Contacts of the helix formed by residues 224 - 229 (chain C) in PDB entry 4J1R
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 ALA 224 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218C CYS* 5.3 0.2 - - - -
222C TYR 3.6 1.4 + - - -
223C ARG* 1.3 76.4 - - - +
225C PRO* 1.3 75.3 - - + +
226C GLU* 3.4 24.7 - - - +
227C LEU* 3.2 24.6 + - + +
228C ILE* 3.5 6.9 + - - +
238C ILE* 3.8 22.9 + - + +
241C TRP* 3.5 20.5 - - + -
242C SER* 5.0 0.8 + - - -
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Residues in contact with PRO 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 ARG 3.7 0.2 - - - -
224C ALA* 1.3 83.1 - - + +
226C GLU* 1.3 73.8 + - - +
228C ILE* 3.0 25.0 + - + +
229C PHE* 3.0 19.3 + - - -
241C TRP* 3.4 46.7 - - + -
266C LEU* 4.8 6.3 - - + -
269C ILE* 4.3 5.4 - - + -
284C MET* 3.8 19.1 - - + -
323C TYR* 4.2 17.9 - - + -
328C ARG* 3.6 5.6 - - - +
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Residues in contact with GLU 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ALA* 3.5 11.7 - - + -
225C PRO* 1.3 77.3 - - - +
227C LEU* 1.3 61.4 + - - +
229C PHE* 3.2 10.5 + - - +
231C ALA* 2.9 30.1 + - + +
234C TYR* 4.4 14.9 - - + +
235C THR 5.7 0.3 + - - -
237C SER* 4.4 0.5 + - - -
238C ILE* 3.3 22.9 - - + +
284C MET* 3.7 40.5 - - + +
325C PRO* 3.8 16.5 - - + +
328C ARG* 2.9 41.8 + - - -
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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
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215C SER* 3.3 29.0 - - - +
216C PTR 5.3 0.2 - - - -
217C ILE* 3.8 21.8 - - + +
218C CYS* 4.3 5.8 - - + -
223C ARG* 3.7 23.2 - - + -
224C ALA* 3.2 26.4 + - + +
225C PRO 3.2 0.6 - - - -
226C GLU* 1.3 78.8 - - + +
228C ILE* 1.3 58.5 + - - +
230C GLY* 2.9 19.2 + - - -
231C ALA 4.5 2.5 - - - +
234C TYR* 3.5 50.0 - - + -
238C ILE* 4.1 15.5 - - + -
288C TYR* 4.8 0.3 + - - -
64D ASN* 4.6 3.6 + - - -
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Residues in contact with ILE 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 ARG* 4.1 17.3 - - - +
224C ALA 3.5 14.4 - - - +
225C PRO* 3.0 10.4 + - + +
227C LEU* 1.3 75.0 - - - +
229C PHE* 1.3 58.4 + - - +
230C GLY 3.1 0.7 - - - -
262C GLY 3.2 22.2 - - - +
263C VAL* 4.4 3.6 - - - -
265C GLN* 3.6 31.0 - - + -
266C LEU* 3.9 35.2 - - + +
269C ILE* 4.0 17.0 - - + -
288C TYR* 3.3 9.4 - - - -
291C PHE* 3.9 7.3 - - + -
64D ASN* 3.1 24.4 + - - +
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Residues in contact with PHE 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 PRO 3.0 23.7 + - - +
226C GLU* 3.5 11.0 - - - +
227C LEU 3.1 0.8 - - - -
228C ILE* 1.3 77.3 - - - +
230C GLY* 1.3 57.7 + - - +
231C ALA 3.2 0.7 - - - -
266C LEU* 3.7 29.6 - - + -
276C PRO* 4.9 6.3 - - + -
281C ILE* 4.2 22.4 - - + -
284C MET* 3.5 32.1 - - + -
286C PRO* 3.2 30.1 - - + +
287C ASN 2.8 24.3 + - - -
288C TYR* 3.3 16.0 + - - -
289C THR 4.0 11.9 - - - -
291C PHE* 3.4 30.5 - + - -
323C TYR* 6.3 0.2 - + - -
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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