Contacts of the helix formed by residues 225 - 235 (chain A) in PDB entry 1DGD
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 TYR 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A PHE* 3.4 38.7 - + - -
167A ILE* 3.6 15.8 - - - +
168A PRO 4.4 2.6 + - - -
170A PRO* 3.6 27.9 - - + +
185A TYR* 4.0 27.1 - + + -
186A LEU* 4.1 7.8 - - + +
189A LEU* 3.8 28.1 - - + +
221A LEU* 3.7 22.4 - - + -
222A PRO* 3.0 26.8 + - + +
223A ASP 3.1 2.4 + - - -
224A GLY* 1.3 79.5 - - - +
226A MET* 1.3 60.2 + - - +
228A ALA* 3.0 5.5 + - - +
229A LEU* 2.8 38.9 + - + +
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Residues in contact with MET 226 (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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211A PRO* 5.3 7.0 - - + -
221A LEU* 3.9 29.2 - - + -
222A PRO 4.4 1.4 + - - -
224A GLY 3.5 0.6 - - - +
225A TYR* 1.3 77.0 - - - +
227A ALA* 1.3 56.6 - - - +
229A LEU* 3.5 12.3 - - - +
230A LYS* 2.9 30.0 + - - +
240A LEU* 4.5 8.5 - - - -
242A LEU* 3.6 38.8 - - + -
258A CYS* 4.7 3.4 - - + -
261A ASP* 4.0 33.8 + - + +
263A VAL* 3.5 36.0 - - + +
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Residues in contact with ALA 227 (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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224A GLY* 3.5 15.8 + - - +
226A MET* 1.3 77.5 - - - +
228A ALA* 1.3 64.8 + - - +
230A LYS* 3.4 5.8 + - - +
231A ARG* 3.1 35.8 + - - +
261A ASP 6.0 0.2 - - - +
263A VAL* 3.8 18.0 - - + +
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Residues in contact with ALA 228 (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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186A LEU* 3.8 15.3 - - + -
189A LEU* 3.6 19.1 - - + -
224A GLY 3.1 10.5 + - - +
225A TYR 3.0 8.5 + - - +
227A ALA* 1.3 81.5 - - - +
229A LEU* 1.3 57.5 + - - +
231A ARG* 3.0 28.8 + - - +
232A LYS* 2.8 34.2 + - + +
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Residues in contact with LEU 229 (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 PHE* 4.6 1.1 - - + -
189A LEU* 3.9 15.9 - - + +
193A PHE* 4.1 15.9 - - + -
207A PHE* 3.9 48.7 - - + -
209A ALA* 4.4 8.3 - - + -
221A LEU* 5.1 0.7 - - + -
225A TYR* 2.8 34.6 + - + +
226A MET* 3.5 20.0 - - - +
227A ALA 3.2 0.2 - - - -
228A ALA* 1.3 76.1 - - - +
230A LYS* 1.3 64.5 + - - +
232A LYS* 2.9 15.1 + - - +
233A CYS* 3.0 16.3 + - - -
240A LEU* 4.0 17.7 - - + -
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Residues in contact with LYS 230 (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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226A MET 2.9 17.0 + - - +
227A ALA* 3.7 6.3 - - - +
229A LEU* 1.3 75.3 - - - +
231A ARG* 1.3 57.4 + - + +
233A CYS* 3.3 8.0 + - + +
234A GLU* 2.8 69.6 + - - +
238A MET 5.7 0.4 + - - -
240A LEU* 3.7 32.3 - - + +
263A VAL* 4.8 10.5 - - + -
264A THR 3.8 20.6 - - - +
265A PRO* 4.9 0.4 - - - -
266A ASP* 3.9 24.6 + - - -
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Residues in contact with ARG 231 (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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186A LEU* 6.2 1.8 - - - +
224A GLY 5.5 0.4 + - - -
227A ALA* 3.1 19.0 + - - +
228A ALA* 3.0 39.4 + - - +
230A LYS* 1.3 74.5 - - + +
232A LYS* 1.3 67.9 + - + +
234A GLU* 3.2 15.9 + - - +
235A ALA* 3.1 24.1 + - - +
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Residues in contact with LYS 232 (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* 4.1 17.9 - - + -
190A ASP* 2.9 44.3 + - - +
193A PHE* 3.9 36.8 - - + +
228A ALA* 2.8 20.7 + - - +
229A LEU 2.9 7.2 + - - +
231A ARG* 1.3 78.9 - - - +
233A CYS* 1.3 61.9 + - - +
235A ALA* 3.5 1.6 + - - +
236A ARG* 3.0 51.4 + - - +
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Residues in contact with CYS 233 (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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193A PHE* 5.2 1.3 - - - -
207A PHE* 3.8 31.2 - - - -
229A LEU* 3.0 18.7 + - - -
230A LYS* 3.5 11.2 - - + +
231A ARG 3.2 0.2 - - - -
232A LYS* 1.3 75.4 - - - +
234A GLU* 1.3 67.4 + - + +
236A ARG* 3.0 12.0 + - - -
237A GLY 3.0 10.4 + - - -
238A MET* 3.0 38.9 + - + +
239A LEU 4.4 3.6 - - - -
240A LEU* 4.2 22.9 - - + -
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Residues in contact with GLU 234 (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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230A LYS* 2.8 58.1 + - - +
231A ARG* 3.2 17.7 + - - +
233A CYS* 1.3 75.8 - - + +
235A ALA* 1.3 64.2 + - - +
236A ARG 3.1 0.9 + - - -
237A GLY* 3.2 11.2 + - - +
238A MET 4.8 3.4 - - - +
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Residues in contact with ALA 235 (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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231A ARG 3.1 15.3 + - - +
232A LYS* 3.7 6.5 - - - +
234A GLU* 1.3 79.3 - - - +
236A ARG* 1.3 69.5 + - + +
237A GLY 3.5 0.4 + - - -
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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