Contacts of the helix formed by residues 223 - 236 (chain C) in PDB entry 3G33
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 SER 223 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183C LEU* 3.3 18.1 - - - +
221C GLY 4.1 1.0 - - - -
222C ASN* 1.3 83.6 + - - +
224C GLU* 1.3 65.5 + - - +
225C ALA* 3.7 12.0 + - - +
226C ASP* 3.7 10.2 + - - +
227C GLN* 3.2 16.6 + - - +
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Residues in contact with GLU 224 (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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183C LEU* 3.9 15.0 - - + -
190C VAL 5.9 0.4 - - - -
191C LEU* 3.5 34.9 - - + +
193C GLN* 5.2 11.9 + - - +
223C SER* 1.3 77.2 - - - +
225C ALA* 1.3 58.6 + - - +
227C GLN* 3.1 10.3 + - - +
228C LEU* 2.7 30.0 + - - +
249C LEU* 5.5 4.1 - - + +
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Residues in contact with ALA 225 (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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223C SER* 3.5 7.0 + - - +
224C GLU* 1.3 77.8 - - - +
226C ASP* 1.3 62.3 + - - +
228C LEU* 3.4 11.3 + - - +
229C GLY* 3.3 16.3 + - - -
249C LEU* 4.7 19.7 - - + +
254C PHE* 4.2 10.0 - - + -
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Residues in contact with ASP 226 (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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220C CYS 4.2 2.8 - - - +
221C GLY* 3.4 5.5 - - - -
222C ASN* 2.6 39.6 + - + +
223C SER* 3.6 14.3 + - - +
224C GLU 3.2 0.8 - - - -
225C ALA* 1.3 77.5 - - - +
227C GLN* 1.3 64.4 + - - +
229C GLY* 3.2 10.9 + - - -
230C LYS* 3.2 27.7 + - - +
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Residues in contact with GLN 227 (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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183C LEU* 2.8 33.0 + - + +
184C TRP* 3.0 26.3 - - - +
186C ARG* 5.2 0.7 - - + +
191C LEU* 3.5 24.0 - - + -
219C PHE* 3.3 19.0 - - - +
221C GLY* 2.9 37.2 + - - +
223C SER 3.2 12.0 + - - +
224C GLU* 3.1 11.5 + - - +
226C ASP* 1.3 77.7 - - - +
228C LEU* 1.3 62.2 + - - +
230C LYS* 3.4 4.7 + - - +
231C ILE* 3.1 30.4 + - + +
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Residues in contact with LEU 228 (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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188C PRO* 4.3 13.0 - - + -
191C LEU* 3.6 38.4 - - + +
192C LEU* 3.7 32.5 - - + -
224C GLU 2.7 31.0 - - - +
225C ALA* 3.7 8.1 - - - +
226C ASP 3.3 0.4 - - - -
227C GLN* 1.3 72.6 - - - +
229C GLY* 1.3 67.3 + - - +
231C ILE* 2.9 8.8 + - + +
232C PHE* 2.9 55.8 + - + -
249C LEU* 4.6 3.4 - - + -
254C PHE* 3.7 9.2 - - + -
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Residues in contact with GLY 229 (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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225C ALA 3.3 7.8 + - - -
226C ASP* 3.2 10.2 + - - -
228C LEU* 1.3 80.7 - - - +
230C LYS* 1.3 59.9 + - - +
231C ILE 3.4 0.2 + - - -
232C PHE* 3.7 2.7 + - - +
233C ASP* 3.0 31.2 + - - +
254C PHE* 4.0 15.2 - - - -
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Residues in contact with LYS 230 (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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219C PHE* 3.6 29.7 - - + -
220C CYS* 3.4 34.5 - - - +
226C ASP* 3.2 27.4 + - - +
227C GLN* 3.8 6.7 - - - +
228C LEU 3.2 0.2 - - - -
229C GLY* 1.3 76.7 - - - +
231C ILE* 1.3 61.4 + - - +
233C ASP* 3.8 11.7 + - - +
234C LEU* 4.0 10.2 - - - +
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Residues in contact with ILE 231 (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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184C TRP 5.7 0.2 - - - +
186C ARG 4.6 0.9 - - - +
188C PRO* 4.5 8.7 - - + -
191C LEU* 4.2 22.7 - - + -
203C TRP* 3.4 48.9 - - + +
219C PHE* 3.7 23.5 - - + -
227C GLN* 3.1 24.0 - - + +
228C LEU* 2.9 12.2 + - + +
230C LYS* 1.3 75.1 - - - +
232C PHE* 1.3 72.8 + - + +
233C ASP 3.1 1.8 - - - -
234C LEU* 3.2 13.9 + - - +
235C ILE* 3.3 24.8 + - + +
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Residues in contact with PHE 232 (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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188C PRO* 5.8 0.2 - - + -
192C LEU* 4.9 0.7 - - + -
228C LEU* 2.9 55.1 + - + +
229C GLY* 4.4 3.1 - - - +
231C ILE* 1.3 81.3 - - + +
233C ASP* 1.3 57.4 + - - +
234C LEU 3.1 1.0 + - - -
235C ILE* 4.3 7.6 - - + -
236C GLY* 3.1 30.9 + - - +
237C LEU* 4.3 10.3 - - + +
238C PRO* 3.7 35.9 - - + -
243C TRP* 3.8 19.5 - + - -
254C PHE* 3.7 40.4 - + + -
255C PRO 5.8 0.2 - - - +
257C ARG* 3.4 15.3 - - + +
283C PHE* 4.0 15.7 - + - -
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Residues in contact with ASP 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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229C GLY 3.0 20.4 + - - +
230C LYS* 4.0 9.8 - - - +
231C ILE 3.1 1.4 - - - -
232C PHE* 1.3 77.4 - - - +
234C LEU* 1.3 60.1 + - + +
257C ARG* 3.2 37.9 + - - +
258C GLY 5.3 1.1 - - - +
260C ARG* 3.2 39.8 + - - +
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Residues in contact with LEU 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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218C LEU* 4.6 11.2 - - + +
219C PHE* 3.5 30.5 - - + -
230C LYS 4.0 7.6 - - - +
231C ILE 3.2 6.1 + - - +
232C PHE 3.1 0.6 - - - -
233C ASP* 1.3 91.2 - - + +
235C ILE* 1.3 66.9 + - + +
236C GLY 3.3 1.1 + - - -
258C GLY 4.2 0.4 - - - +
260C ARG* 3.1 50.5 + - + +
265C VAL* 3.7 42.6 - - + -
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Residues in contact with ILE 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 TRP* 4.0 13.0 - - + -
219C PHE* 5.3 2.5 - - + -
231C ILE* 3.3 35.4 + - + +
232C PHE* 4.3 6.5 - - + -
234C LEU* 1.3 80.0 - - + +
236C GLY* 1.3 73.3 + - - +
259C PRO* 3.7 20.4 - - - +
278C LEU* 6.5 1.3 - - + -
281C LEU* 3.7 38.4 - - + +
283C PHE* 4.3 22.2 - - + +
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Residues in contact with GLY 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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232C PHE* 3.1 21.1 + - - -
234C LEU 3.3 2.6 - - - -
235C ILE* 1.3 94.2 - - - +
237C LEU* 1.3 66.3 + - - -
238C PRO* 3.4 7.4 - - - +
257C ARG 3.4 11.7 - - - -
258C GLY 3.7 14.6 - - - -
259C PRO* 4.1 1.6 - - - -
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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