35.0 + - - +
231B ASN* 6.2 1.1 - - - +
233B VAL* 3.9 7.9 - - + -
234B THR 2.9 30.7 - - - +
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Residues in contact with GLN 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 2.8 20.7 + - - +
199B ASP* 3.2 7.5 + - - +
201B ALA* 1.3 74.0 - - - +
203B LYS* 1.3 59.0 + - - +
205B THR* 3.4 1.7 + - - -
206B GLU* 2.9 49.7 + - - +
233B VAL* 3.5 14.3 - - + +
251B ALA* 3.5 34.6 + - + +
254B GLN* 3.1 33.9 + - - +
255B ALA* 4.4 2.2 - - + -
258B ARG* 3.6 4.4 - - - +
6C TYR* 3.5 21.6 + - + +
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Residues in contact with LYS 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ASP* 2.9 52.3 + - - +
200B ARG* 3.3 6.9 + - - +
202B GLN* 1.3 76.1 - - - +
204B VAL* 1.3 65.2 + - - +
206B GLU* 3.4 4.5 + - - +
207B THR* 2.8 30.4 + - - -
2C THR 3.6 21.3 - - - +
3C TYR* 5.7 0.2 - - - -
4C PHE* 2.7 46.0 + - + +
5C ASN* 4.4 5.9 + - - +
6C TYR* 3.6 39.0 - - + +
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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
----------------------------------------------------------
153B ILE* 3.9 27.8 - - + -
158B PRO* 3.6 30.5 - - + -
190B VAL* 3.9 15.5 - - + -
200B ARG* 2.9 52.6 + - + +
201B ALA 3.9 1.1 - - - +
203B LYS* 1.3 75.5 - - - +
205B THR* 1.3 57.0 + - - +
207B THR* 3.1 3.6 + - - -
208B VAL* 2.9 33.5 + - + +
2C THR* 4.0 14.6 - - + -
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Residues in contact with THR 205 (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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190B VAL* 4.1 15.1 - - + +
201B ALA* 3.0 19.1 + - - +
202B GLN 3.9 2.9 - - - -
204B VAL* 1.3 75.3 - - - +
206B GLU* 1.3 62.9 + - - +
208B VAL* 3.3 1.4 + - + +
209B LEU* 3.0 53.1 + - + +
230B PRO* 5.7 2.0 - - + -
231B ASN* 3.2 34.5 + - - +
233B VAL* 3.9 21.4 - - + +
255B ALA* 4.3 6.3 - - + -
256B LEU* 5.9 1.3 - - + -
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Residues in contact with GLU 206 (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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202B GLN* 2.9 30.5 + - - +
203B LYS* 3.8 5.7 - - - +
205B THR* 1.3 74.8 - - - +
207B THR* 1.3 63.7 + - - +
209B LEU* 4.8 0.4 - - - -
210B ALA* 3.2 21.8 + - - +
255B ALA* 3.5 26.9 - - - +
258B ARG* 2.9 36.6 + - + -
259B THR* 3.3 19.1 - - + +
4C PHE* 4.7 5.9 - - + -
6C TYR* 2.8 32.5 + - - -
217C SER* 4.8 1.2 + - - -
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Residues in contact with THR 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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163B ILE* 3.9 17.3 - - + -
203B LYS 2.8 22.8 + - - -
204B VAL 3.6 3.8 - - - -
206B GLU* 1.3 77.9 - - - +
208B VAL* 1.3 63.2 + - - +
210B ALA* 3.4 6.0 + - - +
211B ALA* 3.3 20.3 + - - +
0C ACE 3.9 28.7 - - + -
1C THR 3.5 18.2 + - - +
2C THR* 4.0 14.4 - - + -
4C PHE* 4.2 6.4 - - - -
214C LYS* 5.9 0.3 - - - -
217C SER* 5.2 3.8 - - - +
220C HIS* 5.6 0.3 - - - -
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Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 3.1 38.6 - - + -
158B PRO* 4.5 1.8 - - + -
163B ILE* 4.4 22.2 - - + +
188B PRO* 4.0 22.4 - - + +
190B VAL* 4.1 15.5 - - + -
204B VAL* 2.9 27.3 + - + +
205B THR* 3.8 4.5 - - - +
207B THR* 1.3 76.6 - - - +
209B LEU* 1.3 61.7 + - + +
211B ALA* 3.2 5.5 + - - +
212B VAL* 2.9 29.5 + - + +
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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
----------------------------------------------------------
188B PRO* 4.2 25.6 - - + +
205B THR* 3.0 40.4 + - + +
208B VAL* 1.3 75.7 - - + +
210B ALA* 1.3 65.3 + - - +
212B VAL* 3.3 3.5 + - + -
213B TYR* 3.1 37.7 + - + +
228B LEU* 4.4 17.3 - - + -
230B PRO* 4.9 7.4 - - + -
255B ALA 4.5 4.3 - - - +
256B LEU* 3.9 24.9 - - + -
259B THR* 3.3 31.6 - - + +
260B VAL* 4.2 2.2 - - + -
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Residues in contact with ALA 210 (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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206B GLU 3.2 16.8 + - - +
207B THR 3.7 4.9 - - - +
208B VAL 3.3 0.2 - - - -
209B LEU* 1.3 75.7 - - - +
211B ALA* 1.3 63.3 + - - +
213B TYR* 3.5 3.5 + - - +
214B LYS* 3.1 24.4 + - - +
259B THR* 4.0 13.6 - - + +
213C TYR 5.5 0.9 - - - +
214C LYS* 4.1 11.3 - - + +
217C SER* 3.3 32.8 - - - +
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Residues in contact with ALA 211 (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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163B ILE* 3.3 35.2 - - + +
164B LEU* 5.6 1.3 - - - -
167B ALA* 3.6 12.7 - - + +
207B THR 3.3 5.3 + - - +
208B VAL 3.2 5.5 + - - +
209B LEU 3.2 0.4 - - - -
210B ALA* 1.3 77.7 - - - +
212B VAL* 1.3 65.3 + - - +
214B LYS* 3.2 2.5 + - - +
215B ALA* 2.9 24.8 + - - +
214C LYS* 4.1 16.8 - - - +
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Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ALA* 4.0 16.9 - - + +
170B LEU* 4.2 13.2 - - + -
186B VAL* 3.9 25.6 - - + -
188B PRO* 4.1 28.9 - - + -
208B VAL* 2.9 22.1 + - + +
209B LEU* 3.3 10.5 + - + +
211B ALA* 1.3 77.5 - - - +
213B TYR* 1.3 69.1 + - + +
215B ALA* 3.4 3.1 + - - +
216B LEU* 3.0 38.7 + - + +
228B LEU* 5.2 0.2 - - + -
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Residues in contact with TYR 213 (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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186B VAL* 5.3 2.3 - - + +
209B LEU* 3.1 29.9 + - + +
210B ALA* 4.4 2.9 - - - +
212B VAL* 1.3 83.4 - - + +
214B LYS* 1.3 65.7 + - - +
216B LEU* 3.4 28.4 - - + +
217B SER* 3.1 22.3 + - - -
223B LEU* 4.0 12.2 - - + +
226B THR* 5.3 1.5 + - - -
227B LEU 5.3 0.3 - - - -
228B LEU* 3.5 37.6 - - + +
259B THR 3.7 18.4 - - - +
260B VAL* 3.9 21.2 - - + +
261B PRO* 3.7 18.4 - - + -
264B VAL* 3.6 30.6 - - + +
210C ALA* 5.6 0.5 - - - +
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Residues in contact with LYS 214 (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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160A TYR* 4.8 9.7 + - - -
210B ALA 3.1 18.9 + - - +
211B ALA 3.2 4.2 + - - +
213B TYR* 1.3 78.0 - - - +
215B ALA* 1.3 56.1 + - - +
217B SER* 3.2 2.9 + - - -
218B ASP* 2.7 63.7 + - - +
160C TYR* 5.7 3.6 - - - -
207C THR 5.8 0.2 - - - -
210C ALA* 4.1 20.2 - - + +
211C ALA* 3.9 30.6 - - - +
214C LYS* 3.8 32.8 - - + -
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Residues in contact with ALA 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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167B ALA* 3.3 35.0 - - + +
168B ASN* 4.2 6.3 - - - +
171B ALA* 3.5 6.2 - - + +
211B ALA 2.9 15.9 + - - +
212B VAL 3.6 3.4 - - - +
214B LYS* 1.3 75.5 - - - +
216B LEU* 1.4 64.7 + - - +
218B ASP* 3.2 9.3 + - - -
219B HIS* 3.0 32.3 + - + -
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Residues in contact with LEU 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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170B LEU 4.6 1.8 - - - +
171B ALA* 3.7 30.3 - - + +
174B ALA* 4.3 8.7 - - + -
186B VAL* 4.5 15.7 - - + -
212B VAL* 3.0 30.5 + - + +
213B TYR* 3.4 37.9 - - + +
214B LYS 3.3 0.4 - - - -
215B ALA* 1.4 75.7 - - - +
217B SER* 1.3 62.3 + - - +
219B HIS 3.5 0.9 + - - -
220B HIS 3.1 3.6 + - - -
221B VAL* 2.9 54.1 + - + +
223B LEU* 4.1 17.5 - - + -
226B THR* 5.4 3.6 - - + +
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Residues in contact with SER 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TYR 3.1 13.3 + - - -
214B LYS* 3.4 9.9 - - - -
215B ALA 3.1 0.4 - - - -
216B LEU* 1.3 77.0 - - - +
218B ASP* 1.3 69.1 + - - +
220B HIS* 3.0 24.7 + - - +
221B VAL 5.8 0.7 - - - -
223B LEU* 5.9 0.2 - - - +
206C GLU 4.8 2.4 + - - -
207C THR* 5.2 4.5 - - - +
210C ALA* 3.4 30.2 - - - +
259C THR* 6.4 0.4 - - - -
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Residues in contact with ASP 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A TYR* 4.2 19.8 + - + -
161A GLN* 3.6 23.5 - - + +
164A LEU* 3.9 25.4 - - + +
1B THR* 5.0 2.0 + - - +
214B LYS* 2.7 55.2 + - - +
215B ALA* 3.2 8.7 + - - +
217B SER* 1.3 77.9 + - - +
219B HIS* 1.3 63.4 + - + +
220B HIS* 3.6 9.9 + - - -
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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
------------------------------------------------------------
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