Contacts of the helix formed by residues 223 - 235 (chain A) in PDB entry 3I5Y
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 ASP 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A THR* 1.3 71.9 + - - +
224A PHE* 1.3 67.5 + - - +
225A ARG* 3.0 37.2 + - - +
226A ALA* 3.8 23.3 - - + +
227A ALA* 3.2 22.3 + - - +
245A ARG* 4.2 0.4 - - - -
9B U 3.2 39.5 + - + +
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Residues in contact with PHE 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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222A THR 3.2 2.4 + - - -
223A ASP* 1.3 70.6 + - - +
225A ARG* 1.3 65.7 + - - +
227A ALA* 3.3 5.3 + - + +
228A MET* 3.0 45.7 + - + +
245A ARG* 3.6 26.9 - - - +
248A ASP* 3.2 31.2 - - - -
249A VAL* 3.6 28.7 - - + -
252A LYS* 4.6 2.0 - - + -
253A TYR* 4.1 8.5 - + - -
8B U 6.2 0.2 - - - -
9B U 3.0 17.7 + - - +
10B U 3.4 64.4 - + + -
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Residues in contact with ARG 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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223A ASP* 3.0 26.6 + - - +
224A PHE* 1.3 78.7 - - - +
226A ALA* 1.3 60.6 + - - +
228A MET* 3.1 4.6 + - - +
229A ASN* 2.8 54.0 + - - +
10B U 4.0 28.8 - - + +
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Residues in contact with ALA 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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223A ASP* 3.4 27.6 + - + +
224A PHE 3.2 0.6 - - - -
225A ARG* 1.3 80.0 - - - +
227A ALA* 1.3 59.3 + - - +
229A ASN* 3.4 14.0 + - - +
230A LYS* 3.1 26.2 + - - +
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Residues in contact with ALA 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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216A VAL* 4.2 3.7 - - + +
217A SER 4.5 8.5 - - - +
218A LEU* 4.0 22.7 - - + -
222A THR* 5.1 7.2 - - - +
223A ASP 3.2 13.2 + - - +
224A PHE* 3.6 9.6 - - + +
226A ALA* 1.3 76.5 - - - +
228A MET* 1.3 59.2 + - + +
230A LYS* 3.2 11.3 + - - +
231A MET* 2.9 30.6 + - - +
245A ARG* 5.1 3.6 - - - +
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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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218A LEU* 4.9 4.5 - - + -
224A PHE* 3.0 54.5 + - + +
225A ARG* 3.5 11.2 - - - +
227A ALA* 1.3 78.0 - - + +
229A ASN* 1.3 61.4 + - - +
231A MET* 3.2 18.6 + - + +
232A ASN* 2.7 43.4 + - - +
249A VAL* 3.6 24.2 - - + -
253A TYR* 4.0 37.7 - - + +
257A PHE* 4.8 6.1 - - + -
10B U 4.9 4.3 - - - +
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Residues in contact with ASN 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 ARG* 2.8 43.0 + - - +
226A ALA* 3.5 13.4 - - - +
227A ALA 3.3 0.2 - - - -
228A MET* 1.3 75.3 - - - +
230A LYS* 1.3 57.2 + - - +
232A ASN* 3.3 10.6 + - - +
233A LYS* 2.8 33.9 + - - +
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Residues in contact with LYS 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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197A GLU* 4.0 14.3 + - - -
201A LYS* 4.8 13.7 - - - +
215A CYS 3.2 25.7 + - - -
216A VAL* 3.7 16.7 - - + +
226A ALA 3.1 14.3 + - - +
227A ALA* 3.3 13.5 - - - +
228A MET 3.2 0.2 - - - -
229A ASN* 1.3 75.2 - - - +
231A MET* 1.3 58.1 + - - +
233A LYS* 4.5 6.5 - - + +
234A LEU* 3.0 58.9 + - + +
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Residues in contact with MET 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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181A VAL* 4.1 5.2 - - + -
216A VAL* 3.8 18.2 - - + -
218A LEU* 4.1 16.6 - - + -
227A ALA 2.9 18.6 + - - +
228A MET* 3.2 17.5 + - - +
230A LYS* 1.3 74.4 - - - +
232A ASN* 1.3 58.0 + - - +
235A ARG* 2.9 28.9 + - - -
236A PRO* 3.4 22.3 - - + +
239A VAL* 3.9 22.9 - - + -
249A VAL* 5.6 1.6 - - + -
257A PHE* 3.5 53.8 - - + -
258A PHE* 4.0 11.7 - - + -
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Residues in contact with ASN 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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228A MET* 2.7 37.6 + - - +
229A ASN* 3.6 9.9 + - - +
230A LYS 3.3 0.2 - - - -
231A MET* 1.3 76.1 - - - +
233A LYS* 1.3 63.1 + - - +
235A ARG* 3.4 23.5 + - - +
256A LYS* 3.1 36.8 + - - +
257A PHE* 3.4 7.8 - - - -
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Residues in contact with LYS 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 ASN 2.8 21.6 + - - +
230A LYS* 4.3 5.6 - - + +
232A ASN* 1.3 75.4 - - - +
234A LEU* 1.3 76.3 + - + +
235A ARG* 4.8 1.7 - - - +
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Residues in contact with LEU 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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212A LYS 5.7 0.3 - - - +
214A ALA* 4.0 24.9 - - + +
215A CYS 4.3 4.3 - - - +
216A VAL* 4.1 4.9 - - + -
230A LYS* 3.0 59.3 + - + +
233A LYS* 1.3 99.1 - - + +
235A ARG* 1.3 69.8 + - - +
236A PRO* 4.4 4.7 - - + -
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Residues in contact with ARG 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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178A GLN 4.2 4.7 - - - +
179A TYR* 2.9 63.9 + - + +
180A MET* 3.4 16.2 - - - +
212A LYS 5.7 0.3 - - - +
214A ALA* 4.8 0.7 - - - +
231A MET 2.9 15.6 + - - -
232A ASN* 3.4 24.1 + - - +
233A LYS 4.8 1.8 - - - +
234A LEU* 1.3 78.5 - - - +
236A PRO* 1.3 70.8 - - - +
237A ASN* 3.7 2.6 + - - +
256A LYS* 3.3 40.0 + - - +
257A PHE* 3.8 22.6 - - - -
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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