Contacts of the helix formed by residues 221 - 233 (chain A) in PDB entry 2J6U
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 GLY 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A LYS 2.7 18.3 + - - -
218A GLY 4.6 0.4 - - - -
219A MET 3.7 0.8 - - - -
220A ILE* 1.3 82.0 - - - +
222A GLU* 1.3 66.4 + - - -
223A ALA 3.4 2.4 + - - -
224A LYS 3.5 0.6 + - - -
225A ALA* 3.0 22.3 + - - +
11T C 3.5 21.8 - - - -
12T T 5.9 1.6 - - - -
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Residues in contact with GLU 222 (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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213A PHE* 4.4 6.2 - - + -
217A LYS* 3.6 41.9 - - - +
221A GLY* 1.3 70.7 - - - -
223A ALA* 1.3 64.4 + - - +
225A ALA* 3.0 5.7 + - - +
226A LYS* 3.0 52.8 + - + +
11T C 3.1 10.9 + - - +
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Residues in contact with ALA 223 (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 GLU* 1.3 74.7 - - - +
224A LYS* 1.3 57.9 + - - +
226A LYS* 3.5 5.7 + - - +
227A TYR* 3.1 27.5 + - - +
10T C 3.5 39.9 - - - +
11T C 2.5 24.1 + - - +
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Residues in contact with LYS 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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188A GLY* 3.0 31.3 + - - +
189A ILE* 4.2 13.2 - - + -
193A THR* 4.1 19.7 + - + -
220A ILE* 3.5 38.4 - - + +
221A GLY 3.5 1.0 + - - +
222A GLU 3.4 0.2 - - - -
223A ALA* 1.3 76.0 - - - +
225A ALA* 1.3 63.9 + - - +
227A TYR* 3.8 14.7 - - + +
228A LEU* 3.3 23.8 + - + +
11P T 5.0 2.6 + - - -
12P T 3.8 17.4 - - - -
10T C 5.6 4.8 - - - -
11T C 4.2 1.0 + - - +
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Residues in contact with ALA 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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213A PHE* 3.7 18.6 - - + -
216A LEU* 3.2 30.9 - - + +
217A LYS* 4.3 5.8 - - - -
220A ILE* 4.3 0.9 - - - +
221A GLY 3.0 15.0 + - - +
222A GLU* 3.0 13.2 + - - +
224A LYS* 1.3 75.0 - - - +
226A LYS* 1.3 65.8 + - - +
227A TYR 3.3 0.2 + - - -
228A LEU* 3.3 3.5 + - - +
229A ILE* 3.0 29.7 + - - +
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Residues in contact with LYS 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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213A PHE* 4.2 21.2 - - + -
222A GLU* 3.0 49.1 + - + +
223A ALA* 4.1 5.2 - - - +
225A ALA* 1.3 76.4 - - - +
227A TYR* 1.3 56.6 + - - +
229A ILE* 3.8 7.6 - - - +
230A SER* 2.8 37.3 + - - +
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Residues in contact with TYR 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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152A VAL* 3.6 21.3 - - + +
186A VAL* 3.9 7.6 - - + +
187A PRO* 2.7 32.7 + - - +
188A GLY* 5.2 2.7 - - - -
189A ILE* 5.0 3.6 - - + -
223A ALA 3.1 19.3 + - - +
224A LYS* 3.8 17.0 - - + +
226A LYS* 1.3 76.0 - - - +
228A LEU* 1.3 82.6 + - + +
230A SER* 3.2 9.3 + - - -
231A LEU* 3.2 41.2 + - + +
236A TYR* 3.8 31.0 - + - -
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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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183A ILE* 4.2 10.3 - - + -
186A VAL* 4.0 12.3 - - + -
189A ILE* 3.9 14.8 - - + -
197A LEU* 3.8 28.9 - - + -
205A LEU* 3.7 24.8 - - + +
208A THR* 3.8 21.3 + - + -
216A LEU* 5.7 0.9 - - + -
220A ILE* 4.3 10.5 - - + -
224A LYS 3.3 17.7 + - - +
225A ALA* 4.0 2.7 - - - +
227A TYR* 1.3 99.2 - - + +
229A ILE* 1.3 61.0 + - - +
231A LEU* 3.2 5.1 + - + +
232A ALA* 2.8 28.9 + - - +
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Residues in contact with ILE 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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208A THR* 4.1 23.8 - - - +
209A LEU* 4.8 5.4 - - + -
213A PHE* 3.7 35.9 - - + -
216A LEU* 4.5 8.5 - - + -
225A ALA 3.0 24.3 + - - +
226A LYS* 3.9 5.8 - - + +
228A LEU* 1.3 75.3 - - - +
230A SER* 1.3 58.1 + - - +
232A ALA* 3.5 6.9 - - - +
233A ARG* 2.8 71.6 + - + +
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Residues in contact with SER 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 LYS* 2.8 20.8 + - - +
227A TYR* 3.2 11.6 - - - -
228A LEU 3.1 0.2 - - - -
229A ILE* 1.3 78.1 - - - +
231A LEU* 1.3 60.5 + - - +
233A ARG* 3.4 2.9 + - - +
234A ASP 3.0 3.8 + - - -
235A GLU* 2.7 39.0 + - - +
236A TYR* 3.9 26.2 - - - +
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Residues in contact with LEU 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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152A VAL* 3.9 18.4 - - + -
153A PHE* 3.6 29.9 - - + -
178A ILE* 3.4 16.8 - - - +
186A VAL* 4.0 14.8 - - + -
205A LEU* 3.9 17.7 - - + -
227A TYR* 3.2 47.4 + - + +
228A LEU* 3.6 10.5 - - + +
230A SER* 1.3 79.0 - - - +
232A ALA* 1.3 63.7 + - - +
234A ASP* 3.1 10.7 + - - +
236A TYR* 3.7 29.2 - - + -
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Residues in contact with ALA 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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178A ILE* 3.5 27.0 - - - +
205A LEU* 3.7 12.7 - - - +
208A THR* 3.3 27.1 - - - +
209A LEU* 3.7 27.2 - - + +
228A LEU 2.8 11.6 + - - +
229A ILE 3.5 4.5 - - - +
231A LEU* 1.3 74.9 - - - +
233A ARG* 1.3 58.6 + - - +
234A ASP* 2.9 9.1 + - - +
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Residues in contact with ARG 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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209A LEU* 3.6 20.3 - - + +
229A ILE* 2.8 47.6 + - - +
230A SER* 4.0 2.2 - - - +
232A ALA* 1.3 70.6 - - - +
234A ASP* 1.3 70.4 + - - +
235A GLU* 3.0 40.1 + - + +
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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