Contacts of the helix formed by residues 203 - 211 (chain A) in PDB entry 2PY5
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 THR 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A LYS 2.7 16.8 + - - -
200A ASP* 3.9 6.7 + - - +
201A ILE 3.3 6.6 - - - +
202A ILE* 1.3 87.0 + - - +
204A THR* 1.3 59.3 + - - +
205A LYS* 3.8 9.5 + - - +
206A LYS* 3.2 16.3 + - - +
207A PHE* 2.9 26.2 + - - +
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Residues in contact with THR 204 (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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199A LYS* 3.6 23.5 + - + +
203A THR* 1.3 69.3 - - - +
205A LYS* 1.3 66.6 + - - +
207A PHE* 3.5 8.9 - - + +
208A LYS* 2.9 58.8 + - + +
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Residues in contact with LYS 205 (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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203A THR* 3.2 8.9 - - - +
204A THR* 1.3 79.3 - - - +
206A LYS* 1.3 62.9 + - - +
208A LYS* 3.5 8.5 + - - +
209A LYS* 3.3 21.7 + - + +
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Residues in contact with LYS 206 (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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202A ILE* 3.3 40.9 - - + +
203A THR* 3.2 6.9 + - - +
205A LYS* 1.3 77.2 - - - +
207A PHE* 1.3 67.0 + - - +
209A LYS* 3.0 8.8 + - + +
210A VAL* 2.9 31.0 + - + +
359A LEU* 4.1 12.6 + - - +
9005A EDO 3.7 10.1 - - - -
9006A EDO 2.8 46.3 + - - -
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Residues in contact with PHE 207 (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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195A LEU* 4.0 6.7 - - + -
198A PHE* 3.8 19.3 - + - -
199A LYS* 3.7 42.2 - - + -
202A ILE* 3.7 20.1 - - + +
203A THR 2.9 14.7 + - - +
204A THR* 3.2 13.4 + - + +
206A LYS* 1.3 76.1 - - - +
208A LYS* 1.3 61.9 + - + +
211A PHE* 2.8 64.6 + + + +
393A PHE* 4.3 4.0 - + - -
425A VAL* 4.1 28.3 - - + -
8011A EDO 4.1 11.9 - - - -
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Residues in contact with LYS 208 (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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204A THR* 2.9 43.4 + - + +
205A LYS* 3.8 8.0 - - - +
207A PHE* 1.3 79.1 - - + +
209A LYS* 1.3 61.4 + - - +
212A PRO* 3.9 9.7 - - - +
8011A EDO 2.6 48.2 + - - +
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Residues in contact with LYS 209 (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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205A LYS* 3.3 12.6 + - + +
206A LYS* 3.0 13.5 + - + +
208A LYS* 1.3 82.3 - - - +
210A VAL* 1.3 65.7 + - + +
212A PRO* 4.0 9.0 - - - +
265A TYR* 5.6 0.2 - - - -
266A GLY* 4.9 3.1 - - - -
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Residues in contact with VAL 210 (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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202A ILE* 4.8 1.1 - - + -
206A LYS* 2.9 37.0 + - + +
207A PHE* 4.3 0.9 - - - -
209A LYS* 1.3 82.3 - - + +
211A PHE* 1.3 97.2 + - + +
212A PRO* 3.3 6.1 - - - -
265A TYR* 3.4 18.8 - - + +
266A GLY 2.7 27.6 + - - +
359A LEU* 4.5 9.0 - - + -
9005A EDO 3.5 28.7 - - - +
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Residues in contact with PHE 211 (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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198A PHE* 3.9 29.2 - + - -
202A ILE* 4.3 2.9 - - + -
207A PHE* 2.8 49.9 + + + +
208A LYS 4.0 1.1 - - - -
210A VAL* 1.3 103.2 - - + +
212A PRO* 1.3 63.1 - - - +
264A PRO 4.1 4.7 - - - -
265A TYR* 4.3 4.0 - - + -
359A LEU* 4.0 9.9 - - + -
360A PHE* 5.1 0.2 - + - -
393A PHE* 4.1 10.8 - + - -
425A VAL 4.3 5.1 - - - +
426A TYR* 3.5 39.9 - + + -
429A MET* 3.7 31.6 - - + -
8011A EDO 2.7 25.7 + - - -
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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