Contacts of the helix formed by residues 197 - 217 (chain B) in PDB entry 3LSG
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 PRO 197 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ASP* 3.7 17.5 - - - +
234A ASN* 4.3 14.6 - - + +
235A TYR* 4.2 31.2 - - + +
238A THR* 4.5 8.1 - - + -
187B SER 5.7 0.4 - - - +
190B PHE* 3.8 1.3 - - + -
191B LYS* 3.9 15.7 - - + +
196B ILE* 1.3 93.0 - - + +
198B PHE* 1.3 66.2 + - - +
199B GLN 4.4 0.9 - - - +
200B ASP* 3.1 27.1 + - - +
201B TYR 3.0 17.0 + - - -
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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
----------------------------------------------------------
232A ASP* 4.0 8.4 + - - +
161B ILE* 3.9 21.1 - - + -
170B PHE* 3.9 24.5 - + - -
171B THR* 3.7 12.1 - - - -
172B LEU* 3.3 51.6 - - + -
175B LEU* 3.6 27.8 - - + -
187B SER* 5.7 0.4 + - - -
190B PHE* 3.3 31.7 - + + +
197B PRO* 1.3 71.7 - - - +
199B GLN* 1.3 64.3 + - + +
201B TYR* 3.0 2.8 + - - +
202B LEU* 2.7 60.4 + - + +
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Residues in contact with GLN 199 (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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1A PO4 4.7 3.3 + - - +
230A PHE* 5.4 3.7 - - - -
231A GLU* 5.4 4.7 - - - +
232A ASP* 3.8 19.0 + - - +
235A TYR* 3.3 60.7 + - + +
172B LEU* 5.0 9.9 - - - +
197B PRO* 3.2 2.0 - - - +
198B PHE* 1.3 91.3 - - + +
200B ASP* 1.3 60.6 + - - +
202B LEU* 3.5 9.5 + - + +
203B LEU* 3.0 27.9 + - - +
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Residues in contact with ASP 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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235A TYR* 3.5 24.1 + - - -
238A THR* 4.4 8.5 + - - +
242A LYS* 5.4 6.3 + - - -
196B ILE* 4.2 15.5 - - + +
197B PRO* 3.1 34.2 + - + +
199B GLN* 1.3 75.3 - - - +
201B TYR* 1.3 64.3 + - - +
203B LEU* 3.3 16.0 + - + +
204B GLN* 3.0 22.7 + - - +
243B TYR* 5.5 1.0 - - - -
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Residues in contact with TYR 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLN* 3.2 31.9 + - + +
161B ILE* 4.0 27.8 - - + -
162B GLU* 4.9 1.3 + - - -
190B PHE* 3.6 26.9 - + + -
194B PHE* 3.6 29.8 - + + -
196B ILE* 3.8 19.2 - - + +
197B PRO 3.0 5.6 + - - +
198B PHE 3.0 7.9 + - - +
200B ASP* 1.3 75.6 - - - +
202B LEU* 1.3 65.3 + - - +
204B GLN* 3.1 19.6 + - - +
205B LYS* 3.1 56.3 + - + +
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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
----------------------------------------------------------
161B ILE* 4.6 3.8 - - + -
165B TYR* 3.6 32.8 - - + -
170B PHE* 3.7 28.9 - - + +
171B THR* 5.3 0.2 - - - -
198B PHE* 2.7 41.7 + - + +
199B GLN* 3.7 9.9 - - + +
201B TYR* 1.3 77.3 - - - +
203B LEU* 1.3 64.1 + - - +
205B LYS* 3.2 5.4 + - - +
206B ARG* 3.2 56.7 + - - +
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Residues in contact with LEU 203 (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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1A PO4 5.9 0.7 - - - +
235A TYR* 6.1 0.4 - - - +
199B GLN 3.0 18.2 + - - +
200B ASP* 3.6 15.9 - - - +
202B LEU* 1.3 76.0 - - - +
204B GLN* 1.3 64.4 + - - +
206B ARG* 3.1 8.2 + - - +
207B MSE 2.9 48.4 + - + +
230B PHE* 4.1 20.6 - - + -
239B LYS* 3.9 38.4 - - + +
243B TYR* 4.0 21.5 - - + -
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Residues in contact with GLN 204 (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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196B ILE* 4.0 19.5 - - + +
200B ASP 3.0 13.9 + - - +
201B TYR* 3.1 24.4 + - - +
203B LEU* 1.3 77.9 - - - +
205B LYS* 1.3 69.0 + - - +
207B MSE 3.3 1.7 + - - +
208B GLU* 3.0 52.5 + - - +
243B TYR* 3.3 32.5 + - + +
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Residues in contact with LYS 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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158B GLN* 5.0 4.2 - - - +
161B ILE* 4.4 10.5 - - + -
162B GLU* 3.3 35.7 + - - -
165B TYR* 3.8 23.2 - - + -
201B TYR* 3.1 53.9 + - + +
202B LEU* 3.2 5.1 + - - +
204B GLN* 1.3 81.9 - - - +
206B ARG* 1.3 58.6 + - - +
208B GLU* 3.4 21.0 + - - +
209B LYS* 3.0 28.8 + - - +
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Residues in contact with ARG 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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165B TYR* 2.7 35.8 + - + +
167B ASP 2.8 31.3 + - - -
168B SER* 4.0 4.4 + - - +
170B PHE* 4.0 7.3 + - - +
202B LEU* 3.2 47.6 + - + +
203B LEU* 3.1 10.4 + - - +
205B LYS* 1.3 74.8 - - - +
207B MSE 1.3 62.3 + - - +
209B LYS 3.4 0.3 + - - -
210B ALA* 2.9 26.3 + - - +
228B VAL* 3.0 35.0 + - + +
229B GLY 3.7 15.6 + - - -
230B PHE* 4.2 22.4 - - + -
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Residues in contact with MSE 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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203B LEU* 2.9 28.2 + - + +
204B GLN 3.8 4.0 - - - +
206B ARG* 1.3 78.2 - - - +
208B GLU* 1.3 65.6 + - - +
210B ALA* 3.0 13.8 + - - +
211B LYS 3.0 10.6 + - - -
228B VAL* 4.8 0.2 - - + -
230B PHE* 3.5 37.7 - - + -
236B PHE* 3.7 22.7 - - + -
239B LYS 4.2 5.8 - - - +
240B PHE* 3.6 39.5 - - - +
243B TYR* 3.7 26.7 - - + -
244B TYR* 3.2 25.5 + - + +
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Residues in contact with GLU 208 (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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204B GLN* 3.0 45.2 + - + +
205B LYS* 3.7 27.0 + - - +
207B MSE 1.3 75.5 - - + +
209B LYS* 1.3 64.6 + - - +
211B LYS* 3.2 6.0 + - - +
212B LEU* 3.1 21.3 + - - +
243B TYR* 5.1 3.2 + - + +
244B TYR* 3.8 9.9 - - - +
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Residues in contact with LYS 209 (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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165B TYR* 3.4 34.2 + - + +
166B THR* 4.9 7.1 + - - -
205B LYS 3.0 18.5 + - - +
206B ARG 3.8 4.0 - - - +
207B MSE 3.2 0.2 - - - -
208B GLU* 1.3 77.0 - - - +
210B ALA* 1.3 63.6 + - - +
212B LEU* 3.3 24.9 + - + -
213B LEU* 3.0 45.9 + - + +
227B GLN* 5.3 4.7 + - - +
228B VAL* 3.7 18.2 - - + -
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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 ARG 2.9 14.9 + - - +
207B MSE 3.0 14.1 + - - +
209B LYS* 1.3 77.7 - - - +
211B LYS* 1.3 56.8 + - - +
213B LEU* 3.3 3.3 + - - +
214B LEU* 2.9 35.1 + - + +
224B ILE* 4.1 12.2 - - + +
228B VAL* 3.9 2.2 - - + +
236B PHE* 3.8 33.7 - - + -
240B PHE* 4.1 10.1 - - + -
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Residues in contact with LYS 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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207B MSE 3.0 7.3 + - - +
208B GLU* 3.2 8.0 + - - +
210B ALA* 1.3 74.1 - - - +
212B LEU* 1.3 65.2 + - - +
214B LEU* 3.1 2.1 + - - -
215B LEU* 2.9 26.9 + - - +
240B PHE* 4.1 10.1 - - + -
244B TYR* 3.3 60.3 - - + +
246B ILE* 5.0 5.6 - - - +
251B TYR* 3.4 52.6 - - + +
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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
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208B GLU 3.1 12.9 + - - +
209B LYS* 3.3 30.9 + - + +
211B LYS* 1.3 76.4 - - - +
213B LEU* 1.3 60.9 + - + +
215B LEU* 4.6 7.4 - - + -
216B THR* 2.8 53.7 + - + +
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Residues in contact with LEU 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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209B LYS* 3.0 35.8 + - + +
210B ALA 3.6 4.3 - - - +
212B LEU* 1.3 77.9 - - + +
214B LEU* 1.3 56.8 + - - +
216B THR* 4.1 4.0 - - - +
217B THR* 2.6 46.3 + - + +
219B LEU* 3.9 16.8 - - + -
224B ILE* 4.0 25.8 - - + -
227B GLN* 4.2 24.2 - - + +
228B VAL* 3.7 29.4 - - + -
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Residues in contact with LEU 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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210B ALA* 2.9 23.0 + - + +
211B LYS 3.1 1.1 + - - +
213B LEU* 1.3 76.7 - - - +
215B LEU* 1.3 60.5 + - - +
217B THR 3.4 5.4 - - - +
221B ASN* 4.1 3.1 - - - +
224B ILE* 3.2 24.5 - - + -
236B PHE* 5.4 1.8 - - + -
240B PHE* 3.7 31.4 - - + -
248B PRO* 3.8 27.1 - - + +
251B TYR* 3.7 26.9 - - + -
252B ARG* 2.9 54.9 + - + +
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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
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211B LYS 2.9 16.9 + - - +
212B LEU* 3.8 8.7 - - + +
214B LEU* 1.3 80.6 - - - +
216B THR* 1.3 73.4 + - + +
217B THR 3.6 0.9 - - - +
251B TYR* 3.7 24.2 - - + +
252B ARG* 5.5 0.7 - - - +
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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
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212B LEU* 2.8 44.6 + - + +
213B LEU* 4.1 2.3 - - - +
215B LEU* 1.3 96.4 - - + +
217B THR* 1.3 70.3 + - - +
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Residues in contact with THR 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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213B LEU* 2.6 27.7 + - + +
214B LEU 3.4 7.8 - - - +
215B LEU 4.7 0.7 - - - +
216B THR* 1.3 94.4 - - - +
218B GLU* 1.3 66.9 + - - +
219B LEU* 3.1 39.4 + - + +
252B ARG* 2.8 17.0 + - - -
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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