Contacts of the helix formed by residues 218 - 226 (chain F) in PDB entry 1PQ3
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 218 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327E ARG 4.5 2.2 - - - -
328E GLU* 4.0 27.8 + - - +
197F GLY 4.5 0.4 - - - -
198F LEU* 3.2 25.8 - - - +
216F TYR* 3.9 6.6 - - - -
217F PHE* 1.3 78.8 - - - +
219F MET* 1.3 66.3 + - - +
220F ARG* 3.4 12.2 + - - +
221F ASP* 2.8 39.3 + - - -
222F ILE* 3.0 9.0 + - - +
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Residues in contact with MET 219 (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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274E ARG* 3.4 32.8 - - - +
327E ARG* 4.1 16.1 - - - +
197F GLY* 3.4 35.7 - - - +
198F LEU 2.8 11.2 + - - +
199F ARG* 3.6 18.8 - - + +
218F SER* 1.3 70.3 - - - +
220F ARG* 1.3 57.3 + - - +
222F ILE* 3.2 12.2 + - + +
223F ASP* 3.0 32.9 + - - +
269F GLY 3.4 16.6 - - - +
270F GLY* 3.4 26.0 - - - -
271F LEU* 3.6 19.7 - - + +
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Residues in contact with ARG 220 (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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278E TYR* 4.1 11.8 + - + -
281E GLU* 3.0 38.9 + - - +
282E GLU* 2.6 33.8 + - - -
285E ASN* 3.1 26.6 - - - +
326E THR* 5.7 6.4 + - + -
327E ARG* 3.5 31.5 - - + +
328E GLU* 6.0 1.6 - - + -
218F SER* 2.9 11.3 + - - +
219F MET* 1.3 76.7 - - - +
221F ASP* 1.3 72.9 + - - +
223F ASP* 3.1 4.9 + - - +
224F ARG* 3.1 25.8 + - + +
3071F SO4 3.6 32.8 + - - +
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Residues in contact with ASP 221 (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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328E GLU* 4.4 3.3 - - - +
216F TYR* 3.7 12.9 - - - +
217F PHE* 3.5 24.7 - - + -
218F SER* 2.8 37.5 + - - +
220F ARG* 1.3 78.8 - - - +
222F ILE* 1.3 57.3 + - - +
224F ARG* 3.4 14.9 + - - +
225F LEU* 3.0 39.0 + - + +
230F VAL* 4.4 1.3 - - - +
3071F SO4 3.4 22.2 + - - -
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Residues in contact with ILE 222 (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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274E ARG* 4.0 17.0 - - - +
196F ILE* 4.1 19.7 - - + -
197F GLY 4.2 4.5 - - - +
217F PHE* 4.3 5.2 - - + +
218F SER 3.0 10.8 + - - +
219F MET* 3.5 22.0 - - - +
220F ARG 3.1 0.4 - - - -
221F ASP* 1.3 73.7 - - - +
223F ASP* 1.3 59.8 + - - +
224F ARG 3.1 1.8 - - - -
226F GLY* 2.8 27.9 + - - -
227F ILE* 4.2 24.9 - - + +
230F VAL* 4.0 20.6 - - + -
271F LEU* 3.8 25.4 - - + -
275F GLU* 4.1 13.0 - - - +
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Residues in contact with ASP 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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227E ILE* 4.4 12.4 - - + +
228E GLN* 4.3 9.2 + - - +
274E ARG* 2.5 55.7 + - - +
275E GLU* 5.3 0.7 - - - -
278E TYR* 3.9 18.2 - - + -
327E ARG* 2.5 37.9 + - - -
219F MET 3.0 12.4 + - - -
220F ARG 3.1 6.0 + - - +
222F ILE* 1.3 75.4 - - - +
224F ARG* 1.3 60.3 + - - +
226F GLY* 4.7 1.4 + - - -
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Residues in contact with ARG 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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228E GLN* 3.1 50.1 + - + +
278E TYR* 3.8 19.3 - - + +
220F ARG* 3.1 17.1 + - + +
221F ASP* 3.8 14.4 + - - +
222F ILE 3.1 0.6 - - - -
223F ASP* 1.3 81.3 - - - +
225F LEU* 1.3 80.0 + - + +
226F GLY 3.6 0.2 - - - -
233F ARG* 4.2 1.8 - - - +
3071F SO4 3.4 38.1 + - - -
3074F SO4 2.5 51.4 + - - -
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Residues in contact with LEU 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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228E GLN* 5.3 2.7 - - - +
217F PHE* 4.3 23.3 - - + -
221F ASP* 3.0 19.9 + - + +
224F ARG* 1.3 111.3 - - + +
226F GLY* 1.3 62.3 - - - +
229F LYS* 3.1 33.9 + - + +
230F VAL* 4.5 4.0 - - + -
233F ARG* 3.6 31.6 - - - +
3074F SO4 3.6 17.9 - - - +
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Residues in contact with GLY 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 ILE* 2.8 18.2 + - - -
223F ASP 4.6 1.7 + - - -
224F ARG 3.6 1.0 - - - -
225F LEU* 1.3 80.3 - - - +
227F ILE* 1.3 66.8 + - - -
228F GLN* 3.1 4.9 + - - -
229F LYS 3.1 1.6 + - - -
230F VAL* 3.1 22.7 + - - +
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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