Contacts of the helix formed by residues 225 - 234 (chain C) in PDB entry 6ACQ
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 GLY 225 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213C ASP* 3.0 32.3 - - - -
216C MET* 4.5 1.6 - - - -
217C LYS* 3.7 4.6 - - - +
224C MET* 1.3 73.0 - - - +
226C PRO* 1.3 73.8 - - - +
227C LEU 3.2 0.5 + - - -
228C GLU* 2.9 16.1 + - - +
229C LEU* 2.9 22.8 + - - +
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Residues in contact with PRO 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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190B ILE* 4.2 3.8 - - + -
194C MET* 4.2 19.9 - - + +
195C ILE* 3.6 29.2 - - + +
198C ALA* 3.7 28.3 - - + -
212C ILE* 4.2 4.7 - - + -
213C ASP* 3.3 6.7 - - - +
216C MET* 3.5 33.4 - - + -
222C HIS* 5.8 0.9 - - - +
224C MET 3.9 1.5 - - - +
225C GLY* 1.3 83.5 - - - +
227C LEU* 1.3 59.8 + - - +
229C LEU* 3.5 7.2 - - + +
230C GLY 2.8 23.0 + - - -
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Residues in contact with LEU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C ILE* 4.3 5.8 - - + +
198C ALA* 3.7 31.4 - - + +
199C VAL* 4.2 3.4 - - - +
202C LEU* 4.6 9.4 - - + -
209C VAL* 3.6 36.1 - - + +
212C ILE* 4.1 18.2 - - + -
213C ASP* 2.8 22.6 + - - +
226C PRO* 1.3 71.3 - - - +
228C GLU* 1.3 64.4 + - - +
230C GLY* 3.1 2.8 + - - +
231C ASP* 3.1 24.6 + - - -
277C PHE* 3.8 42.4 - - + -
278C TYR* 4.3 4.5 - - + -
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Residues in contact with GLU 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C ASP* 2.9 14.3 + - - +
217C LYS* 3.2 26.7 + - - -
223C PRO 5.5 0.2 - - - -
224C MET* 3.7 23.2 - - + +
225C GLY* 2.9 34.0 + - - +
227C LEU* 1.3 76.6 - - - +
229C LEU* 1.3 56.8 + - - +
231C ASP* 3.4 6.2 + - - +
232C PHE* 3.1 25.8 + - - +
271C ARG* 5.7 1.6 + - - -
278C TYR* 3.4 28.8 + - + -
280C TYR* 4.4 4.3 + - - +
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Residues in contact with LEU 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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220B ALA* 6.3 0.2 - - + -
222B HIS* 6.1 1.1 - - - +
191C LEU* 4.1 28.5 - - + -
194C MET* 4.8 7.2 - - + -
195C ILE* 4.0 19.3 - - + -
224C MET* 3.5 37.5 - - + +
225C GLY 2.9 18.7 + - - +
226C PRO* 3.5 4.9 - - + +
228C GLU* 1.3 77.0 - - - +
230C GLY* 1.3 60.9 + - - +
232C PHE* 3.1 5.1 + - + +
233C ILE* 2.9 44.9 + - + +
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Residues in contact with GLY 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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195C ILE* 4.0 8.5 - - - -
226C PRO 2.8 15.3 + - - -
227C LEU 3.1 4.0 + - - -
229C LEU* 1.3 75.4 - - - +
231C ASP* 1.3 57.3 - - - +
233C ILE* 4.0 0.2 - - - -
234C GLY 2.8 35.9 + - - +
235C LEU* 3.4 17.5 + - - +
238C CYS* 3.9 16.2 - - - -
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Residues in contact with ASP 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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227C LEU 3.1 12.2 + - - +
228C GLU 3.5 6.1 - - - +
230C GLY* 1.3 76.9 - - - +
232C PHE* 1.3 60.7 + - - +
234C GLY* 3.7 5.2 + - - -
235C LEU* 3.7 6.2 - - - +
269C LEU 4.0 0.8 - - - +
270C GLY* 3.4 18.8 - - - -
271C ARG* 2.9 24.8 + - - +
272C LYS* 4.7 1.6 + - - +
276C GLY* 3.4 5.5 - - - -
277C PHE* 2.9 26.8 + - - -
278C TYR* 2.9 33.3 + - - -
280C TYR* 3.0 27.6 + - + +
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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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141C ASN 6.0 2.0 - - - -
224C MET* 3.8 23.8 - - + -
228C GLU 3.1 15.6 + - - +
229C LEU* 3.1 13.2 + - + +
231C ASP* 1.3 77.4 - - - +
233C ILE* 1.3 67.8 + - + +
234C GLY 3.2 1.1 - - - -
271C ARG* 3.2 45.4 - - + +
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Residues in contact with ILE 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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191C LEU* 4.2 11.0 - - + -
192C ILE* 4.1 23.8 - - + -
195C ILE* 4.1 6.7 - - + -
229C LEU* 2.9 41.7 + - + +
230C GLY 4.0 2.9 - - - +
232C PHE* 1.3 82.0 - - + +
234C GLY* 1.3 61.0 + - - +
237C ILE* 3.5 39.6 - - + +
238C CYS* 4.2 6.5 - - - -
241C ILE* 5.9 0.4 - - + -
272C LYS* 4.9 1.7 - - - -
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Residues in contact with GLY 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 GLY 2.8 9.6 + - - -
231C ASP 3.7 3.8 + - - -
232C PHE 3.2 3.4 - - - -
233C ILE* 1.3 80.8 - - - +
235C LEU* 1.3 61.2 + - - -
236C ASP* 3.3 13.9 - - - -
237C ILE* 3.1 3.8 + - - +
238C CYS* 3.0 26.3 + - - -
269C LEU 3.4 10.3 - - - -
272C LYS* 4.0 11.0 - - - -
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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