Contacts of the helix formed by residues 233 - 247 (chain G) in PDB entry 3KDO
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 233 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B ALA 2.9 28.1 - - - +
100B ASN* 4.1 4.2 + - - -
101B LEU* 4.3 3.6 + - - +
102B PRO* 3.8 18.7 - - - +
261B TRP 4.3 6.1 - - - +
262B GLY 3.8 3.9 - - - +
265B ARG* 3.8 39.7 + - + +
232G ALA* 1.3 81.7 - - - +
234G LEU* 1.3 67.4 + - - +
235G LEU 3.3 0.7 - - - +
236G GLU* 3.1 21.0 + - - +
237G MET* 3.1 15.8 + - - +
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Residues in contact with LEU 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B LEU* 3.1 33.2 - - + -
262B GLY 3.0 17.5 + - - +
263B ALA* 4.2 10.5 - - + +
265B ARG* 6.3 0.2 - - - +
266B TYR* 3.9 35.9 - - + +
233G ASP* 1.3 72.5 - - - +
235G LEU* 1.3 65.2 + - + +
237G MET* 3.3 10.4 + - + +
238G GLU* 3.1 27.3 + - + +
263G ALA* 4.5 6.3 - - + -
266G TYR* 4.1 13.9 - - + -
267G ILE* 3.6 30.5 - - + -
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Residues in contact with LEU 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B TYR* 4.2 36.1 - - + -
269B ASP* 5.8 3.6 - - - +
233G ASP* 3.3 1.6 - - + +
234G LEU* 1.3 79.1 - - + +
236G GLU* 1.3 70.4 + - - +
238G GLU* 3.4 25.8 + - - +
239G GLN* 3.2 33.2 + - - +
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Residues in contact with GLU 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLU* 4.8 3.8 - - - +
99B ALA* 5.2 5.9 - - - +
100B ASN* 6.6 0.2 - - + -
232G ALA* 3.6 17.5 - - + -
233G ASP* 3.1 30.2 + - - +
235G LEU* 1.3 80.8 + - - +
237G MET* 1.3 67.2 + - - +
239G GLN* 3.2 18.8 + - - +
240G ARG* 3.0 50.0 + - - +
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Residues in contact with MET 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B GLY* 3.9 17.0 - - - +
230G ILE* 3.2 42.7 - - + +
231G THR* 4.2 4.0 - - - -
232G ALA 3.3 34.8 - - - +
233G ASP 3.1 2.9 + - - +
234G LEU* 3.3 16.4 + - + +
236G GLU* 1.3 75.1 - - - +
238G GLU* 1.3 63.2 + - - +
240G ARG* 3.3 3.4 + - - +
241G LEU* 3.0 29.8 + - - +
254G VAL* 5.1 2.7 - - - -
259G THR* 4.0 33.2 - - + -
263G ALA* 5.2 0.7 - - + -
267G ILE* 4.2 22.0 - - + -
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Residues in contact with GLU 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234G LEU* 3.1 21.1 + - + +
235G LEU* 3.5 29.5 - - - +
236G GLU 3.2 0.2 - - - -
237G MET* 1.3 76.1 - - - +
239G GLN* 1.3 63.2 + - + +
241G LEU* 3.2 4.9 + - - +
242G GLU* 3.1 21.7 + - - +
266G TYR* 2.3 42.3 + - + -
267G ILE* 5.2 1.1 - - + -
270G LEU* 4.0 24.0 - - + +
274G TYR* 5.0 2.9 + - - -
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Residues in contact with GLN 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235G LEU* 3.2 23.1 + - - +
236G GLU* 3.2 19.6 + - - +
238G GLU* 1.3 77.0 - - + +
240G ARG* 1.3 60.5 + - + +
242G GLU* 3.3 13.7 + - - +
243G VAL* 3.0 32.0 + - + +
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Residues in contact with ARG 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLU* 2.7 41.6 + - - -
195G THR* 4.2 4.2 - - - +
196G SER* 3.6 23.8 + - - +
202G PHE* 3.5 45.3 - - + +
229G ASN 4.9 0.8 + - - -
230G ILE* 3.9 22.0 + - + +
231G THR 3.9 6.9 + - - -
232G ALA* 3.8 13.5 - - - +
236G GLU* 3.0 43.4 + - - +
237G MET 3.8 4.0 - - - +
238G GLU 3.2 0.4 - - - -
239G GLN* 1.3 78.1 - - + +
241G LEU* 1.3 63.4 + - - +
243G VAL* 3.5 3.7 + - + -
244G LEU* 3.1 28.9 + - - +
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Residues in contact with LEU 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230G ILE* 3.7 22.0 - - + -
237G MET 3.0 18.1 + - - +
238G GLU 3.2 6.5 + - - +
240G ARG* 1.3 75.9 - - - +
242G GLU* 1.3 58.6 + - - +
244G LEU* 3.3 5.9 + - + +
245G ALA* 3.0 27.4 + - - +
252G ALA* 3.7 30.5 - - + -
267G ILE* 4.2 19.5 - - + +
270G LEU* 3.7 35.4 - - + -
271G ALA* 4.3 11.7 - - + +
274G TYR* 3.8 14.0 - - + -
276G LEU* 3.9 14.5 - - + +
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Residues in contact with GLU 242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238G GLU 3.1 11.9 + - - +
239G GLN* 3.5 14.8 - - - +
241G LEU* 1.3 74.9 - - - +
243G VAL* 1.3 60.7 + - + +
245G ALA* 3.2 1.8 + - - +
246G ASP* 2.8 54.3 + - - +
274G TYR* 4.0 25.0 + - + +
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Residues in contact with VAL 243 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202G PHE* 4.1 10.3 - - + -
203G GLU* 4.4 20.2 - - + -
206G ALA* 4.0 15.9 - - + -
239G GLN* 3.0 22.7 + - + +
240G ARG* 3.6 11.4 - - + +
242G GLU* 1.3 76.2 - - + +
244G LEU* 1.3 62.5 + - - +
246G ASP* 3.4 6.7 + - - +
247G LEU* 3.1 42.1 + - + +
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Residues in contact with LEU 244 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202G PHE* 3.6 14.4 - - + -
206G ALA* 4.7 1.1 - - + -
226G TRP* 3.6 18.8 - - + -
228G ALA* 3.7 8.3 - - + -
230G ILE* 4.2 9.0 - - + -
240G ARG 3.1 14.9 + - - +
241G LEU* 3.5 7.2 - - - +
242G GLU 3.2 0.2 - - - -
243G VAL* 1.3 79.7 - - - +
245G ALA* 1.3 61.6 + - - +
247G LEU* 3.4 1.0 + - - -
248G GLY 3.2 2.8 + - - -
249G LEU* 2.9 61.1 + - + +
251G HIS 3.3 22.4 - - - +
252G ALA* 3.7 22.4 - - + -
276G LEU* 3.9 12.3 - - + -
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Residues in contact with ALA 245 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241G LEU 3.0 13.2 + - - +
242G GLU 3.2 4.5 + - - +
244G LEU* 1.3 76.5 - - - +
246G ASP* 1.3 61.8 + - - +
248G GLY* 2.8 22.4 + - - -
249G LEU 5.0 0.7 - - - +
274G TYR* 3.5 46.4 - - + +
276G LEU* 4.5 6.7 - - - +
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Residues in contact with ASP 246 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242G GLU* 2.8 43.9 + - - +
243G VAL* 3.8 6.9 + - - +
245G ALA* 1.3 75.4 - - - +
247G LEU* 1.3 63.3 + - + +
248G GLY 3.3 1.0 + - - -
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Residues in contact with LEU 247 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206G ALA* 3.6 42.8 - - + +
207G GLU* 3.4 33.7 - - + +
210G ALA* 4.2 20.1 - - + +
243G VAL* 3.1 25.5 + - + +
244G LEU 4.0 3.6 - - - +
245G ALA 3.2 0.2 - - - -
246G ASP* 1.3 77.4 - - + +
248G GLY* 1.3 63.3 + - - +
249G LEU* 3.5 14.5 + - + +
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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