Contacts of the helix formed by residues 197 - 217 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187E SER 5.7 1.1 - - - +
190E PHE* 4.5 0.4 - - + -
191E LYS* 4.2 22.4 - - + +
196E ILE* 1.3 89.5 - - + +
198E PHE* 1.3 67.2 + - - +
199E GLN* 4.0 13.2 - - + +
200E ASP* 3.0 33.4 + - - +
201E TYR* 3.0 19.6 + - - +
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Residues in contact with PHE 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E ILE* 3.8 15.3 - - + -
170E PHE* 3.7 24.7 - + - -
171E THR* 3.7 4.9 - - - -
172E LEU* 3.2 54.5 - - + -
175E LEU* 3.7 30.5 - - + -
187E SER* 5.7 2.7 + - - +
190E PHE* 3.5 38.6 - + + +
197E PRO* 1.3 71.1 - - - +
199E GLN* 1.3 70.9 + - + +
201E TYR* 3.1 2.6 + - - +
202E LEU* 2.8 56.1 + - + +
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Residues in contact with GLN 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E LEU* 4.0 28.7 - - - +
187E SER* 5.4 2.2 + - - -
197E PRO* 4.0 9.2 - - + +
198E PHE* 1.3 96.7 + - + +
200E ASP* 1.3 64.2 + - - +
202E LEU* 3.6 4.9 + - - +
203E LEU* 3.0 28.1 + - - +
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Residues in contact with ASP 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196E ILE* 4.4 12.2 - - + +
197E PRO* 3.0 40.6 + - + +
199E GLN* 1.3 81.4 - - - +
201E TYR* 1.3 59.7 + - - +
203E LEU* 3.4 10.0 + - - +
204E GLN* 2.9 30.1 + - - +
243E TYR* 5.6 1.2 - - - -
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Residues in contact with TYR 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A GLN* 4.2 8.7 + - - +
253A GLU* 2.6 45.8 + - + -
158E GLN* 4.0 11.9 + - + +
161E ILE* 3.7 39.3 - - + -
190E PHE* 3.4 33.4 - + + -
194E PHE* 3.7 19.1 - + + -
196E ILE* 3.9 20.7 - - + +
197E PRO 3.0 6.2 + - - +
198E PHE 3.4 7.6 - - - +
200E ASP* 1.3 75.6 - - - +
202E LEU* 1.3 64.0 + - - +
204E GLN* 3.3 9.8 + - - +
205E LYS* 3.1 44.7 + - + +
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Residues in contact with LEU 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E ILE* 4.3 9.0 - - + -
165E TYR* 3.6 32.3 - - + -
170E PHE* 3.6 28.3 - - + +
171E THR* 5.1 0.4 - - - -
198E PHE* 2.8 43.3 + - + +
199E GLN* 3.8 5.8 - - - +
201E TYR* 1.3 77.0 - - - +
203E LEU* 1.3 64.0 + - - +
205E LYS* 3.2 3.9 + - + +
206E ARG* 3.0 56.4 + - - +
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Residues in contact with LEU 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E GLN 3.0 19.4 + - - +
200E ASP* 3.6 9.9 - - - +
202E LEU* 1.3 76.9 - - - +
204E GLN* 1.3 57.4 + - - +
206E ARG* 3.2 6.3 + - - +
207E MSE 2.8 53.0 + - + +
230E PHE* 4.0 27.1 - - + -
239E LYS* 3.5 38.4 - - + +
243E TYR* 4.2 19.1 - - + -
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Residues in contact with GLN 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A LYS* 5.6 8.3 - - - +
196E ILE* 4.0 20.1 - - + +
200E ASP 2.9 17.4 + - - +
201E TYR* 3.6 9.5 - - - +
202E LEU 3.3 0.2 - - - -
203E LEU* 1.3 75.6 - - - +
205E LYS* 1.3 60.2 + - - +
207E MSE 3.8 0.2 - - - -
208E GLU* 2.8 63.3 + - - +
243E TYR* 3.2 31.2 - - + +
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Residues in contact with LYS 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A GLN* 3.5 19.2 - - + +
253A GLU* 5.1 4.5 - - - +
161E ILE* 4.0 19.1 - - + -
162E GLU* 2.8 34.3 + - - +
165E TYR* 4.0 29.5 - - + -
201E TYR* 3.1 41.6 + - + +
202E LEU* 3.2 7.8 + - - +
204E GLN* 1.3 77.3 - - + +
206E ARG* 1.3 64.8 + - - +
208E GLU* 4.1 6.4 - - - +
209E LYS* 3.2 23.4 + - - +
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Residues in contact with ARG 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E TYR* 2.8 34.5 + - + +
167E ASP 3.0 28.3 + - - -
168E SER* 4.2 4.2 + - - +
170E PHE* 3.6 18.6 + - - +
202E LEU* 3.0 41.7 + - + +
203E LEU* 3.6 9.1 - - - +
205E LYS* 1.3 77.0 - - - +
207E MSE 1.3 57.4 + - - +
209E LYS* 3.4 2.8 + - - +
210E ALA* 3.0 27.9 + - - +
228E VAL* 3.1 28.9 + - + +
229E GLY 3.9 12.1 + - - -
230E PHE* 3.9 30.3 - - + -
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Residues in contact with MSE 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E LEU* 2.8 32.4 + - + +
204E GLN 3.8 2.2 - - - +
205E LYS 3.3 0.2 - - - -
206E ARG* 1.3 77.0 - - + +
208E GLU* 1.3 57.5 + - - +
210E ALA* 3.3 3.8 + - - +
211E LYS* 3.0 23.9 + - - +
228E VAL* 4.9 0.2 - - + -
230E PHE* 3.5 35.2 - - + -
236E PHE* 3.9 22.2 - - + -
239E LYS* 4.0 7.0 - - + +
240E PHE* 3.7 37.2 - - + +
243E TYR* 3.6 44.4 - - + -
244E TYR* 3.3 11.9 + - + -
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Residues in contact with GLU 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A LYS* 4.9 12.8 - - - +
204E GLN* 2.8 58.3 + - + +
205E LYS* 4.1 5.7 - - - +
207E MSE 1.3 73.9 - - + +
209E LYS* 1.3 60.9 + - - +
211E LYS* 3.5 4.9 + - + +
212E LEU* 3.0 26.5 + - - +
243E TYR* 4.7 3.0 + - + +
244E TYR* 3.4 15.9 - - - +
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Residues in contact with LYS 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E TYR* 3.4 30.2 + - + +
166E THR* 5.7 2.6 - - - +
205E LYS 3.2 18.1 + - - +
206E ARG 3.6 4.3 - - - +
208E GLU* 1.3 75.2 - - - +
210E ALA* 1.3 65.0 + - - +
212E LEU* 3.1 22.1 + - + -
213E LEU* 2.9 46.4 + - + +
227E GLN* 5.0 7.5 + - - +
228E VAL* 3.6 19.1 - - + -
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Residues in contact with ALA 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206E ARG 3.0 14.1 + - - +
207E MSE 3.3 10.1 + - - +
209E LYS* 1.3 76.2 - - - +
211E LYS* 1.3 57.7 + - - +
213E LEU* 3.2 3.3 + - - +
214E LEU* 2.9 31.8 + - + +
224E ILE* 3.7 27.4 - - + +
228E VAL* 3.7 4.8 - - + +
236E PHE* 3.9 17.5 - - + -
240E PHE* 3.8 16.4 - - + -
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Residues in contact with LYS 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D LEU* 4.2 16.2 - - + -
160D ILE* 5.5 3.0 - - - +
178D LYS 3.0 27.3 + - - -
179D LEU* 4.0 24.4 - - - +
180D ASP* 5.8 1.3 - - - +
207E MSE 3.0 15.9 + - - +
208E GLU* 3.7 6.5 - - + +
210E ALA* 1.3 74.2 - - - +
212E LEU* 1.3 66.4 + - - +
214E LEU* 3.1 4.9 + - - +
215E LEU* 3.0 41.4 + - + +
240E PHE* 3.8 12.3 - - + -
244E TYR* 3.7 37.7 + - + +
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Residues in contact with LEU 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ASN* 5.9 2.9 - - - +
188B ILE* 5.8 1.6 - - + -
191B LYS* 6.2 1.8 - - - +
180D ASP 5.9 0.4 - - - +
181D LEU* 4.6 12.1 - - + -
208E GLU 3.0 15.5 + - - +
209E LYS* 3.4 28.0 - - + +
211E LYS* 1.3 78.6 - - - +
213E LEU* 1.3 60.4 + - + +
215E LEU* 3.3 4.4 + - - -
216E THR* 2.7 57.1 + - + +
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Residues in contact with LEU 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E LYS* 2.9 40.6 + - + +
210E ALA 3.6 4.7 - - - +
212E LEU* 1.3 80.7 - - + +
214E LEU* 1.3 57.4 + - - +
216E THR* 5.4 0.4 - - - +
217E THR* 2.8 55.5 + - + +
219E LEU* 4.2 8.7 - - + -
224E ILE* 4.0 33.7 - - + -
227E GLN* 4.1 26.0 - - + +
228E VAL* 4.0 15.7 - - + -
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Residues in contact with LEU 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D SER* 6.0 0.7 - - - -
152D ASN* 3.6 42.0 - - + +
153D ALA* 3.3 27.4 - - + +
156D LEU* 5.1 3.4 - - + -
210E ALA* 2.9 12.6 + - + +
211E LYS* 3.1 8.7 + - - +
213E LEU* 1.3 77.1 - - - +
215E LEU* 1.3 63.1 + - + +
216E THR 3.6 0.2 + - - -
217E THR 3.7 10.7 - - - +
219E LEU 5.2 4.5 - - - +
221E ASN* 4.1 10.1 - - - +
224E ILE* 3.9 19.5 - - + +
236E PHE* 6.2 2.5 - - + -
240E PHE* 3.5 38.8 - - + -
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Residues in contact with LEU 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ALA* 4.3 8.0 - - + +
156D LEU* 3.8 26.5 - - + -
157D ILE* 4.2 21.8 - - + -
179D LEU* 3.8 34.1 - - + +
181D LEU* 3.7 20.2 - - + -
185D TYR* 3.4 10.6 + - - -
189D MSE 3.6 25.6 - - + +
211E LYS* 3.0 40.7 + - + +
212E LEU* 3.9 6.5 - - - +
214E LEU* 1.3 77.1 - - + +
216E THR* 1.3 61.1 + - - +
217E THR 5.0 0.2 - - - -
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Residues in contact with THR 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B ILE* 3.8 26.5 - - + -
192B LYS* 3.5 25.9 - - - +
181D LEU* 3.9 17.0 - - + -
185D TYR* 3.3 19.6 + - + +
212E LEU* 2.7 43.3 + - + +
213E LEU* 4.2 0.9 - - - +
215E LEU* 1.3 84.0 - - - +
217E THR* 1.3 70.7 + - - +
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Residues in contact with THR 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B LYS* 4.2 20.6 - - + +
213E LEU* 2.8 42.1 + - + +
214E LEU* 3.7 10.7 - - - +
215E LEU 5.0 0.3 - - - -
216E THR* 1.3 91.3 - - - +
218E GLU* 1.3 68.8 + - - +
219E LEU* 3.0 35.4 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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