Contacts of the helix formed by residues 263 - 275 (chain J) 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 ALA 263 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234D LEU* 4.3 13.0 - - + -
259D THR 4.3 1.2 + - - -
262D GLY 4.9 2.7 - - - -
263D ALA* 3.4 30.5 - - + +
234J LEU* 4.2 19.7 - - + -
237J MET* 5.4 0.4 - - + -
259J THR* 5.0 6.8 + - + +
260J GLY 3.9 2.4 + - - -
262J GLY* 1.3 75.8 - - - +
264J LEU* 1.3 59.6 + - - +
265J ARG 3.3 2.7 - - - -
266J TYR* 3.3 4.3 + - - +
267J ILE* 2.9 33.8 + - + +
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Residues in contact with LEU 264 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254J VAL* 4.5 9.2 - - + -
256J VAL* 4.1 29.6 - - + +
259J THR* 4.2 18.8 - - + +
260J GLY 3.3 15.9 + - - +
261J TRP* 4.0 8.0 + - + +
262J GLY 3.7 1.2 - - - -
263J ALA* 1.3 78.4 - - - +
265J ARG* 1.3 59.5 + - - +
267J ILE* 3.3 10.7 + - + +
268J ARG* 2.8 30.2 + - + +
305J TYR* 3.5 36.8 - - + -
308J ILE* 4.1 23.6 - - + -
310J ILE* 4.6 9.9 - - + -
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Residues in contact with ARG 265 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D ASP* 4.0 38.6 + - + +
99J ALA* 4.9 13.8 + - - +
135J GLU 2.8 30.3 + - - -
136J PHE* 3.9 31.1 - - - +
137J ASP* 4.0 18.8 + - - +
261J TRP 4.9 2.2 + - - -
262J GLY 5.5 0.6 + - - -
263J ALA 3.3 0.2 - - - -
264J LEU* 1.3 78.1 - - - +
266J TYR* 1.3 58.5 + - - +
268J ARG* 3.3 2.1 + - + +
269J ASP* 2.8 53.0 + - - +
308J ILE* 4.1 29.5 - - + +
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Residues in contact with TYR 266 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D ASP* 6.1 0.6 - - - +
234D LEU* 3.5 39.6 - - + +
235D LEU* 4.2 35.9 - - + -
234J LEU* 4.0 12.8 - - + -
238J GLU* 2.7 38.8 + - + +
263J ALA 3.3 7.3 + - - +
264J LEU 3.2 0.4 - - - -
265J ARG* 1.3 79.7 - - - +
267J ILE* 1.3 60.9 + - + +
269J ASP* 3.3 8.6 + - + +
270J LEU* 2.8 50.5 + - + +
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Residues in contact with ILE 267 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230J ILE* 4.4 2.7 - - + -
234J LEU* 4.0 24.9 - - + +
237J MET* 4.1 32.8 - - + -
238J GLU* 5.3 0.7 - - + -
241J LEU* 4.2 19.5 - - + +
254J VAL* 4.2 25.6 - - + -
259J THR* 4.8 4.3 - - + -
263J ALA* 2.9 23.1 + - + +
264J LEU* 3.5 16.2 - - + +
266J TYR* 1.3 81.9 - - + +
268J ARG* 1.3 59.3 + - - +
270J LEU* 3.3 6.2 + - + +
271J ALA* 2.8 31.3 + - + +
278J ILE* 5.6 2.7 - - + -
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Residues in contact with ARG 268 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137J ASP* 3.6 26.1 + - - +
138J GLY 2.9 23.0 + - - -
140J ALA* 4.0 19.3 - - - +
264J LEU* 2.8 16.8 + - + +
265J ARG* 3.6 5.6 - - - +
267J ILE* 1.3 77.9 - - - +
269J ASP* 1.3 80.0 + - - +
271J ALA* 3.5 1.9 + - - +
272J ALA* 2.9 46.4 + - - +
278J ILE* 3.6 18.4 - - + +
308J ILE* 3.4 33.1 + - + +
309J GLY* 3.8 21.5 + - - +
310J ILE* 5.2 2.7 - - + -
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Residues in contact with ASP 269 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D LEU* 6.0 1.7 - - - +
137J ASP* 4.5 6.3 - - - +
265J ARG* 2.8 37.9 + - - +
266J TYR* 3.7 9.9 - - + +
268J ARG* 1.3 103.8 + - - +
270J LEU* 1.3 61.3 + - - +
272J ALA* 3.4 1.9 + - - +
273J ASP* 3.0 39.9 + - - +
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Residues in contact with LEU 270 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238J GLU* 3.9 32.1 - - + +
241J LEU* 3.7 20.2 - - + -
266J TYR* 2.8 39.7 + - + +
267J ILE* 3.3 6.0 + - + +
269J ASP* 1.3 73.8 - - - +
271J ALA* 1.3 65.2 + - - +
273J ASP* 3.2 14.4 + - + +
274J TYR* 3.1 55.2 + - + +
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Residues in contact with ALA 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241J LEU* 4.2 23.0 - - + +
252J ALA* 5.2 1.1 - - + -
267J ILE* 2.8 18.5 + - + +
268J ARG 3.7 2.2 - - - +
270J LEU* 1.3 75.9 - - - +
272J ALA* 1.3 61.5 + - - +
274J TYR* 3.1 5.8 + - - +
275J GLY 3.0 4.5 + - - -
276J LEU* 2.9 35.9 + - + +
278J ILE* 3.7 29.8 - - + -
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Residues in contact with ALA 272 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J ALA* 4.2 19.3 - - + -
141J PHE* 5.6 1.5 - - - -
268J ARG* 2.9 41.0 + - - +
269J ASP 3.6 4.9 - - - +
270J LEU 3.2 0.2 - - - -
271J ALA* 1.3 78.2 - - - +
273J ASP* 1.3 60.3 + - - +
275J GLY* 2.9 19.9 + - - +
276J LEU 4.3 5.1 + - - +
278J ILE* 5.3 0.6 - - + +
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Residues in contact with ASP 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269J ASP* 3.0 27.2 + - - +
270J LEU* 3.2 15.2 + - + +
272J ALA* 1.3 77.6 - - - +
274J TYR* 1.3 66.4 + - + +
275J GLY 3.5 0.3 + - - -
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Residues in contact with TYR 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238J GLU 5.0 1.3 + - - -
241J LEU* 3.9 34.5 - - + -
242J GLU* 4.0 25.7 - - + +
245J ALA* 3.5 24.8 - - + +
270J LEU* 3.1 46.3 + - + +
271J ALA 3.6 7.0 - - - +
272J ALA 3.1 0.2 - - - -
273J ASP* 1.3 80.8 - - + +
275J GLY* 1.3 61.5 + - - +
276J LEU* 3.8 18.4 - - + +
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Residues in contact with GLY 275 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141J PHE* 3.3 26.2 - - - -
149J MET* 5.6 0.5 - - - +
249J LEU 4.9 2.9 - - - +
250J LYS* 4.2 5.0 - - - +
272J ALA 2.9 16.3 + - - -
273J ASP 3.2 1.0 + - - -
274J TYR* 1.3 79.9 - - - +
276J LEU* 1.3 62.0 + - - +
277J ALA 4.0 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