Contacts of the helix formed by residues 197 - 217 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C SER 5.8 0.9 - - - +
190C PHE* 3.7 0.9 - - + -
191C LYS* 4.5 21.7 - - + -
196C ILE* 1.3 93.2 - - + +
198C PHE* 1.3 67.9 + - - +
199C GLN* 3.8 13.0 - - - +
200C ASP* 3.0 38.0 + - + +
201C TYR* 3.0 11.4 + - - +
232D ASP* 6.2 0.2 - - - +
234D ASN* 6.1 1.8 - - + -
235D TYR* 4.1 17.0 - - + +
238D THR* 4.8 14.4 - - + +
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Residues in contact with PHE 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ILE* 3.9 14.8 - - + -
170C PHE* 3.8 24.0 - + - -
171C THR* 3.7 5.2 - - - -
172C LEU* 3.3 60.6 - - + -
175C LEU* 3.6 25.1 - - + -
186C LEU* 5.6 0.4 - - + -
187C SER* 5.5 2.7 + - - +
190C PHE* 3.3 46.5 - + + +
197C PRO* 1.3 70.9 - - - +
199C GLN* 1.3 70.2 + - + +
201C TYR* 3.2 3.5 + - - +
202C LEU* 2.9 47.9 + - + +
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Residues in contact with GLN 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C LEU* 3.8 13.8 - - - +
187C SER* 5.6 0.2 + - - -
197C PRO* 3.0 5.7 + - - +
198C PHE* 1.3 96.7 + - + +
200C ASP* 1.3 57.5 + - - +
202C LEU* 3.5 5.3 + - - +
203C LEU* 3.0 28.2 + - - +
231D GLU* 4.4 15.9 + - - +
232D ASP* 2.9 28.2 + - - +
235D TYR* 3.4 53.9 - - + +
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Residues in contact with ASP 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C ILE* 4.3 8.9 - - + +
197C PRO* 3.0 38.6 + - + +
199C GLN* 1.3 75.2 - - - +
201C TYR* 1.3 64.7 + - - +
203C LEU* 3.8 14.8 - - - +
204C GLN* 3.0 24.3 + - - +
243C TYR* 5.1 1.0 + - - -
235D TYR* 3.9 20.4 + - - -
238D THR* 4.8 2.9 + - - -
239D LYS* 5.4 2.4 + - - -
242D LYS* 6.0 0.3 + - - -
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Residues in contact with TYR 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C GLN* 3.7 26.2 + - - +
161C ILE* 3.9 31.6 - - + -
190C PHE* 3.5 27.8 - + + -
194C PHE* 3.7 26.7 - + - -
196C ILE* 3.7 20.8 - - + +
197C PRO 3.0 5.1 + - - -
198C PHE 3.5 7.2 - - - +
200C ASP* 1.3 75.3 - - - +
202C LEU* 1.3 70.1 + - - +
204C GLN* 3.2 13.4 + - - +
205C LYS* 3.1 54.6 + - + +
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Residues in contact with LEU 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ILE* 4.1 15.3 - - + -
165C TYR* 3.7 31.4 - - + -
170C PHE* 3.7 26.5 - - + +
171C THR* 5.2 0.4 - - - -
198C PHE* 2.9 36.3 + - + +
199C GLN* 3.8 6.1 - - - +
201C TYR* 1.3 82.7 - - + +
203C LEU* 1.3 62.5 + - - +
205C LYS* 3.2 5.6 + - + +
206C ARG* 3.0 55.5 + - - +
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Residues in contact with LEU 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C GLN 3.0 17.8 + - - +
200C ASP* 3.8 15.3 - - - +
202C LEU* 1.3 77.3 - - - +
204C GLN* 1.3 56.9 + - - +
206C ARG* 3.1 9.8 + - - +
207C MSE 3.0 37.1 + - + +
230C PHE* 3.5 32.1 - - + -
235C TYR* 5.7 1.1 - - + -
239C LYS* 3.9 34.3 - - + +
243C TYR* 3.8 26.7 - - + -
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Residues in contact with GLN 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C ILE* 4.5 14.1 - - + +
200C ASP 3.0 18.6 + - - +
201C TYR* 3.5 12.7 - - - +
202C LEU 3.2 0.2 - - - -
203C LEU* 1.3 77.1 - - - +
205C LYS* 1.3 58.4 + - - +
207C MSE 3.3 4.0 + - - +
208C GLU* 2.9 56.7 + - + +
243C TYR* 3.4 26.4 + - + +
244C TYR* 5.5 0.9 - - - +
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Residues in contact with LYS 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C GLN 5.4 1.5 + - - -
161C ILE* 5.0 3.8 - - + +
162C GLU* 3.0 42.8 + - - +
165C TYR* 4.7 15.3 - - + -
201C TYR* 3.1 50.5 + - + +
202C LEU* 3.2 13.2 + - + +
204C GLN* 1.3 76.9 - - + +
206C ARG* 1.3 59.3 + - + +
208C GLU* 3.3 20.8 + - - +
209C LYS* 2.9 30.7 + - - +
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Residues in contact with ARG 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C TYR* 2.9 37.0 + - + +
167C ASP 3.1 22.6 + - - -
168C SER* 4.0 4.8 + - - +
170C PHE* 3.9 12.1 + - - +
202C LEU* 3.0 47.7 + - + +
203C LEU* 3.6 9.4 - - - +
205C LYS* 1.3 75.8 - - - +
207C MSE 1.3 61.1 + - - +
209C LYS* 3.5 2.1 + - - -
210C ALA* 2.9 27.9 + - - +
228C VAL* 3.0 30.3 + - - +
229C GLY 3.2 17.1 + - - -
230C PHE* 3.6 26.8 - - + +
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Residues in contact with MSE 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C LEU* 3.0 27.3 + - + +
204C GLN 3.7 2.9 - - - +
206C ARG* 1.3 78.4 - - - +
208C GLU* 1.3 64.0 + - - +
210C ALA* 3.3 2.9 + - + +
211C LYS* 3.0 27.5 + - - +
230C PHE* 3.5 28.0 - - + -
236C PHE* 3.5 36.8 - - + -
239C LYS* 4.7 2.9 - - - -
240C PHE* 3.9 37.3 - - - -
243C TYR* 3.9 24.0 - - + -
244C TYR* 3.2 24.5 - - + +
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Residues in contact with GLU 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C GLN* 2.9 46.8 + - + +
205C LYS* 3.7 23.0 - - - +
207C MSE 1.3 76.8 - - - +
209C LYS* 1.3 62.8 + - - +
211C LYS* 3.2 11.1 + - + +
212C LEU* 3.1 20.8 + - - +
244C TYR* 4.6 8.5 - - - +
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Residues in contact with LYS 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C TYR* 3.3 34.7 + - + +
205C LYS 2.9 17.8 + - - +
206C ARG 3.9 0.9 - - - +
208C GLU* 1.3 77.9 - - - +
210C ALA* 1.3 60.0 + - - +
212C LEU* 3.2 28.4 + - + +
213C LEU* 3.0 43.7 + - + +
227C GLN* 5.3 2.9 - - - +
228C VAL* 3.4 21.5 - - + -
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Residues in contact with ALA 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C ARG 2.9 17.4 + - - +
207C MSE 3.7 8.3 - - + +
208C GLU 3.2 0.2 - - - -
209C LYS* 1.3 76.0 - - - +
211C LYS* 1.3 58.2 + - - +
213C LEU* 3.3 2.6 + - - +
214C LEU* 2.9 36.3 + - - +
224C ILE* 3.8 19.2 - - + +
228C VAL* 3.7 6.5 - - + +
236C PHE* 3.6 31.9 - - + -
240C PHE* 4.7 3.4 - - + -
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Residues in contact with LYS 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C MSE 3.0 14.1 + - - +
208C GLU* 3.2 11.6 + - + +
210C ALA* 1.3 74.2 - - - +
212C LEU* 1.3 66.0 + - - +
214C LEU* 3.3 5.0 + - - +
215C LEU* 3.0 29.0 + - - +
240C PHE* 3.9 11.7 - - + -
244C TYR* 3.2 57.8 - - + +
251C TYR* 3.5 48.0 + - + +
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Residues in contact with LEU 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C GLU 3.1 12.0 + - - +
209C LYS* 3.4 37.0 - - + +
211C LYS* 1.3 79.4 - - - +
213C LEU* 1.3 57.3 + - + +
215C LEU* 3.1 3.2 + - + -
216C THR* 2.5 60.4 + - + +
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Residues in contact with LEU 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C LYS* 3.0 36.0 + - - +
210C ALA 3.3 4.2 + - - +
212C LEU* 1.3 80.2 - - + +
214C LEU* 1.3 57.0 + - - +
216C THR* 3.7 5.8 - - - +
217C THR* 2.5 55.1 + - + +
219C LEU* 4.5 9.0 - - + -
224C ILE* 4.1 20.4 - - + -
227C GLN* 3.7 29.2 - - + +
228C VAL* 4.1 24.5 - - + -
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Residues in contact with LEU 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C ALA 2.9 26.8 + - - +
211C LYS* 3.6 4.0 - - - +
212C LEU 3.2 0.2 - - - -
213C LEU* 1.3 78.0 - - - +
215C LEU* 1.3 62.4 + - - +
217C THR 3.6 7.1 - - - +
221C ASN* 4.0 2.7 - - - +
224C ILE* 3.6 22.2 - - + -
236C PHE* 4.7 4.3 - - + -
240C PHE* 3.6 38.1 - - + -
248C PRO* 3.7 27.1 - - + +
251C TYR* 4.0 11.9 - - + -
252C ARG* 3.3 57.1 + - + +
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Residues in contact with LEU 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C LYS 3.0 12.8 + - - +
212C LEU* 3.9 3.8 - - - +
214C LEU* 1.3 77.3 - - - +
216C THR* 1.3 66.8 + - + +
217C THR 3.7 0.7 - - - -
251C TYR* 3.7 51.8 - - + +
252C ARG* 4.2 12.6 - - - +
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Residues in contact with THR 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C LEU* 2.5 51.5 + - + +
213C LEU* 3.7 5.9 - - - +
215C LEU* 1.3 85.4 - - + +
217C THR* 1.3 66.2 + - - +
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Residues in contact with THR 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C LEU* 2.5 39.5 + - + +
214C LEU 3.6 6.2 - - - +
215C LEU 3.7 0.5 - - - -
216C THR* 1.3 92.3 - - - +
218C GLU* 1.3 69.8 + - - +
219C LEU* 3.2 33.6 + - + +
252C ARG* 3.0 15.9 + - - -
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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