Contacts of the helix formed by residues 220 - 231 (chain B) in PDB entry 5IJ7
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 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194B ASP* 3.2 26.0 + - - -
219B PRO* 1.4 76.9 - - - +
221B ASP* 1.3 64.8 + - - +
222B LYS* 3.2 34.9 + - - +
223B ILE* 3.5 20.7 - - - +
224B PHE* 3.3 14.2 - - - -
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Residues in contact with ASP 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B PRO 4.3 5.0 - - - +
220B SER* 1.3 73.7 + - - +
222B LYS* 1.4 64.7 + - - +
223B ILE 3.1 2.5 + - - -
224B PHE* 3.1 7.7 + - - +
225B GLU* 3.0 35.3 + - - +
237B ALA* 5.5 0.5 - - - +
241B LYS* 3.2 40.3 + - + +
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Residues in contact with LYS 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLU* 2.8 35.5 + - - +
10B LYS 4.9 2.9 - - - +
15B TRP* 3.4 46.1 - - + +
194B ASP* 2.9 29.9 + - - -
197B ASP* 4.6 1.6 + - - -
220B SER* 3.2 20.1 + - - +
221B ASP* 1.4 75.7 - - - +
223B ILE* 1.3 56.9 + - - +
225B GLU* 3.4 20.7 - - - +
226B ALA* 3.1 28.2 + - - +
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Residues in contact with ILE 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B TRP* 3.6 31.6 - - + -
175B VAL* 4.3 16.8 - - + +
178B LEU* 3.5 51.5 - - + +
179B GLY* 3.9 7.2 - - - +
194B ASP* 3.8 13.2 - - + +
219B PRO* 4.9 2.5 - - + -
220B SER* 3.5 28.4 + - - +
221B ASP 3.1 0.4 - - - -
222B LYS* 1.3 74.3 - - - +
224B PHE* 1.4 61.3 + - + +
226B ALA* 3.1 7.9 + - - +
227B ILE* 3.0 35.6 + - + +
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Residues in contact with PHE 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B PHE* 4.3 3.1 - + - -
175B VAL* 3.7 24.7 - - + -
219B PRO* 3.7 24.0 - - + -
220B SER 3.3 23.1 - - - -
221B ASP* 3.1 8.2 + - - +
223B ILE* 1.4 76.5 - - + +
225B GLU* 1.3 56.7 + - - +
227B ILE* 3.4 6.0 + - + +
228B SER* 3.0 28.2 + - - -
237B ALA* 3.7 20.3 - - + +
240B LEU* 3.4 48.6 - - + +
241B LYS* 3.6 23.1 - - + -
244B TYR* 3.6 32.5 - + + -
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Residues in contact with GLU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B ASP* 3.0 28.5 + - - +
222B LYS* 3.4 22.2 - - - +
224B PHE* 1.3 75.1 - - - +
226B ALA* 1.3 52.2 + - - +
228B SER* 4.0 5.2 - - - -
229B SER* 2.7 31.4 + - - -
237B ALA* 3.8 21.5 - - + +
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Residues in contact with ALA 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PRO 5.4 0.4 - - - +
15B TRP* 3.7 38.6 - - + +
16B ARG* 4.1 6.3 - - + +
19B VAL* 3.9 6.3 - - + -
222B LYS 3.1 19.3 + - - +
223B ILE* 3.1 8.2 + - - +
225B GLU* 1.3 75.5 - - - +
227B ILE* 1.4 64.0 + - - +
229B SER* 3.2 20.9 + - - -
230B MET* 3.5 12.6 + - - +
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Residues in contact with ILE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 4.0 10.3 - - + -
166B ILE* 4.8 1.8 - - + -
171B PHE* 4.4 12.6 - - + -
174B LEU* 3.9 17.7 - - + -
175B VAL* 3.8 31.0 - - + -
178B LEU* 3.8 28.9 - - + -
223B ILE* 3.0 22.1 + - + +
224B PHE* 3.4 7.8 + - + +
226B ALA* 1.4 75.3 - - - +
228B SER* 1.4 55.5 + - - +
230B MET 3.2 2.1 + - - -
231B PHE* 2.9 50.2 + - + +
234B LYS* 6.2 0.7 - - + -
240B LEU* 3.8 16.6 - - + -
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Residues in contact with SER 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B PHE 3.0 17.6 + - - -
225B GLU* 4.0 7.2 - - - -
226B ALA 3.3 0.2 - - - -
227B ILE* 1.4 74.6 - - - +
229B SER* 1.3 61.1 + - - +
231B PHE 4.1 7.0 - - - -
232B PRO* 3.1 26.9 - - - +
235B GLY 3.5 14.3 + - - -
236B THR* 3.7 12.3 + - - -
237B ALA* 3.8 17.5 + - - -
240B LEU* 3.9 6.4 - - - +
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Residues in contact with SER 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ARG* 3.5 29.0 + - - +
225B GLU 2.7 23.1 + - - -
226B ALA* 3.2 11.1 + - - -
228B SER* 1.3 77.6 - - - +
230B MET* 1.3 68.3 + - - +
232B PRO* 3.8 12.8 - - - +
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Residues in contact with MET 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ARG* 3.6 48.0 - - + +
19B VAL* 4.0 23.1 - - + -
20B LYS* 5.0 11.4 - - - -
226B ALA 3.5 10.5 + - - +
227B ILE 3.2 6.1 + - - +
229B SER* 1.3 82.0 - - - +
231B PHE* 1.3 71.6 + - + +
232B PRO* 3.5 9.4 - - - +
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Residues in contact with PHE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 3.7 25.1 - - + -
23B TYR* 3.5 39.3 - + + -
166B ILE* 3.6 40.2 - - + -
174B LEU* 4.1 4.9 - - + -
227B ILE* 2.9 30.4 + - + +
228B SER* 3.3 11.4 - - - +
230B MET* 1.3 86.6 - - + +
232B PRO* 1.4 64.1 - - - +
233B ASP* 3.2 4.3 + - - +
234B LYS* 3.4 26.0 + - + +
235B GLY 4.0 4.2 + - - +
240B LEU* 5.6 1.4 - - + +
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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