Contacts of the helix formed by residues 232 - 245 (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 ASP 232 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225C ALA* 4.2 6.4 - - - +
230C PHE* 3.1 5.0 + - - +
231C GLU* 1.3 78.3 - - - +
233C VAL* 1.3 63.6 + - - +
234C ASN* 3.3 3.6 - - - +
235C TYR* 3.0 25.5 + - - +
236C PHE* 3.2 20.3 + - - +
172D LEU* 3.3 13.6 - - + +
183D SER 4.4 2.5 - - - +
184D GLY* 5.8 1.1 - - - -
187D SER* 2.7 39.3 + - - +
197D PRO* 5.3 1.4 - - - +
199D GLN* 2.9 33.5 + - - +
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Residues in contact with VAL 233 (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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182B SER* 5.9 2.9 - - - +
221C ASN* 3.5 19.3 - - + +
222C TYR* 3.3 48.7 - - + +
225C ALA* 3.8 10.2 - - - +
232C ASP* 1.3 72.0 - - - +
234C ASN* 1.3 66.1 + - - +
236C PHE* 3.5 1.4 - - + +
237C ILE* 2.8 40.3 + - + +
187D SER* 4.5 1.8 - - - +
188D ILE* 4.3 21.8 - - + -
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Residues in contact with ASN 234 (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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232C ASP* 3.3 10.2 + - - +
233C VAL* 1.3 84.8 - - - +
235C TYR* 1.3 62.4 + - - +
237C ILE* 4.0 5.7 - - - +
238C THR* 3.1 31.2 + - - +
187D SER* 3.5 11.4 + - - +
188D ILE* 3.9 21.2 - - - +
191D LYS* 2.8 52.9 + - - +
197D PRO* 4.3 11.4 - - + +
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Residues in contact with TYR 235 (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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203C LEU* 5.7 1.8 - - + -
230C PHE* 3.7 26.2 - + + -
231C GLU* 4.6 6.3 - - - -
232C ASP* 3.0 19.8 + - - +
233C VAL 3.4 0.2 - - - -
234C ASN* 1.3 76.5 - - - +
236C PHE* 1.3 58.0 + - - +
238C THR* 3.2 7.2 + - - -
239C LYS* 2.8 73.2 + - + +
197D PRO* 4.1 13.4 - - + +
199D GLN* 3.5 58.9 - - + +
200D ASP* 3.8 18.9 + - - -
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Residues in contact with PHE 236 (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 3.5 30.7 - - + -
210C ALA* 3.6 23.3 - - + -
214C LEU* 4.7 4.0 - - + -
221C ASN* 3.9 25.4 - - + -
224C ILE* 4.0 12.8 - - + -
225C ALA* 3.7 25.1 - - + -
228C VAL* 5.1 0.4 - - + -
230C PHE* 3.8 21.9 - + + -
232C ASP 3.2 14.5 + - - +
233C VAL* 3.5 9.0 - - + +
234C ASN 3.2 0.2 - - - -
235C TYR* 1.3 77.6 - - - +
237C ILE* 1.3 63.2 + - + +
239C LYS* 3.7 0.7 - - - +
240C PHE* 2.8 49.8 + + - +
248C PRO* 4.1 20.0 - - + -
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Residues in contact with ILE 237 (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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221C ASN* 3.4 32.8 - - + +
233C VAL* 2.8 40.3 + - + +
234C ASN* 4.0 5.8 - - - +
236C PHE* 1.3 77.2 - - + +
238C THR* 1.3 65.6 + - + +
240C PHE* 3.3 5.3 + - - +
241C LYS* 3.0 28.6 + - + +
247C THR* 5.8 5.2 - - + -
248C PRO* 4.4 15.1 - - + +
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Residues in contact with THR 238 (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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234C ASN* 3.1 21.2 + - - +
235C TYR* 3.2 12.5 + - - -
237C ILE* 1.3 80.6 - - + +
239C LYS* 1.3 66.2 + - - +
241C LYS* 3.3 7.0 + - - +
242C LYS* 3.1 23.6 + - - +
191D LYS* 4.2 22.9 - - - +
197D PRO* 3.8 19.4 - - + +
200D ASP* 4.9 3.0 + - - -
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Residues in contact with LYS 239 (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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203C LEU* 3.9 32.5 - - + +
207C MSE 4.7 3.4 - - - -
230C PHE* 4.3 13.2 - - + -
235C TYR* 2.8 68.9 + - + +
236C PHE 3.7 3.8 - - - +
238C THR* 1.3 74.6 + - - +
240C PHE* 1.3 52.0 + - - +
242C LYS* 3.4 34.5 + - + +
243C TYR* 2.8 44.9 + - + +
239D LYS* 5.1 8.7 - - - +
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Residues in contact with PHE 240 (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 3.9 28.4 - - + -
210C ALA* 4.7 0.9 - - + -
211C LYS* 3.9 17.0 - - + -
214C LEU* 3.6 28.5 - - + -
236C PHE* 2.8 36.1 + + + +
237C ILE 3.5 4.9 - - - +
239C LYS* 1.3 72.9 - - - +
241C LYS* 1.3 57.2 + - - +
243C TYR* 4.2 0.9 - - - -
244C TYR* 2.9 47.4 + + - +
246C ILE* 3.2 25.2 - - + +
247C THR 3.8 4.5 - - - -
248C PRO* 3.5 29.6 - - + -
251C TYR* 4.0 17.3 - + + -
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Residues in contact with LYS 241 (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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237C ILE* 3.0 14.8 + - + +
238C THR* 3.5 10.8 - - - +
239C LYS 3.2 0.2 - - - -
240C PHE* 1.3 73.3 - - - +
242C LYS* 1.3 59.1 + - - +
245C GLN* 2.6 62.3 + - - +
246C ILE* 3.6 26.2 + - - +
247C THR* 3.9 20.4 - - + -
248C PRO* 5.2 0.2 - - - +
250C GLN* 5.4 1.8 - - - -
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Residues in contact with LYS 242 (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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238C THR 3.1 13.7 + - - +
239C LYS* 3.8 33.3 - - + +
241C LYS* 1.3 80.3 - - - +
243C TYR* 1.3 63.4 + - - +
245C GLN* 4.2 5.4 + - - +
239D LYS* 5.3 7.7 - - - +
242D LYS* 5.4 13.4 - - - +
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Residues in contact with TYR 243 (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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200C ASP 5.1 0.5 + - - -
203C LEU* 3.8 29.4 - - + -
204C GLN* 3.4 32.6 + - + +
207C MSE 3.9 16.4 - - + -
239C LYS* 2.8 31.4 + - + +
240C PHE* 3.8 5.6 - - - +
242C LYS* 1.3 76.7 - - - +
244C TYR* 1.3 110.9 + + - +
245C GLN* 4.1 6.1 + - - +
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Residues in contact with TYR 244 (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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204C GLN* 4.8 1.0 + - - +
207C MSE 3.2 29.8 - - + +
208C GLU* 4.1 8.5 + - - +
211C LYS* 3.2 45.2 - - + +
240C PHE* 2.9 37.1 + + - +
243C TYR* 1.3 118.1 - + + +
245C GLN* 1.3 91.6 + - - +
246C ILE* 3.0 22.4 + - + +
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Residues in contact with GLN 245 (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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241C LYS* 2.6 42.2 + - - +
242C LYS 4.2 4.0 + - - +
243C TYR 3.7 6.2 + - - +
244C TYR* 1.3 98.3 + - - +
246C ILE* 1.3 56.7 + - + +
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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