Contacts of the helix formed by residues 224 - 236 (chain A) in PDB entry 1RY2
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 SER 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A GLY 3.6 1.7 + - - -
223A PHE* 1.3 78.8 - - - +
225A SER* 1.3 59.9 + - - +
226A ASN* 3.6 18.3 + - - +
227A SER* 3.0 27.3 + - - -
228A LEU* 3.0 24.3 + - - +
258A ILE* 4.9 5.2 - - - -
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Residues in contact with SER 225 (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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224A SER* 1.3 71.7 - - - +
226A ASN* 1.3 67.0 + - - +
228A LEU* 4.1 2.9 - - - -
229A ARG* 3.0 26.5 + - - +
258A ILE* 3.1 42.9 - - - +
261A ASP* 3.6 16.7 + - - +
262A ALA* 3.2 20.8 - - - +
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Residues in contact with ASN 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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224A SER* 3.7 17.3 - - - +
225A SER* 1.3 89.4 + - - +
227A SER* 1.3 59.3 + - - +
229A ARG* 3.6 25.9 + - - +
230A ASP* 3.3 32.1 + - - +
265A GLU* 5.7 0.6 + - - -
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Residues in contact with SER 227 (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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219A VAL* 5.2 0.4 - - - -
223A PHE* 3.8 21.6 - - - +
224A SER* 3.0 23.2 + - - -
226A ASN* 1.3 77.5 - - - +
228A LEU* 1.3 64.5 + - - +
230A ASP* 3.7 3.4 + - - +
231A ARG* 3.1 52.7 + - - +
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Residues in contact with LEU 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 ALA* 5.6 2.7 - - + -
194A VAL 6.0 0.2 - - - -
195A TYR* 3.8 47.6 - - + -
219A VAL* 4.1 24.4 - - + +
224A SER 3.0 12.3 + - - +
225A SER* 3.5 9.4 - - - +
226A ASN 3.3 0.2 - - - -
227A SER* 1.3 78.5 - - - +
229A ARG* 1.3 62.7 + - - +
231A ARG* 3.4 1.4 + - - +
232A ILE* 3.0 47.4 + - + +
240A VAL* 5.6 2.9 - - + -
258A ILE* 4.2 4.9 - - + +
259A VAL* 4.0 33.4 - - + -
262A ALA* 4.0 7.4 - - + -
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Residues in contact with ARG 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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225A SER 3.0 15.5 + - - +
226A ASN* 3.6 28.1 + - - +
228A LEU* 1.3 74.7 - - - +
230A ASP* 1.3 90.7 + - - +
232A ILE* 3.1 4.6 + - - +
233A ASN* 2.8 44.5 + - - +
262A ALA* 3.9 14.1 - - + +
265A GLU* 2.5 56.0 + - + -
266A THR* 4.0 17.3 - - - +
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Residues in contact with ASP 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 ASN* 3.3 11.2 + - - +
227A SER* 4.2 4.3 - - - +
229A ARG* 1.3 117.7 + - - +
231A ARG* 1.3 60.5 + - + +
233A ASN* 3.7 7.7 - - - +
234A ASP* 2.8 33.3 + - - +
327A PRO* 6.0 7.2 - - + -
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Residues in contact with ARG 231 (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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217A SER* 5.9 1.4 - - - -
218A VAL 5.5 0.4 - - - -
219A VAL* 3.7 37.6 - - + +
223A PHE* 3.3 18.6 - - - -
227A SER* 3.1 43.0 + - - +
228A LEU 3.7 3.4 - - - +
230A ASP* 1.3 78.6 - - + +
232A ILE* 1.3 58.7 + - - +
235A GLY* 2.9 24.6 + - - -
237A SER* 5.2 0.5 + - - -
319A TYR* 3.7 50.0 + - + +
321A SER* 2.4 36.6 + - - -
327A PRO* 4.1 25.0 - - + +
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Residues in contact with ILE 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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193A ALA* 4.1 13.2 - - + -
219A VAL* 5.8 0.9 - - + -
228A LEU* 3.0 42.4 + - + +
229A ARG* 3.6 5.2 - - - +
231A ARG* 1.3 74.8 - - + +
233A ASN* 1.3 60.9 + - - +
235A GLY 3.2 0.2 + - - -
236A ASP* 2.9 26.5 + - - -
237A SER* 3.2 41.6 + - - +
240A VAL* 4.0 22.4 - - + -
259A VAL* 6.2 0.7 - - + -
262A ALA* 5.4 0.9 - - + -
263A LEU* 4.3 14.6 - - + -
266A THR* 3.6 20.0 - - + +
269A VAL* 4.0 2.7 - - + -
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Residues in contact with ASN 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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229A ARG* 2.8 35.3 + - - +
230A ASP* 3.7 7.8 - - - +
232A ILE* 1.3 74.7 - - - +
234A ASP* 1.3 62.1 + - - +
236A ASP* 3.4 9.6 + - - +
265A GLU 3.5 14.3 - - - +
266A THR* 3.2 34.7 - - - +
267A PRO* 3.9 9.0 - - - +
268A GLY 5.4 0.4 - - - +
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Residues in contact with ASP 234 (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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230A ASP 2.8 20.3 + - - +
233A ASN* 1.3 74.6 - - - +
235A GLY* 1.3 58.1 + - - +
236A ASP* 3.5 2.8 + - - +
319A TYR* 2.3 41.7 + - + +
327A PRO 4.8 3.4 - - - +
329A GLY 4.8 1.0 + - - -
537A TRP* 2.9 40.9 + - - +
538A LYS* 4.7 7.8 - - - +
539A ASN* 5.1 4.6 + - - -
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Residues in contact with GLY 235 (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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191A THR* 2.8 33.6 + - - -
217A SER* 5.9 0.4 - - - -
231A ARG 2.9 19.5 + - - -
232A ILE 3.2 1.5 + - - -
234A ASP* 1.3 77.3 - - - +
236A ASP* 1.3 66.9 + - - +
237A SER* 3.2 3.6 - - - -
317A LEU* 4.7 2.0 - - - -
319A TYR* 3.2 12.0 + - - -
537A TRP* 3.6 11.2 + - - -
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Residues in contact with ASP 236 (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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191A THR* 4.2 9.6 + - - +
232A ILE 2.9 6.3 + - - -
233A ASN 3.4 6.7 + - - +
234A ASP 3.4 5.3 - - - +
235A GLY* 1.3 80.2 - - - +
237A SER* 1.3 59.3 + - - +
238A LYS* 3.1 30.6 + - - +
537A TRP* 4.6 9.6 + - + +
538A LYS* 4.1 20.6 + - - +
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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