Contacts of the helix formed by residues 222 - 234 (chain A) in PDB entry 4BJ3
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 ASN 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A TYR* 3.4 15.1 - - - -
188A ALA 2.8 14.2 + - - +
189A ASN* 3.0 28.9 + - - +
190A ASN* 6.0 0.2 - - - -
191A PRO* 6.1 0.2 - - - +
220A LEU* 4.2 19.8 - - - +
221A THR* 1.3 68.0 - - - +
223A THR* 1.3 62.8 + - - +
225A GLY* 4.2 5.1 - - - +
226A ALA* 3.5 12.2 + - - +
258A HIS* 3.8 17.3 - - - +
259A ASP* 3.2 25.7 - - - +
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Residues in contact with THR 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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187A TYR* 2.9 34.1 + - + +
221A THR* 3.1 10.1 + - - +
222A ASN* 1.3 70.6 - - - +
224A PHE* 1.3 65.4 + - + +
225A GLY 3.1 1.6 - - - -
226A ALA* 3.1 5.4 + - - +
227A ILE* 2.9 46.5 + - + +
251A VAL* 4.5 5.2 - - + -
253A THR* 4.0 7.7 + - + +
257A SER* 3.5 24.9 - - - -
259A ASP* 3.1 4.6 + - - -
303A ILE* 4.2 17.3 - - + -
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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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223A THR* 1.3 77.4 - - + +
225A GLY* 1.3 58.7 + - - +
226A ALA 3.3 0.2 - - - -
227A ILE* 4.0 18.2 - - + -
228A GLN* 3.3 24.6 + - - +
257A SER* 3.9 13.9 - - - -
259A ASP* 3.1 32.6 + - - +
260A GLY* 3.6 23.6 - - - -
262A MET* 3.3 25.3 - - + +
263A LEU* 3.6 39.3 - - + -
266A VAL* 3.6 14.0 - - + +
267A ILE* 4.6 6.3 - - + -
299A GLU* 5.1 4.9 - - - -
303A ILE* 4.0 30.3 - - + -
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Residues in contact with GLY 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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191A PRO* 4.7 5.4 - - - +
222A ASN* 3.7 5.6 + - - -
223A THR 3.1 0.6 - - - -
224A PHE* 1.3 77.6 - - - +
226A ALA* 1.3 58.1 + - - +
228A GLN* 3.9 6.8 - - - +
229A TYR* 3.3 21.5 + - - +
259A ASP* 3.0 18.5 + - - -
262A MET* 4.0 10.3 - - - -
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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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149A VAL* 4.2 7.8 - - + +
185A ILE* 5.6 1.4 - - + +
187A TYR* 3.5 42.6 - - + -
191A PRO* 3.8 13.9 - - + +
222A ASN 3.5 7.3 + - - +
223A THR 3.1 6.8 + - - +
225A GLY* 1.3 76.9 - - - +
227A ILE* 1.3 59.2 + - - +
228A GLN 3.2 1.3 - - - -
229A TYR* 3.1 9.4 + - - +
230A ALA* 2.8 29.8 + - - +
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Residues in contact with ILE 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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149A VAL* 4.5 8.3 - - + -
223A THR* 2.9 37.0 + - + +
224A PHE* 4.2 16.2 - - + -
226A ALA* 1.3 75.5 - - - +
228A GLN* 1.3 62.0 + - - +
230A ALA* 3.3 8.8 + - - +
231A ARG* 3.1 21.5 + - - +
249A MET* 3.6 23.1 - - + +
251A VAL* 3.8 29.8 - - + -
266A VAL* 3.6 18.6 - - + -
267A ILE* 5.3 2.2 - - + -
270A CYS* 4.0 9.0 - - - -
303A ILE* 3.9 18.2 - - + -
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Residues in contact with GLN 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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224A PHE 3.3 17.2 + - - +
225A GLY* 3.9 7.2 - - - +
226A ALA 3.2 0.4 - - - -
227A ILE* 1.3 77.8 - - - +
229A TYR* 1.3 65.0 + - - +
231A ARG* 3.3 35.1 + - - +
232A LYS* 3.3 40.1 + - + +
262A MET* 4.1 16.6 - - - +
266A VAL* 4.1 15.9 - - + +
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Residues in contact with TYR 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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185A ILE* 3.9 26.5 - - + -
191A PRO* 3.7 38.4 - - + -
192A ARG* 5.8 0.2 - - - -
193A VAL* 4.0 17.8 + - + +
225A GLY 3.3 13.6 + - - +
226A ALA 3.1 9.1 + - - +
228A GLN* 1.3 77.7 - - - +
230A ALA* 1.3 63.5 + - - +
232A LYS* 3.3 3.3 + - - -
233A TYR* 3.2 63.9 + + + +
234A ALA 5.7 0.9 - - - -
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Residues in contact with ALA 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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147A VAL* 4.4 6.1 - - + -
149A VAL* 3.9 24.7 - - + -
185A ILE* 4.6 5.8 - - + -
226A ALA 2.8 15.5 + - - +
227A ILE 3.6 5.8 - - - +
228A GLN 3.2 0.2 - - - -
229A TYR* 1.3 80.7 - - - +
231A ARG* 1.3 62.5 + - - +
234A ALA* 3.1 38.5 + - + +
235A TYR* 3.5 9.9 - - + -
249A MET* 4.4 7.0 - - - -
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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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227A ILE 3.1 12.8 + - - +
228A GLN* 3.5 37.3 - - - +
229A TYR 3.3 0.4 - - - -
230A ALA* 1.3 78.1 - - - +
232A LYS* 1.3 100.3 + - - +
235A TYR* 4.3 18.3 - - - +
247A LYS* 5.1 4.3 + - - -
249A MET* 5.5 1.5 - - - -
266A VAL* 4.4 11.3 + - - +
269A GLN* 3.3 62.4 - - - +
270A CYS* 4.3 8.7 - - - +
273A ASP* 3.8 20.2 + - - +
275A ILE* 3.9 19.1 - - + +
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Residues in contact with LYS 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 GLN* 3.3 36.1 - - + +
229A TYR* 3.3 1.9 + - - -
230A ALA 3.2 0.8 - - - -
231A ARG* 1.3 114.0 - - - +
233A TYR* 1.3 101.9 + - + +
235A TYR 5.2 0.4 - - - -
236A SER* 4.4 9.5 + - - -
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Residues in contact with TYR 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 TYR* 3.2 58.5 + + + +
232A LYS* 1.3 113.6 - - + +
234A ALA* 1.3 55.8 + - - +
235A TYR 3.1 5.6 - - - -
236A SER* 2.7 21.2 + - - +
239A SER* 2.6 26.1 + - - +
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Residues in contact with ALA 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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147A VAL* 3.7 33.4 - - + +
185A ILE* 4.0 14.1 - - + -
196A ASN* 4.6 7.3 + - - +
197A LEU* 3.3 21.7 - - - +
229A TYR* 4.2 1.8 + - - -
230A ALA* 3.1 25.4 + - - +
233A TYR* 1.3 77.8 - - - +
235A TYR* 1.3 58.2 + - + +
239A SER* 3.4 14.5 - - - -
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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