Contacts of the helix formed by residues 260 - 275 (chain C) 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 GLY 260 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256C VAL 3.1 10.5 + - - -
257C VAL 3.4 9.6 + - - -
258C ILE 3.3 1.4 - - - -
259C THR* 1.3 83.7 - - - +
261C TRP* 1.3 69.6 + - - -
262C GLY 3.3 3.1 + - - -
264C LEU* 3.3 24.6 + - - +
257F VAL 5.8 0.2 - - - -
258F ILE 4.6 0.4 - - - -
260F GLY* 3.6 16.4 - - - -
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Residues in contact with TRP 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C LEU* 4.0 10.8 - - + -
102C PRO* 3.9 23.2 - - + +
105C LEU* 3.6 24.2 - - + +
260C GLY* 1.3 73.9 - - - -
262C GLY* 1.3 66.4 + - - +
263C ALA 3.3 0.7 + - - -
264C LEU* 3.7 11.2 + - + +
265C ARG* 4.7 0.9 + - - +
288C PHE* 6.4 1.1 - + - -
301C LEU* 4.2 18.4 - - + -
304C LEU* 3.8 35.2 - - + -
305C TYR* 3.5 48.2 - + - -
308C ILE* 3.9 21.4 - - + +
233F ASP* 4.0 7.6 - - - +
257F VAL 5.4 0.7 - - - -
258F ILE* 3.3 35.0 + - + +
284F MET* 4.3 17.7 - - + +
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Residues in contact with GLY 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C PRO* 4.6 2.7 - - - -
261C TRP* 1.3 81.7 - - - +
263C ALA* 1.3 57.3 + - - +
265C ARG 5.4 0.2 + - - -
266C TYR 5.7 0.2 + - - -
232F ALA 4.2 13.0 - - - -
233F ASP* 3.6 3.3 - - - +
234F LEU* 2.9 30.8 + - - -
237F MET* 4.2 9.9 - - - -
258F ILE 3.7 0.6 + - - -
259F THR* 2.8 29.4 + - - +
263F ALA* 4.9 1.1 - - - -
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Residues in contact with ALA 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C LEU* 4.2 17.5 - - + -
237C MET* 5.3 0.2 - - + -
259C THR* 4.8 7.2 - - + +
260C GLY 3.9 2.2 + - - -
262C GLY* 1.3 75.8 - - - +
264C LEU* 1.3 66.4 + - - +
265C ARG 3.4 2.2 - - - -
266C TYR* 3.2 5.9 + - - +
267C ILE* 3.0 28.1 + - + +
234F LEU* 4.4 10.5 - - + -
259F THR 4.1 2.0 + - - -
262F GLY 4.8 2.9 - - - -
263F ALA* 3.4 33.2 - - + +
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Residues in contact with LEU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C VAL* 4.4 6.3 - - + -
256C VAL* 4.0 25.4 - - + +
259C THR* 3.8 24.7 - - + -
260C GLY 3.3 16.3 + - - +
261C TRP* 3.7 8.6 + - + +
262C GLY 3.7 1.2 - - - -
263C ALA* 1.3 77.5 - - - +
265C ARG* 1.3 58.9 + - - +
267C ILE* 3.2 8.6 + - + +
268C ARG* 2.8 30.3 + - - +
305C TYR* 3.3 40.6 - - + -
308C ILE* 3.7 25.4 - - + -
310C ILE* 4.6 8.5 - - + -
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Residues in contact with ARG 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C ALA* 4.7 15.2 - - - +
135C GLU* 2.9 29.5 + - - +
136C PHE* 3.9 30.8 - - - +
137C ASP* 3.8 22.8 + - - +
261C TRP 4.7 2.4 + - - -
263C ALA 3.4 0.4 - - - -
264C LEU* 1.3 78.1 - - - +
266C TYR* 1.3 58.0 + - - +
268C ARG* 3.2 9.9 + - + +
269C ASP* 2.8 45.7 + - - +
308C ILE* 4.2 21.8 + - + +
233F ASP* 3.7 36.5 + - + +
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Residues in contact with TYR 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C LEU* 4.0 11.4 - - + -
238C GLU* 2.4 41.0 + - + +
262C GLY 5.7 0.2 + - - -
263C ALA* 3.2 8.3 + - - +
265C ARG* 1.3 78.5 - - - +
267C ILE* 1.3 61.4 + - + +
269C ASP* 3.2 9.3 + - + +
270C LEU* 2.8 50.6 + - + +
233F ASP* 6.1 0.6 - - - +
234F LEU* 3.5 37.2 - - + +
235F LEU* 3.8 34.1 - - + +
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Residues in contact with ILE 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C ILE* 4.3 3.4 - - + -
234C LEU* 3.9 17.9 - - + -
237C MET* 3.9 38.8 - - + -
238C GLU* 5.2 2.5 - - + -
241C LEU* 4.2 20.5 - - + +
254C VAL* 4.2 28.5 - - + -
259C THR* 4.8 4.5 - - + -
263C ALA* 3.0 18.7 + - + +
264C LEU* 3.5 10.8 - - + +
266C TYR* 1.3 81.5 - - + +
268C ARG* 1.3 58.0 + - - +
270C LEU* 3.2 5.2 + - - +
271C ALA* 2.9 29.6 + - + +
278C ILE* 5.9 2.5 - - + -
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Residues in contact with ARG 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ASP* 3.6 23.1 + - - +
138C GLY 2.8 25.8 + - - -
139C PRO 4.3 0.2 - - - -
140C ALA* 4.0 20.4 - - - +
264C LEU 2.8 13.3 + - - +
265C ARG* 3.3 13.7 - - - +
267C ILE* 1.3 78.9 - - - +
269C ASP* 1.3 79.2 + - - +
271C ALA* 3.8 1.6 - - - +
272C ALA* 3.0 49.2 + - - +
278C ILE* 3.7 27.6 - - + +
308C ILE* 3.2 32.3 + - + +
309C GLY* 3.9 10.2 + - - +
310C ILE* 5.3 2.9 - - + -
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Residues in contact with ASP 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ASP* 4.4 7.7 - - - +
265C ARG* 2.8 39.1 + - - +
266C TYR* 3.7 9.6 - - + +
268C ARG* 1.3 99.4 + - - +
270C LEU* 1.3 65.3 + - - +
272C ALA* 3.7 1.1 - - - +
273C ASP* 3.1 34.8 + - - +
235F LEU* 6.1 0.2 - - - +
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Residues in contact with LEU 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C GLU* 3.8 31.2 - - + -
241C LEU* 3.4 22.9 - - + -
266C TYR* 2.8 38.7 + - + +
267C ILE* 3.5 6.1 - - + +
269C ASP* 1.3 74.8 - - - +
271C ALA* 1.3 65.8 + - - +
273C ASP* 3.3 11.7 + - + +
274C TYR* 3.0 60.4 + - + +
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Residues in contact with ALA 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C LEU* 4.4 15.8 - - + +
252C ALA* 4.9 2.2 - - + -
267C ILE* 2.9 17.6 + - + +
268C ARG 3.8 3.8 - - - +
270C LEU* 1.3 74.0 - - - +
272C ALA* 1.3 66.0 + - - +
274C TYR* 3.0 10.5 + - - +
275C GLY 2.9 17.8 + - - -
276C LEU* 2.9 33.1 + - + +
278C ILE* 3.8 18.2 - - + -
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Residues in contact with ALA 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C ALA* 4.3 18.3 - - + +
141C PHE* 5.8 1.5 - - - -
268C ARG* 3.0 43.2 + - - +
269C ASP* 3.7 3.8 - - - +
271C ALA* 1.3 75.6 - - - +
273C ASP* 1.3 59.8 + - - +
275C GLY* 2.9 19.8 + - - +
276C LEU 4.3 5.6 + - - +
278C ILE* 5.2 1.0 - - + +
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Residues in contact with ASP 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C ASP* 3.1 27.4 + - - +
270C LEU* 3.6 13.1 - - + +
272C ALA* 1.3 77.9 - - - +
274C TYR* 1.3 64.9 + - + +
275C GLY 3.4 0.3 + - - -
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Residues in contact with TYR 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C GLU 4.8 2.0 + - - -
241C LEU* 3.9 26.2 - - + -
242C GLU* 3.8 26.5 + - + +
245C ALA* 3.4 30.8 - - + +
246C ASP* 6.1 0.2 - - - -
270C LEU* 3.0 52.9 + - + +
271C ALA 3.0 8.1 + - - +
273C ASP* 1.3 79.3 - - + +
275C GLY* 1.3 61.4 + - - +
276C LEU* 3.7 21.1 - - + +
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Residues in contact with GLY 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C PHE* 3.6 22.7 - - - -
249C LEU 4.9 2.9 - - - +
250C LYS* 4.4 4.0 - - - +
271C ALA 2.9 2.4 + - - -
272C ALA 2.9 13.7 + - - -
273C ASP 3.2 1.2 - - - -
274C TYR* 1.3 82.0 - - - +
276C LEU* 1.3 63.3 + - - +
277C ALA 4.2 0.2 + - - -
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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