Contacts of the helix formed by residues 222 - 235 (chain F) in PDB entry 6PB4
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 ALA 222 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218F ARG 5.2 2.2 - - - +
219F GLU* 3.9 13.2 - - - +
221F PHE* 1.3 79.8 - - - +
223F GLU* 1.3 68.1 + - - +
224F LEU 3.4 1.1 - - - +
225F ARG* 4.0 5.2 + - - +
226F ALA* 3.4 18.9 + - - +
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Residues in contact with GLU 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F GLU 3.3 4.5 - - - +
220F LYS* 3.0 61.0 + - - +
222F ALA* 1.3 83.3 + - - +
224F LEU* 1.3 79.4 - - + +
226F ALA* 3.1 9.2 + - - +
227F GLN* 2.9 38.3 + - + +
255F VAL* 4.8 10.3 - - + -
258F GLN* 4.6 2.1 + - - -
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Residues in contact with LEU 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F LEU* 4.3 13.9 - - + -
145F LEU* 3.8 24.8 - - + +
148F TYR* 3.4 28.0 - - + -
220F LYS 2.9 27.4 - - - +
221F PHE* 4.8 4.7 - - + -
222F ALA 3.4 0.6 - - - +
223F GLU* 1.3 88.1 - - - +
225F ARG* 1.3 56.9 + - - +
227F GLN* 3.2 9.3 + - + +
228F TYR* 2.9 26.5 + - - +
255F VAL* 4.1 17.0 - - + -
259F PHE* 3.9 29.2 - - + -
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Residues in contact with ARG 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F LEU* 4.2 16.1 - - + +
149F ASP* 3.3 32.0 + - - -
221F PHE* 4.4 17.8 + - - +
222F ALA* 4.0 7.7 + - - +
223F GLU 3.4 0.2 - - - -
224F LEU* 1.3 78.8 - - - +
226F ALA* 1.3 56.8 + - - +
228F TYR* 3.3 12.4 + - + +
229F VAL* 2.9 39.7 + - + +
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Residues in contact with ALA 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F ALA 3.4 13.7 + - - +
223F GLU* 3.1 14.2 + - - +
225F ARG* 1.3 78.6 - - - +
227F GLN* 1.3 65.8 + - + +
229F VAL* 3.1 11.8 - - - +
230F VAL* 3.0 27.5 + - - +
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Residues in contact with GLN 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223F GLU* 2.9 25.6 + - + +
224F LEU* 3.6 9.0 - - + +
226F ALA* 1.3 78.4 - - - +
228F TYR* 1.3 53.6 + - - +
230F VAL* 3.2 12.1 - - - +
231F THR* 2.3 39.8 + - - -
248F GLU 4.9 1.0 - - - +
251F LYS* 3.1 38.1 + - - +
252F LEU* 4.0 26.0 - - + +
255F VAL* 4.8 23.5 - - + +
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Residues in contact with TYR 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F THR* 3.2 29.8 - - + +
145F LEU* 3.7 19.7 - - + -
224F LEU 2.9 12.5 + - - +
225F ARG* 3.3 13.7 - - + +
226F ALA 3.2 0.2 - - - -
227F GLN* 1.3 75.9 - - - +
229F VAL* 1.3 75.4 + - + +
231F THR* 2.9 20.9 + - - -
232F ARG* 2.9 68.9 + - + +
252F LEU* 5.1 2.8 - - - +
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Residues in contact with VAL 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225F ARG* 2.9 30.4 + - + +
226F ALA* 3.1 21.8 - - - +
228F TYR* 1.3 90.0 - - + +
230F VAL* 1.3 60.9 + - + +
232F ARG* 3.4 3.6 + - - +
233F ASP* 2.8 36.0 + - - +
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Residues in contact with VAL 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226F ALA 3.0 22.1 + - - +
227F GLN* 3.2 24.5 - - - +
229F VAL* 1.3 79.1 - - + +
231F THR* 1.3 59.2 + - - +
233F ASP* 3.7 13.1 + - + +
234F THR* 3.5 23.2 + - + +
248F GLU* 4.3 24.1 - - + +
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Residues in contact with THR 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F ILE* 4.6 0.7 - - + -
227F GLN* 2.3 28.1 + - - -
228F TYR* 2.9 7.5 + - - -
230F VAL* 1.3 77.8 - - - +
232F ARG* 1.3 77.6 + - - +
233F ASP 3.1 2.9 + - - -
234F THR* 3.4 8.8 + - - -
235F ILE* 3.4 40.6 - - + +
248F GLU 5.6 0.9 + - - -
249F ILE* 4.7 6.5 - - + -
252F LEU* 3.8 35.7 - - + +
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Residues in contact with ARG 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F PRO* 2.9 30.1 + - - +
139F GLU* 3.4 23.7 + - - +
141F ILE* 4.7 2.0 - - - +
142F THR* 2.9 31.1 + - - -
228F TYR* 2.9 57.3 + - + +
229F VAL* 3.4 5.8 + - - +
231F THR* 1.3 97.2 - - - +
233F ASP* 1.3 62.9 + - - +
234F THR 3.4 0.2 - - - -
235F ILE* 4.4 12.0 + - - +
236F LYS* 4.8 7.6 + - - +
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Residues in contact with ASP 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229F VAL* 2.8 28.2 + - - +
230F VAL* 3.7 12.7 - - + +
231F THR 3.1 0.8 - - - -
232F ARG* 1.3 81.8 - - - +
234F THR* 1.3 65.0 + - + +
235F ILE 3.6 0.2 - - - -
236F LYS* 4.2 4.2 + - - +
237F ALA* 4.1 12.5 + - - +
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Residues in contact with THR 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F VAL* 3.5 18.9 + - + +
231F THR* 3.4 10.4 + - - -
233F ASP* 1.3 79.7 - - + +
235F ILE* 1.3 68.1 + - - +
236F LYS 3.0 5.8 - - - -
237F ALA* 3.1 24.5 + - + +
239F GLY 3.5 6.1 - - - +
242F HIS* 6.1 0.2 - - - +
245F ALA* 4.2 29.8 + - + +
248F GLU* 4.0 17.5 + - - +
249F ILE* 5.5 1.7 - - - +
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Residues in contact with ILE 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F PRO* 4.0 29.8 - - + -
141F ILE* 4.6 2.7 - - + -
231F THR* 3.4 39.2 + - + +
232F ARG* 4.4 10.9 + - - +
233F ASP 3.6 0.6 - - - -
234F THR* 1.3 78.6 - - - +
236F LYS* 1.3 55.4 + - - +
239F GLY* 2.6 26.1 - - - +
240F ARG* 3.7 33.7 + - + +
245F ALA* 6.0 1.6 - - + -
246F GLN* 6.1 1.6 - - - +
249F ILE* 4.0 25.6 - - + -
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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