Contacts of the helix formed by residues 197 - 217 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C ASP* 5.3 1.1 - - - +
234C ASN* 4.3 12.8 - - + +
235C TYR* 4.1 18.8 - - + +
238C THR* 3.8 32.8 - - + +
187D SER 5.9 1.3 - - - +
190D PHE* 4.5 1.1 - - + -
191D LYS* 4.4 12.5 - - + -
196D ILE* 1.3 92.6 - - + +
198D PHE* 1.3 67.2 + - - +
199D GLN* 3.9 14.4 - - - +
200D ASP* 3.1 20.6 + - - +
201D TYR* 3.1 17.3 + - - +
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Residues in contact with PHE 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D ILE* 4.0 21.8 - - + -
170D PHE* 3.9 13.7 - + - -
171D THR* 3.7 9.6 - - - -
172D LEU* 3.2 55.6 - - + -
175D LEU* 3.7 30.5 - - + -
187D SER* 6.0 0.4 + - - -
190D PHE* 3.4 31.3 - + + +
197D PRO* 1.3 71.5 - - - +
199D GLN* 1.3 72.4 + - + +
201D TYR* 3.1 3.3 + - - +
202D LEU* 2.8 57.5 + - + +
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Residues in contact with GLN 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C GLU* 2.9 38.1 + - - +
232C ASP* 2.9 25.6 + - - +
235C TYR* 3.5 50.9 - - + +
172D LEU* 4.3 4.0 - - - +
197D PRO* 3.9 1.7 - - - +
198D PHE* 1.3 101.0 + - + +
200D ASP* 1.3 59.0 + - - +
202D LEU* 3.5 6.1 + - + +
203D LEU* 3.0 27.7 + - - +
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Residues in contact with ASP 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C TYR* 3.8 21.2 + - - -
238C THR* 4.9 3.3 + - - -
196D ILE* 4.3 15.3 - - + +
197D PRO* 3.1 29.4 + - + +
199D GLN* 1.3 76.1 - - - +
201D TYR* 1.3 65.8 + - - +
203D LEU* 3.8 12.8 - - - +
204D GLN* 3.1 24.4 + - - +
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Residues in contact with TYR 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D GLN* 4.0 25.2 + - - +
161D ILE* 3.7 43.7 - - + -
190D PHE* 3.7 16.8 - + + -
194D PHE* 3.7 29.2 - + + -
196D ILE* 3.9 18.5 - - + +
197D PRO 3.1 7.7 + - - +
198D PHE 3.1 8.2 + - - +
200D ASP* 1.3 78.1 - - - +
202D LEU* 1.3 63.2 + - - +
204D GLN* 3.8 13.1 + - - +
205D LYS* 3.2 37.6 + - + +
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Residues in contact with LEU 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D ILE* 4.3 7.2 - - + -
165D TYR* 3.6 29.8 - - + -
170D PHE* 3.7 31.6 - - + +
171D THR* 4.9 0.9 - - - -
198D PHE* 2.8 38.4 + - + +
199D GLN* 3.7 6.5 - - - +
201D TYR* 1.3 79.3 - - - +
203D LEU* 1.3 64.3 + - - +
205D LYS* 3.3 4.4 + - + +
206D ARG* 3.0 60.8 + - - +
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Residues in contact with LEU 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D GLN 3.0 17.8 + - - +
200D ASP* 3.8 13.0 - - - +
202D LEU* 1.3 77.4 - - - +
204D GLN* 1.3 57.7 + - - +
206D ARG* 3.1 6.9 + - - +
207D MSE 2.8 51.5 + - + +
230D PHE* 3.9 26.9 - - + -
239D LYS* 3.9 31.0 - - + +
243D TYR* 4.6 15.7 - - + -
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Residues in contact with GLN 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D ILE* 6.0 2.0 - - + -
200D ASP 3.1 18.1 + - - +
201D TYR* 3.8 13.9 + - - +
203D LEU* 1.3 77.3 - - - +
205D LYS* 1.3 70.7 + - - +
207D MSE 3.2 1.2 + - - +
208D GLU* 2.6 62.8 + - - +
243D TYR* 3.0 33.9 - - + +
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Residues in contact with LYS 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D GLN 5.3 1.0 + - - -
161D ILE* 3.9 17.0 - - + -
162D GLU* 2.9 51.6 + - - +
165D TYR* 3.8 29.2 - - + -
201D TYR* 3.2 27.0 + - + +
202D LEU* 3.6 8.5 - - - +
203D LEU 3.2 0.2 - - - -
204D GLN* 1.3 89.1 - - - +
206D ARG* 1.3 62.9 + - - +
208D GLU* 3.5 4.3 + - - +
209D LYS* 3.2 22.7 + - - +
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Residues in contact with ARG 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D TYR* 2.7 37.2 + - + +
167D ASP 3.0 27.7 + - - -
168D SER* 4.2 3.6 + - - +
170D PHE* 3.5 16.8 + - - +
202D LEU* 3.0 43.9 + - + +
203D LEU* 3.1 9.4 + - - +
205D LYS* 1.3 75.4 - - - +
207D MSE 1.3 61.1 + - - +
209D LYS* 3.4 2.4 + - - +
210D ALA* 3.0 29.1 + - - +
228D VAL* 3.0 27.3 + - + +
229D GLY 3.3 18.7 + - - -
230D PHE* 4.0 23.0 - - + -
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Residues in contact with MSE 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D LEU* 2.8 31.6 + - + +
204D GLN 3.2 2.4 + - - +
206D ARG* 1.3 76.0 - - - +
208D GLU* 1.3 58.9 + - - +
210D ALA* 3.3 2.4 + - + +
211D LYS* 3.0 22.5 + - - +
228D VAL* 5.0 0.2 - - + -
230D PHE* 3.6 36.3 - - + -
236D PHE* 3.9 24.7 - - + -
239D LYS 4.1 2.5 - - - +
240D PHE* 3.7 35.2 - - - +
243D TYR* 3.5 49.1 - - + -
244D TYR* 2.9 14.2 + - + +
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Residues in contact with GLU 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D GLN* 2.6 51.2 + - + +
205D LYS* 3.9 5.4 - - - +
206D ARG 3.3 0.2 - - - -
207D MSE 1.3 75.8 - - + +
209D LYS* 1.3 64.7 + - - +
211D LYS* 3.4 4.0 + - - +
212D LEU* 3.0 23.4 + - - +
243D TYR* 4.8 2.6 + - + +
244D TYR* 3.5 11.0 - - - +
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Residues in contact with LYS 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D TYR* 3.4 31.4 + - + +
166D THR* 4.7 10.9 - - - +
205D LYS 3.2 16.7 + - - +
206D ARG 3.8 4.7 - - - +
208D GLU* 1.3 76.8 - - - +
210D ALA* 1.3 57.8 + - - +
212D LEU* 3.2 22.2 + - + +
213D LEU* 2.9 58.4 + - + +
227D GLN* 4.8 5.3 + - - +
228D VAL* 3.8 16.8 - - + -
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Residues in contact with ALA 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D ARG 3.0 18.4 + - - +
207D MSE 3.6 5.2 - - - +
208D GLU 3.2 0.2 - - - -
209D LYS* 1.3 78.2 - - - +
211D LYS* 1.3 57.3 + - - +
213D LEU* 3.4 2.1 + - - +
214D LEU* 2.9 31.0 + - - +
224D ILE* 3.8 16.2 - - + +
228D VAL* 3.7 4.9 - - + +
236D PHE* 3.5 37.0 - - + -
240D PHE* 4.0 9.2 - - + -
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Residues in contact with LYS 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D MSE 3.0 17.5 + - - +
208D GLU* 3.7 5.6 - - - +
210D ALA* 1.3 76.8 - - - +
212D LEU* 1.3 62.6 + - - +
214D LEU* 3.3 3.9 + - + +
215D LEU* 3.1 50.4 + - + +
240D PHE* 3.7 14.3 - - + -
244D TYR* 3.6 39.6 - - + +
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Residues in contact with LEU 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D GLU 3.0 14.3 + - - +
209D LYS* 3.4 29.2 - - + +
211D LYS* 1.3 76.9 - - - +
213D LEU* 1.3 60.0 + - + +
215D LEU* 3.2 5.9 + - + -
216D THR* 2.6 55.6 + - + +
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Residues in contact with LEU 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D LYS* 2.9 47.0 + - + +
210D ALA 3.8 3.8 - - - +
212D LEU* 1.3 72.2 - - + +
214D LEU* 1.3 66.8 + - - +
216D THR* 4.0 4.5 - - - +
217D THR* 2.7 50.0 + - + +
219D LEU* 4.4 9.6 - - + -
224D ILE* 4.1 19.5 - - + -
227D GLN* 4.1 26.5 - - + +
228D VAL* 4.1 21.1 - - + -
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Residues in contact with LEU 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D ALA 2.9 18.6 + - - +
211D LYS* 3.3 8.3 + - + +
213D LEU* 1.3 77.3 - - - +
215D LEU* 1.3 69.7 + - + +
216D THR 3.7 0.2 + - - -
217D THR 4.0 8.7 - - - +
219D LEU 5.4 3.4 - - - +
221D ASN* 4.8 9.6 - - - +
224D ILE* 4.0 20.6 - - + +
236D PHE* 6.4 1.8 - - + -
240D PHE* 4.3 25.1 - - + -
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Residues in contact with LEU 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D LYS* 3.1 46.2 + - + +
212D LEU* 3.9 5.6 - - - +
213D LEU 3.1 0.2 - - - -
214D LEU* 1.3 89.1 - - + +
216D THR* 1.3 67.1 + - + +
217D THR 3.8 0.9 - - - -
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Residues in contact with THR 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D LEU* 2.6 44.5 + - + +
213D LEU* 4.0 1.2 - - - +
215D LEU* 1.3 88.5 - - + +
217D THR* 1.3 70.5 + - - +
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Residues in contact with THR 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D LEU* 2.7 41.2 + - + +
214D LEU* 4.0 9.2 - - - +
215D LEU 3.8 0.5 - - - -
216D THR* 1.3 91.0 - - - +
218D GLU* 1.3 70.9 + - - +
219D LEU* 3.2 31.4 + - + +
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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