Contacts of the helix formed by residues 197 - 206 (chain A) in PDB entry 1DG3
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 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A LEU* 4.1 1.3 - - - -
194A GLN* 3.2 49.8 - - + +
196A LEU* 1.3 78.8 - - - +
198A PRO* 1.3 75.8 - - - +
199A ASP* 3.6 7.7 + - - +
200A GLU* 2.7 40.5 + - - +
201A TYR 2.9 18.2 + - - -
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Residues in contact with PRO 198 (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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189A LEU* 4.0 15.0 - - + -
196A LEU 4.7 0.2 - - - +
197A THR* 1.3 88.2 - - - +
199A ASP* 1.3 63.3 + - - +
201A TYR* 3.0 5.3 + - + +
202A LEU 2.9 19.1 + - - -
235A CYS* 3.5 39.9 - - - +
236A PHE* 4.6 1.3 - - - +
237A VAL* 4.0 30.5 - - + +
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Residues in contact with ASP 199 (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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197A THR* 3.3 7.0 + - - +
198A PRO* 1.3 79.3 - - - +
200A GLU* 1.3 58.8 + - + +
202A LEU* 3.3 5.2 + - - +
203A THR* 2.9 32.3 + - - -
233A LYS 4.5 3.1 - - - +
234A LYS* 2.8 40.0 + - - +
235A CYS* 2.8 32.6 + - - +
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Residues in contact with GLU 200 (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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194A GLN 3.1 26.9 + - - +
196A LEU* 3.2 16.6 - - + +
197A THR* 2.7 45.9 + - - +
199A ASP* 1.3 74.8 - - + +
201A TYR* 1.3 66.5 + - - +
203A THR* 3.6 7.9 - - - -
204A TYR* 3.0 34.7 + - + -
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Residues in contact with TYR 201 (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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133A THR* 3.4 12.1 - - - -
134A ILE* 3.0 36.2 + - + +
182A LEU* 3.8 19.7 - - + -
185A PHE* 3.8 20.9 - + - -
187A LEU* 3.8 23.4 - - + +
189A LEU* 4.2 17.5 - - + -
196A LEU* 3.3 19.0 - - + +
197A THR 2.9 7.6 + - - +
198A PRO* 3.0 13.4 + - + +
200A GLU* 1.3 78.2 - - - +
202A LEU* 1.3 57.5 + - - +
204A TYR* 3.4 5.2 + - + +
205A SER* 2.9 47.2 + - - -
235A CYS* 4.8 2.5 - - - -
237A VAL* 5.5 0.4 - - + -
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Residues in contact with LEU 202 (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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134A ILE* 3.8 21.3 - - + -
178A PHE* 4.9 6.3 - - + -
180A TRP* 3.9 22.4 - - + -
198A PRO 2.9 12.2 + - - +
199A ASP* 3.6 9.4 - - - +
201A TYR* 1.3 78.0 - - - +
203A THR* 1.3 65.9 + - - +
205A SER* 3.1 6.1 + - - -
206A LEU* 3.0 50.5 + - + +
233A LYS* 4.2 20.4 - - + -
234A LYS* 4.0 16.4 - - - +
235A CYS* 3.8 24.2 - - + -
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Residues in contact with THR 203 (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 ASP* 2.9 18.6 + - - +
200A GLU* 3.3 9.1 + - - -
202A LEU* 1.3 77.2 - - - +
204A TYR* 1.3 65.6 + - + +
206A LEU* 3.2 17.5 + - - +
207A LYS* 3.6 25.3 + - - +
227A ARG* 5.7 0.2 + - - -
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Residues in contact with TYR 204 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A LEU* 4.1 25.8 - - + -
200A GLU* 3.0 28.5 + - + +
201A TYR* 3.8 7.0 - - + +
203A THR* 1.3 79.2 - - + +
205A SER* 1.3 63.5 + - - +
207A LYS* 3.1 45.5 + - + +
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Residues in contact with SER 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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134A ILE* 3.8 33.9 + - - +
139A MET* 4.8 1.2 - - - +
201A TYR* 2.9 45.4 + - - -
202A LEU* 3.1 6.7 + - - -
204A TYR* 1.3 77.1 - - - +
206A LEU* 1.3 59.6 + - - +
207A LYS 3.3 1.1 + - - +
219A PHE* 5.2 0.3 - - - -
223A ARG* 2.8 29.3 + - - +
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Residues in contact with LEU 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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139A MET* 4.0 17.5 - - + -
180A TRP* 5.0 0.2 - - + -
202A LEU* 3.0 42.3 + - + +
203A THR* 3.2 8.9 + - - +
204A TYR 3.1 0.8 - - - -
205A SER* 1.3 77.0 - - - +
207A LYS* 1.3 62.3 + - - +
208A LEU* 3.6 0.3 + - - +
223A ARG* 3.7 19.8 - - + +
226A ILE* 3.9 48.0 - - + -
227A ARG* 3.1 43.1 + - + +
233A LYS* 4.9 8.7 - - + -
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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