Contacts of the helix formed by residues 222 - 233 (chain A) in PDB entry 2J0U
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 PRO 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A ASP* 5.2 0.4 - - + -
194A ASN* 4.5 16.2 - - - +
220A THR* 3.6 19.7 - - - +
221A LEU* 1.3 91.5 - - - +
223A HIS* 1.3 66.2 + - - +
224A GLU* 4.3 9.6 - - + +
225A ILE* 2.9 30.6 + - + +
226A LEU* 2.9 10.8 + - - +
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Residues in contact with HIS 223 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A LEU 3.9 0.8 + - - -
222A PRO* 1.3 70.6 - - - +
224A GLU* 1.3 64.7 + - - +
226A LEU* 2.9 27.6 + - + +
227A GLU* 3.3 15.1 + - + +
367A ARG* 6.1 1.4 + - - -
370A ARG* 5.6 9.2 - - + +
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Residues in contact with GLU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ASN* 3.7 19.7 - - - +
222A PRO* 3.1 6.1 + - + +
223A HIS* 1.3 80.2 + - - +
225A ILE* 1.3 63.1 + - - +
227A GLU* 3.9 4.3 + - - +
228A MET* 3.7 22.5 + - + +
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Residues in contact with ILE 225 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A ALA* 3.5 13.0 - - + +
190A ASP* 3.4 35.2 - - + +
193A LEU* 3.8 26.9 - - + -
194A ASN* 3.3 23.1 - - + +
216A LEU* 4.9 5.4 - - + -
218A SER* 5.0 0.2 - - - +
220A THR 4.8 1.3 - - - +
221A LEU* 4.7 12.3 - - + -
222A PRO* 2.9 22.4 + - + +
224A GLU* 1.3 77.1 - - - +
226A LEU* 1.3 70.5 + - + +
228A MET* 2.7 30.2 - - + +
229A THR* 3.3 13.0 + - + +
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Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ILE* 5.1 9.9 - - + -
221A LEU* 3.6 51.6 - - + +
222A PRO 2.9 7.9 + - - +
223A HIS* 2.9 24.2 + - + +
225A ILE* 1.3 80.7 - - + +
227A GLU* 1.3 55.2 + - - +
229A THR* 2.4 31.5 + - + +
230A ASN* 3.4 9.4 - - - +
238A ARG* 5.8 1.1 + - + -
240A LEU* 6.2 1.1 - - + -
370A ARG* 3.9 13.2 - - + +
371A TYR* 3.8 41.1 - - - +
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Residues in contact with GLU 227 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A HIS* 3.3 11.9 + - + +
224A GLU 4.4 6.1 - - - +
225A ILE 3.3 0.8 - - - -
226A LEU* 1.3 69.9 - - - +
228A MET* 1.3 60.6 + - - +
229A THR 3.0 1.6 - - - -
230A ASN* 2.5 48.1 + - + +
231A LYS* 3.2 4.6 + - - +
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Residues in contact with MET 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A LEU* 3.3 65.3 - - + +
194A ASN* 4.9 2.2 - - - +
198A LYS* 4.3 13.7 - - + -
224A GLU* 3.7 20.4 + - + +
225A ILE* 2.7 25.3 + - + +
227A GLU* 1.3 73.7 - - - +
229A THR* 1.3 51.8 + - - +
231A LYS* 2.9 20.8 + - - +
232A PHE* 2.7 32.9 - - + -
218T TRP* 4.9 6.7 - - - -
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Residues in contact with THR 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ILE* 4.2 22.1 - - + +
216A LEU* 4.4 17.3 - - + -
225A ILE* 3.3 17.2 + - + +
226A LEU* 2.4 34.3 + - + +
227A GLU 2.8 2.8 + - - -
228A MET* 1.3 69.8 - - + +
230A ASN* 1.3 68.8 + - - -
231A LYS 2.9 2.5 + - - -
232A PHE* 3.1 8.7 + - + -
233A MET* 2.8 57.4 + - - +
236A PRO* 5.6 1.2 - - - +
238A ARG* 5.2 2.3 + - - -
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Residues in contact with ASN 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LEU 3.4 10.5 + - - +
227A GLU* 2.5 32.0 + - + +
229A THR* 1.3 81.5 + - - +
231A LYS* 1.3 57.5 + - - +
233A MET* 3.9 10.1 - - - +
238A ARG* 4.1 16.6 + - - -
345A GLN* 5.6 0.3 + - - -
371A TYR 5.2 2.1 + - - +
372A GLY 6.4 0.2 - - - -
373A ARG* 5.5 9.5 - - - +
217T ARG* 5.3 4.0 - - - +
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Residues in contact with LYS 231 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A GLU 3.2 4.0 + - - +
228A MET* 2.9 17.4 + - - +
230A ASN* 1.3 78.3 - - - +
232A PHE* 1.3 56.8 + - - +
233A MET 4.8 0.4 - - - -
217T ARG* 3.7 14.0 - - - +
218T TRP* 2.9 60.0 + - + +
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Residues in contact with PHE 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASP* 4.3 1.4 - - - +
184A LEU* 5.9 0.4 - - + -
186A LEU* 3.6 24.7 - - + -
193A LEU* 4.1 9.4 - - + -
205A TYR* 3.1 42.3 + + + -
212A THR 5.1 0.7 - - - +
214A VAL* 3.5 31.3 - - + +
216A LEU* 4.5 7.4 - - + -
228A MET* 2.7 42.6 - - + -
229A THR* 3.1 7.5 + - + -
231A LYS* 1.3 76.0 - - - +
233A MET* 1.3 71.5 + - + +
218T TRP* 3.1 48.2 - + + -
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Residues in contact with MET 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASP* 3.5 8.5 - - + +
78A VAL 3.4 23.8 - - - +
79A ILE* 3.4 26.7 - - - -
214A VAL* 3.4 31.2 - - + +
216A LEU* 3.4 24.9 - - + +
229A THR* 2.8 36.0 + - + +
230A ASN* 3.9 13.3 - - - +
231A LYS 4.8 0.3 - - - -
232A PHE* 1.3 85.3 - - + +
234A THR* 1.3 71.7 + - - +
236A PRO* 4.1 18.8 - - + -
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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