Contacts of the helix formed by residues 225 - 235 (chain C) in PDB entry 2JC6
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 ASN 225 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223C ASP* 3.2 13.8 + - - +
224C GLU* 1.3 77.8 - - + +
226C ASP* 1.3 58.1 + - - +
227C SER* 3.2 11.9 - - - +
228C LYS* 3.1 25.4 + - + +
229C LEU 3.5 5.9 + - - -
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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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223C ASP 4.4 2.6 - - - +
224C GLU 3.8 8.9 + - - +
225C ASN* 1.3 70.1 - - - +
227C SER* 1.3 60.1 + - - +
228C LYS 3.2 0.2 - - - -
229C LEU* 3.7 25.4 - - + -
230C PHE* 3.1 27.9 + - - +
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Residues in contact with SER 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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225C ASN* 3.2 7.6 + - - +
226C ASP* 1.3 78.1 + - - +
228C LYS* 1.3 58.1 + - - +
230C PHE* 3.7 5.4 - - - +
231C GLU* 3.0 29.0 + - - +
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Residues in contact with LYS 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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223C ASP* 3.6 26.6 + - - +
225C ASN* 3.1 14.8 + - + +
227C SER* 1.3 78.2 - - - +
229C LEU* 1.3 58.2 + - - +
231C GLU* 3.3 9.2 + - + +
232C GLN* 3.0 55.6 + - + +
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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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185C PRO* 5.4 3.8 - - + +
186C GLY* 4.8 11.9 - - - +
221C PHE* 3.4 20.2 - - + +
222C TYR* 3.3 39.7 - - + +
223C ASP* 3.5 18.5 - - + +
225C ASN 3.5 2.4 + - - -
226C ASP* 3.8 26.5 - - + +
227C SER 3.4 0.2 - - - -
228C LYS* 1.3 76.0 - - - +
230C PHE* 1.3 55.0 + - - +
232C GLN* 3.1 12.7 + - - +
233C ILE* 2.8 52.6 + - + +
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Residues in contact with PHE 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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193C LEU* 3.8 53.5 - - + +
226C ASP 3.1 17.5 + - - +
227C SER* 3.7 7.0 - - - +
229C LEU* 1.3 78.5 - - - +
231C GLU* 1.3 58.7 + - + +
233C ILE* 3.5 3.9 + - - +
234C LEU* 2.8 65.0 + - + +
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Residues in contact with GLU 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 SER 3.0 18.6 + - - +
228C LYS* 3.3 10.9 + - + +
229C LEU 3.2 0.2 - - - -
230C PHE* 1.3 79.2 - - + +
232C GLN* 1.3 62.2 + - + +
234C LEU* 4.0 6.3 - - + +
235C LYS* 3.1 30.7 + - - +
237C GLU* 4.9 1.8 - - - +
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Residues in contact with GLN 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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221C PHE* 3.7 10.5 - - + +
222C TYR 4.4 6.4 + - - +
223C ASP* 4.2 10.9 + - - +
228C LYS* 3.0 45.8 + - + +
229C LEU* 3.1 29.7 + - - +
231C GLU* 1.3 74.2 - - + +
233C ILE* 1.3 59.7 + - - +
235C LYS 3.4 0.3 + - - -
236C ALA* 2.8 23.0 + - - -
237C GLU* 2.9 43.1 + - + +
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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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185C PRO 3.7 22.0 - - - +
186C GLY* 3.9 16.8 - - - +
188C VAL 3.4 23.6 - - - +
190C PRO* 3.4 24.6 - - + +
193C LEU* 3.4 24.7 - - + -
205C TRP* 4.6 6.2 - - + -
221C PHE* 3.8 28.9 - - + -
229C LEU* 2.8 38.0 + - + +
230C PHE* 4.7 1.3 - - - +
232C GLN* 1.3 70.2 - - - +
234C LEU* 1.3 63.5 + - - +
236C ALA* 3.0 12.0 + - - -
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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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190C PRO* 3.2 31.2 - - + +
193C LEU* 3.7 6.5 - - + -
194C ALA* 3.5 24.9 - - + +
230C PHE* 2.8 48.4 + - + +
231C GLU* 4.0 6.3 - - - +
233C ILE* 1.3 75.0 - - - +
235C LYS* 1.3 55.0 + - + +
262C LYS* 2.7 37.5 + - - +
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Residues in contact with LYS 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 GLU 3.1 20.0 + - - +
234C LEU* 1.3 75.5 - - + +
236C ALA* 1.3 70.0 + - - +
237C GLU* 3.1 28.1 + - + +
262C LYS* 4.2 13.5 - - - +
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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