Contacts of the helix formed by residues 228 - 241 (chain B) in PDB entry 2DDK
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 HIS 228 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B GLU* 4.6 2.5 + - - -
89B LYS* 6.1 3.1 - - + -
90B CYS* 5.4 1.6 - - - -
176B PRO* 6.0 4.9 - - + +
226B GLY 3.7 16.4 + - - -
227B LEU* 1.3 77.7 - - - +
229B CYS* 1.3 66.0 + - - +
230B TRP* 2.6 53.9 + + + +
231B ASP* 3.0 19.6 + - - +
232B LEU* 3.2 5.2 - - - +
259B CYS* 4.5 17.9 - - - -
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Residues in contact with CYS 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ILE* 4.0 17.5 - - - -
90B CYS* 2.0 55.5 - - + -
99B ILE* 4.0 8.7 - - + -
227B LEU 3.8 0.6 + - - -
228B HIS* 1.3 67.0 - - - +
230B TRP* 1.3 61.9 + - - +
231B ASP 2.8 12.0 + - - -
232B LEU* 2.8 23.5 + - - +
233B ALA* 2.8 15.8 + - - +
256B LEU* 3.8 32.3 + - + +
259B CYS* 5.3 0.2 - - - -
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Residues in contact with TRP 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ILE* 4.5 4.5 - - + -
80B ALA* 3.2 18.6 - - - -
81B GLU* 2.6 69.9 + - + -
82B GLU* 4.5 9.2 - - - -
89B LYS* 5.0 9.9 - - + -
90B CYS* 4.9 4.0 - - - -
99B ILE* 3.2 20.6 - - + +
100B ILE 3.1 22.7 - - - +
101B ASP* 3.4 27.1 + - - +
119B SER* 3.8 12.3 + - - -
228B HIS* 2.6 46.7 + + + +
229B CYS* 1.3 86.4 - - - +
231B ASP* 1.3 68.8 + - - +
233B ALA* 4.5 2.1 + - - +
234B ALA 5.4 0.3 + - - -
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Residues in contact with ASP 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B GLU* 4.5 1.6 - - - +
101B ASP* 2.2 33.1 - - - +
104B ASP* 3.8 14.0 - - - +
119B SER* 4.4 2.4 + - - -
207B SER* 3.3 26.3 + - - +
208B THR* 3.2 22.0 - - - +
211B LEU* 4.3 1.0 - - - +
227B LEU* 4.5 11.7 - - + +
228B HIS* 3.0 16.8 + - - +
229B CYS 2.8 1.2 - - - -
230B TRP* 1.3 89.6 + - - +
232B LEU* 1.3 61.5 + - - +
233B ALA 3.7 0.2 - - - -
235B ALA* 3.9 9.7 - - - +
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B LEU* 4.7 8.7 - - + -
227B LEU* 4.0 22.0 - - + +
228B HIS 3.2 22.9 - - - +
229B CYS* 2.8 21.0 + - + +
231B ASP* 1.3 80.7 - - - +
233B ALA* 1.3 55.5 + - - -
234B ALA 3.5 1.1 - - - -
235B ALA* 4.0 4.7 - - + -
236B THR* 2.6 43.5 + - - +
246B VAL* 6.0 0.2 - - + -
254B LEU* 3.6 22.9 - - + -
255B ASP 5.8 0.2 - - - +
256B LEU* 4.8 13.0 - - + +
259B CYS* 5.7 1.3 - - - -
260B ARG 4.8 3.6 - - - +
261B VAL* 3.5 35.2 - - + -
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Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ILE* 3.5 47.1 - - + +
121B GLY* 4.5 4.0 - - - -
128B LEU* 3.9 27.6 - - + +
130B PHE 5.0 0.2 - - - +
229B CYS* 2.8 11.8 + - - +
230B TRP* 4.8 0.7 - - - -
231B ASP 3.7 1.2 - - - +
232B LEU* 1.3 74.9 - - - +
234B ALA* 1.3 66.6 + - - +
236B THR* 3.2 10.4 + - - -
237B VAL* 3.6 7.1 + - - +
256B LEU* 5.0 8.1 - - + -
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ILE 5.1 0.4 + - - +
119B SER* 3.0 28.1 + - - +
120B ILE 3.7 26.0 - - - +
121B GLY* 3.9 4.6 - - - +
131B GLY* 3.8 9.6 - - - -
132B VAL 4.0 4.9 - - - +
133B ILE* 3.4 14.4 - - + -
230B TRP 5.4 0.6 + - - -
231B ASP 5.3 0.2 - - - -
233B ALA* 1.3 77.6 - - - +
235B ALA* 1.3 62.5 + - - +
237B VAL* 2.9 23.6 - - - +
238B ILE* 3.3 6.6 + - - +
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B SER* 4.4 1.0 + - - -
133B ILE* 3.3 17.3 - - + +
208B THR* 4.5 4.7 - - - +
211B LEU* 3.4 38.1 - - + -
212B CYS* 5.2 1.3 - - - +
231B ASP 3.9 14.6 - - - +
232B LEU* 3.7 3.7 + - + +
233B ALA 3.4 0.2 - - - -
234B ALA* 1.3 78.9 - - - +
236B THR* 1.3 55.5 + - - +
238B ILE* 3.6 4.1 + - - +
239B ILE* 3.0 34.6 + - - +
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Residues in contact with THR 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LEU* 3.5 16.6 - - + +
232B LEU* 2.6 30.2 + - - +
233B ALA 3.6 4.7 - - - -
234B ALA 2.9 0.6 + - - -
235B ALA* 1.3 74.5 - - - +
237B VAL* 1.3 66.0 + - - +
239B ILE* 3.4 1.3 + - - +
240B ARG* 2.7 71.8 + - - +
246B VAL* 4.0 17.7 - - + +
254B LEU* 3.8 17.4 - - + +
256B LEU* 5.5 0.3 - - - +
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Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LEU* 4.6 12.5 - - + +
129B GLU 3.6 11.2 - - - +
130B PHE* 3.0 28.7 - - - +
131B GLY* 2.9 26.5 - - - +
144B GLY 3.8 14.1 - - - +
145B ARG 3.8 3.8 - - - +
146B ARG* 3.9 7.4 - - - +
233B ALA 3.6 5.4 + - - +
234B ALA 2.9 20.0 - - - +
236B THR* 1.3 78.6 - - - +
238B ILE* 1.3 67.9 + - - +
240B ARG* 3.3 5.0 + - - +
241B GLU* 2.9 26.2 + - + +
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Residues in contact with ILE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B GLY 3.8 9.6 - - - +
133B ILE* 3.0 35.2 - - + -
142B TYR* 3.8 31.6 - - + +
143B THR 4.6 2.2 - - - +
144B GLY* 3.6 23.8 - - - +
150B ALA* 3.4 24.4 - - + +
157B LEU* 4.4 9.0 - - + -
212B CYS* 4.7 5.4 - - - -
215B ALA* 3.7 20.2 - - + -
234B ALA 3.3 6.7 + - - +
235B ALA* 3.7 8.1 - - - +
236B THR 3.2 0.4 - - - -
237B VAL* 1.3 78.9 - - - +
239B ILE* 1.3 64.8 + - + +
241B GLU 3.3 6.1 + - - -
242B ALA* 3.4 3.1 + - - +
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Residues in contact with ILE 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B VAL* 4.1 3.8 - - + +
211B LEU* 3.5 41.5 - - + +
214B LEU* 3.4 36.3 - - + -
215B ALA* 4.0 15.0 - - + +
235B ALA 3.0 22.6 + - - +
236B THR 3.4 2.9 + - - +
238B ILE* 1.3 76.6 - - + +
240B ARG* 1.3 60.3 + - - +
242B ALA* 3.1 9.2 + - - +
243B GLY 3.4 0.2 + - - -
244B GLY* 2.9 44.5 + - - -
245B ILE 4.2 1.1 - - - +
246B VAL* 4.1 13.5 - - + -
263B ALA* 4.0 5.8 - - + -
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Residues in contact with ARG 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LEU* 4.3 17.8 + - - +
146B ARG* 5.9 3.6 - - - +
236B THR* 2.7 44.1 + - + +
237B VAL* 4.0 4.5 - - - +
239B ILE* 1.3 70.3 - - - +
241B GLU* 1.3 62.7 + - - +
242B ALA 2.9 10.5 + - - -
243B GLY* 3.1 12.6 + - - -
244B GLY 3.3 13.7 - - - +
245B ILE* 5.2 0.7 - - - +
246B VAL* 4.0 30.4 + - + +
254B LEU* 4.0 16.2 - - - +
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Residues in contact with GLU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ARG 3.0 32.5 - - - +
146B ARG* 3.6 8.7 + - - +
147B GLY* 2.9 25.1 + - - +
149B GLY* 3.1 37.4 + - - +
150B ALA* 2.9 21.0 + - + +
156B ARG* 5.3 2.9 + - - -
157B LEU 4.5 1.4 - - - +
237B VAL* 2.9 23.3 + - + +
238B ILE* 3.7 4.7 - - - +
239B ILE 3.3 0.2 - - - -
240B ARG* 1.3 78.3 - - + +
242B ALA* 1.3 56.6 + - - +
243B GLY 3.6 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