Contacts of the helix formed by residues 219 - 236 (chain C) in PDB entry 3E7G
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 THR 219 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217C CYS* 3.7 0.6 - - - -
218C SER* 1.3 93.1 + - - +
220C ALA* 1.3 60.9 + - - +
221C ARG* 3.7 6.4 + - - +
222C GLU* 3.0 27.0 + - - +
223C MET* 3.0 29.6 + - - +
311C ALA* 3.5 8.3 - - - -
314C ARG* 4.1 9.4 - - - +
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Residues in contact with ALA 220 (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 THR* 1.3 71.2 - - - +
221C ARG* 1.3 66.2 + - - +
223C MET* 3.1 10.9 + - - +
224C PHE* 3.0 18.0 + - - +
309C LEU* 3.6 22.5 - - + +
311C ALA* 3.4 18.7 - - + +
314C ARG* 4.8 1.8 - - - +
317C GLU* 3.6 26.8 + - - +
319C PHE* 3.8 17.5 - - + -
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Residues in contact with ARG 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C THR* 3.3 6.3 + - - +
220C ALA* 1.3 80.5 - - - +
222C GLU* 1.3 62.8 + - - +
224C PHE* 3.1 39.4 + - - +
225C GLU* 3.0 48.7 + - - +
317C GLU* 5.5 0.6 + - - +
319C PHE* 3.6 25.9 - - + -
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Residues in contact with GLU 222 (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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216C SER* 4.4 5.5 + - - +
217C CYS* 3.6 19.2 - - - -
218C SER* 2.8 30.3 + - - -
219C THR* 3.0 24.1 + - - +
220C ALA 3.2 0.2 - - - -
221C ARG* 1.3 75.3 - - - +
223C MET* 1.3 64.0 - - - +
225C GLU* 3.2 16.4 + - + +
226C HIS* 3.0 42.5 + - + +
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Residues in contact with MET 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C CYS* 3.5 17.9 - - - -
219C THR 3.0 16.2 + - - +
220C ALA* 3.3 10.5 - - - +
222C GLU* 1.3 76.7 - - - +
224C PHE* 1.3 61.1 + - - +
226C HIS* 3.1 4.7 + - - +
227C ILE* 2.9 26.9 + - + +
247C PHE* 3.8 39.4 - - + -
257C PHE* 4.0 6.7 - - + -
258C ARG 3.8 24.9 - - - +
259C VAL* 4.5 0.9 - - + -
309C LEU* 4.0 22.4 - - + -
310C GLN 3.4 32.5 - - - +
311C ALA* 3.9 13.2 - - - -
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Residues in contact with PHE 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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220C ALA 3.0 12.0 + - - +
221C ARG* 3.1 38.1 + - - +
223C MET* 1.3 77.1 - - - +
225C GLU* 1.3 62.6 + - + +
227C ILE* 3.2 4.1 + - - +
228C CYS* 2.9 49.2 + - - -
307C LEU* 3.9 22.2 - - + -
309C LEU* 3.6 12.1 - - + +
319C PHE* 3.4 37.0 - + + -
320C GLU 3.5 25.8 - - - -
321C ILE* 4.4 3.1 - - + -
322C PRO* 3.9 9.6 - - + -
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Residues in contact with GLU 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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221C ARG* 3.0 56.6 + - - +
222C GLU* 3.2 17.6 + - + +
224C PHE* 1.3 77.9 - - + +
226C HIS* 1.3 64.6 + - + +
228C CYS* 3.3 7.6 + - - +
229C ARG* 3.0 22.2 + - - +
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Residues in contact with HIS 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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212C PHE* 5.9 4.8 - - - +
213C ASP 5.0 2.9 - - - -
214C ALA* 3.8 29.2 - - + +
216C SER* 6.0 0.4 + - - -
217C CYS* 4.0 14.4 - - - +
222C GLU* 3.0 51.5 + - + +
223C MET 3.4 7.0 - - - +
225C GLU* 1.3 75.2 - - + +
227C ILE* 1.3 58.5 + - - +
229C ARG* 3.3 14.4 + - - +
230C HIS* 3.0 27.4 + - - +
245C THR* 4.4 10.7 + - + +
247C PHE* 4.0 12.8 - + + -
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Residues in contact with ILE 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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223C MET 2.9 19.9 + - - +
224C PHE 3.7 4.3 - - - +
226C HIS* 1.3 74.5 - - - +
228C CYS* 1.3 61.6 + - - +
230C HIS* 3.2 7.3 + - - +
231C VAL* 2.8 40.3 + - + +
245C THR* 5.4 1.1 - - + -
247C PHE* 4.1 17.5 - - + -
259C VAL* 4.1 15.9 - - + -
264C LEU* 4.1 24.7 - - + -
307C LEU* 3.8 24.7 - - + -
309C LEU* 3.7 32.8 - - + -
321C ILE* 5.9 1.3 - - + -
368C PRO* 4.8 7.0 - - + -
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Residues in contact with CYS 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C PHE* 2.9 56.9 + - - +
225C GLU* 3.7 7.0 - - - +
227C ILE* 1.3 77.1 - - - +
229C ARG* 1.3 62.8 + - - +
231C VAL* 3.4 4.5 + - - +
232C ARG* 3.0 27.2 + - - +
321C ILE* 5.3 2.9 - - - -
322C PRO* 4.1 6.7 - - - -
325C LEU* 3.8 28.4 - - + +
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Residues in contact with ARG 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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212C PHE* 3.5 42.9 - - - -
225C GLU 3.0 13.0 + - - +
226C HIS* 3.4 16.4 - - - +
228C CYS* 1.3 75.3 - - - +
230C HIS* 1.3 59.8 + - - +
232C ARG* 3.4 8.7 + - - +
233C TYR* 2.9 40.3 + - - +
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Residues in contact with HIS 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C PHE* 4.1 15.7 - + + -
226C HIS 3.0 9.6 + - - +
227C ILE* 3.5 11.4 - - - +
229C ARG* 1.3 76.3 - - - +
231C VAL* 1.3 60.7 + - - +
233C TYR* 3.2 1.9 + - - +
234C SER* 2.8 39.8 + - - -
243C ALA* 3.4 27.2 + - + +
244C ILE* 3.7 1.5 - - - -
245C THR* 2.7 31.0 + - - +
264C LEU* 4.9 14.0 - - + +
349C LEU* 5.6 1.3 - - + -
368C PRO* 3.5 23.6 - - - +
369C PHE* 4.1 4.3 - - - -
370C ASN* 2.7 26.3 + - + +
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Residues in contact with VAL 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C ILE* 2.8 37.3 + - + +
228C CYS* 3.7 7.4 - - - +
230C HIS* 1.3 73.4 - - - +
232C ARG* 1.3 57.8 + - - +
234C SER* 4.1 0.3 - - - -
235C THR* 2.8 41.2 + - - +
264C LEU* 4.3 15.9 - - + -
265C ILE* 5.0 15.5 - - + -
321C ILE* 5.4 7.0 - - + -
325C LEU* 3.5 37.2 - - + +
349C LEU* 4.2 18.8 - - + +
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Residues in contact with ARG 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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228C CYS 3.0 18.5 + - - +
229C ARG* 3.6 7.5 - - - +
231C VAL* 1.3 75.4 - - - +
233C TYR* 1.3 64.5 + - - +
235C THR* 4.1 3.2 - - - -
236C ASN* 3.1 21.0 + - - -
241C ARG* 5.0 0.2 + - - -
325C LEU* 3.7 35.8 - - + +
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Residues in contact with TYR 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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210C GLN* 3.4 43.3 + - + +
212C PHE* 3.7 26.5 - + + -
229C ARG* 2.9 27.5 + - - +
230C HIS 3.6 2.2 - - - +
232C ARG* 1.3 79.8 - - - +
234C SER* 1.3 72.8 + - - +
236C ASN* 3.4 3.3 - - - +
241C ARG* 3.0 83.7 + - + +
242C SER 4.4 0.6 + - - -
243C ALA* 4.1 4.3 - - + -
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Residues in contact with SER 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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230C HIS* 2.8 30.5 + - - -
231C VAL 4.1 0.9 - - - -
233C TYR* 1.3 73.3 - - - +
235C THR* 1.3 67.3 + - - +
236C ASN* 4.0 0.3 - - - +
240C ILE* 3.3 6.4 - - - +
241C ARG 3.0 41.6 + - - +
243C ALA* 3.3 9.9 - - - +
349C LEU* 3.9 8.1 - - - -
370C ASN* 2.6 32.2 + - - -
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Residues in contact with THR 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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231C VAL* 2.8 38.3 + - - +
232C ARG* 4.1 3.1 - - - -
234C SER* 1.3 73.6 - - - +
236C ASN* 1.3 70.7 + - - +
237C ASN* 4.1 6.5 - - - +
238C GLY* 2.9 15.2 + - - -
239C ASN 3.6 4.9 + - - -
240C ILE* 3.6 12.9 - - + +
325C LEU 4.2 7.4 + - - +
327C LEU* 3.7 41.3 + - + +
348C ALA* 5.7 0.7 - - + -
349C LEU* 4.1 14.3 - - + +
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Residues in contact with ASN 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 ARG 3.1 14.6 + - - -
233C TYR 3.4 15.5 - - - +
234C SER 4.0 0.7 - - - +
235C THR* 1.3 77.0 - - - +
237C ASN* 1.3 73.4 - - - +
239C ASN* 3.0 49.2 + - - +
241C ARG* 3.5 33.9 + - - +
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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
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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