Contacts of the helix formed by residues 223 - 239 (chain A) in PDB entry 2DH3
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 ASP 223 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A GLN* 5.1 7.7 - - - +
222A VAL* 1.3 78.1 + - - +
224A THR* 1.3 66.0 + - - +
225A VAL 3.3 0.7 + - - -
226A ALA* 3.4 6.3 + - - +
227A THR* 3.0 26.7 + - - -
258A PHE* 5.7 0.8 - - - -
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Residues in contact with THR 224 (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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171A VAL* 4.2 22.0 - - + -
222A VAL 2.6 5.2 + - - -
223A ASP* 1.3 79.5 - - - +
225A VAL* 1.3 60.8 + - - -
227A THR* 3.5 8.8 + - - -
228A LYS* 3.4 31.2 + - + +
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Residues in contact with VAL 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A VAL* 4.3 17.9 - - + -
176A LEU* 5.3 0.4 - - + +
209A PRO* 4.0 22.7 - - + -
217A TRP* 4.2 19.5 - - + +
218A PHE* 3.8 37.0 - - + -
221A GLN 4.1 11.4 - - - +
222A VAL* 2.6 25.9 + - + +
224A THR* 1.3 71.2 - - - +
226A ALA* 1.3 61.8 + - - +
228A LYS* 3.4 20.5 + - + +
229A VAL* 3.5 14.6 + - - +
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Residues in contact with ALA 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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217A TRP* 6.2 0.7 - - - -
222A VAL* 3.6 17.2 + - + +
223A ASP* 3.4 7.6 + - - +
225A VAL* 1.3 76.7 - - - +
227A THR* 1.3 65.5 + - - +
229A VAL* 3.3 5.2 + - - +
230A LYS* 3.2 24.9 + - - +
258A PHE* 3.3 38.4 - - + -
262A TRP* 4.1 13.8 + - + +
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Residues in contact with THR 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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223A ASP 3.0 15.4 + - - -
224A THR* 3.7 10.4 - - - -
226A ALA* 1.3 75.7 - - - +
228A LYS* 1.3 66.5 + - - +
230A LYS* 3.3 19.1 + - + +
231A ASP* 3.3 25.1 + - - +
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Residues in contact with LYS 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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171A VAL* 3.6 37.2 + - + +
172A ALA* 4.7 5.6 + - - +
174A THR* 2.9 30.0 + - + +
175A ASP* 5.0 3.0 - - - +
176A LEU* 3.9 21.9 - - + +
177A LEU* 5.5 1.0 - - - +
218A PHE* 6.1 2.0 - - + -
224A THR* 3.4 22.2 + - + +
225A VAL* 3.6 11.9 - - + +
226A ALA 3.3 0.4 - - - -
227A THR* 1.3 78.5 - - - +
229A VAL* 1.3 61.0 + - - +
231A ASP* 3.4 7.2 + - - +
232A ALA* 3.2 22.2 + - - +
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Residues in contact with VAL 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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176A LEU* 4.1 17.3 - - + -
207A LEU* 4.7 17.5 - - + +
209A PRO* 4.5 6.3 - - + -
217A TRP* 4.4 18.8 - - + -
225A VAL 3.5 14.8 - - - +
226A ALA 3.3 7.1 + - - +
227A THR 3.2 0.4 - - - -
228A LYS* 1.3 75.5 - - - +
230A LYS* 1.3 63.8 + - - +
232A ALA* 3.3 3.2 + - - +
233A LEU* 3.2 32.8 + - + +
246A VAL* 5.4 6.1 - - + -
262A TRP* 3.8 38.1 - - + +
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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 ALA 3.2 15.4 + - - +
227A THR* 3.5 16.4 - - + +
229A VAL* 1.3 78.1 - - - +
231A ASP* 1.3 66.5 + - - +
233A LEU* 3.6 9.8 + - - +
234A GLU* 3.5 52.3 + - - +
261A GLU* 3.3 35.4 - - - +
262A TRP* 4.0 10.5 - - + +
265A ILE* 3.8 18.4 - - + +
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Residues in contact with ASP 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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177A LEU* 4.2 15.1 - - + +
227A THR* 3.3 20.7 + - - +
228A LYS* 3.9 8.1 - - - +
229A VAL 3.3 0.4 - - - -
230A LYS* 1.3 80.0 + - - +
232A ALA* 1.3 59.9 + - - +
234A GLU* 3.5 16.3 + - - +
235A PHE* 3.0 29.1 + - - +
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Residues in contact with ALA 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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176A LEU* 3.9 19.5 - - + -
177A LEU* 3.5 21.5 - - + +
207A LEU* 4.2 12.6 - - + -
228A LYS 3.2 14.6 + - - +
229A VAL* 3.3 6.7 + - - +
231A ASP* 1.3 77.1 - - - +
233A LEU* 1.3 58.6 + - - +
235A PHE* 3.2 0.5 + - - +
236A TRP* 2.8 46.9 + - + +
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Residues in contact with LEU 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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207A LEU* 4.0 6.5 - - + -
229A VAL* 3.2 19.5 + - + +
230A LYS* 3.8 4.9 - - - +
231A ASP 3.4 0.2 - - - -
232A ALA* 1.3 77.9 - - - +
234A GLU* 1.3 62.7 + - - +
237A LEU* 3.1 34.1 + - + +
244A PHE* 3.2 49.8 - - + -
262A TRP* 3.8 49.1 - - + +
265A ILE* 4.3 19.5 - - + -
266A THR* 4.3 6.3 - - - +
275A LEU* 5.5 2.9 - - + -
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Residues in contact with GLU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A LYS* 3.5 35.0 + - - +
231A ASP* 3.5 21.1 + - - +
232A ALA 3.3 0.2 - - - -
233A LEU* 1.3 80.7 - - - +
235A PHE* 1.3 62.2 + - - +
237A LEU* 4.3 7.2 - - - +
238A GLN* 3.7 30.4 + - - +
265A ILE* 4.2 19.5 - - + +
269A PHE* 5.6 0.7 - - - -
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Residues in contact with PHE 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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177A LEU* 3.6 39.9 - - + -
186A LYS* 4.4 20.0 - - + -
231A ASP 3.0 17.7 + - - +
232A ALA 3.5 3.4 - - - +
233A LEU 3.2 0.2 - - - -
234A GLU* 1.3 75.9 - - - +
236A TRP* 1.3 106.1 + + - +
238A GLN* 3.4 17.2 + - - +
239A ALA* 3.4 10.7 + - + +
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Residues in contact with TRP 236 (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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163A ILE* 5.3 4.0 - - + -
164A HIS* 6.1 1.1 - - + -
176A LEU 3.1 27.9 + - - -
177A LEU* 4.0 15.2 - - - +
178A GLN 5.4 0.2 - - - -
179A ILE* 3.9 30.3 - - + -
186A LYS* 4.7 9.6 - - + -
189A PHE* 3.8 40.2 - + - -
205A LEU* 3.9 24.3 - - + +
207A LEU* 4.4 4.6 - - + +
232A ALA* 2.8 39.2 + - + +
235A PHE* 1.3 94.6 - + - +
237A LEU* 1.3 63.5 + - - +
238A GLN 3.3 0.2 - - - -
239A ALA* 3.3 16.4 + - + +
240A GLY 3.2 14.7 + - - -
241A VAL* 3.2 17.8 + - + +
244A PHE* 3.9 16.8 - + + -
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Residues in contact with LEU 237 (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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233A LEU* 3.1 28.3 + - + +
234A GLU* 4.3 4.5 - - - +
236A TRP* 1.3 76.2 - - - +
238A GLN* 1.3 59.8 + - - +
240A GLY* 3.0 20.1 + - - -
241A VAL* 3.8 12.3 + - + +
243A GLY 5.1 0.7 - - - +
244A PHE* 3.8 24.0 - - + -
265A ILE* 4.4 18.2 - - + +
266A THR* 4.4 9.4 - - + -
269A PHE* 3.6 49.0 - - + -
273A ARG* 3.7 36.2 + - + +
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Residues in contact with GLN 238 (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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234A GLU* 3.7 18.4 + - - +
235A PHE* 3.4 10.4 + - - +
236A TRP 3.3 0.6 - - - -
237A LEU* 1.3 76.2 - - - +
239A ALA* 1.3 58.6 + - - +
240A GLY* 3.2 1.3 + - - -
269A PHE* 4.2 20.3 - - + -
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Residues in contact with ALA 239 (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 LYS* 4.1 23.6 - - - +
189A PHE* 4.9 3.8 - - + -
190A ASP* 4.2 8.3 - - - +
193A LEU* 3.1 19.0 - - - +
197A LYS* 5.4 0.3 + - - -
235A PHE* 3.4 9.3 + - + +
236A TRP* 3.3 34.0 + - + +
237A LEU 3.2 0.4 - - - -
238A GLN* 1.3 77.4 - - - +
240A GLY* 1.3 57.1 + - - +
241A VAL 3.8 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