Contacts of the helix formed by residues 260 - 274 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B VAL 3.1 13.5 + - - +
257B VAL 3.8 10.1 - - - -
258B ILE 3.2 1.6 - - - -
259B THR* 1.3 80.9 - - - +
261B TRP* 1.3 68.9 + - - -
262B GLY 3.3 3.0 + - - -
263B ALA 3.8 0.2 + - - -
264B LEU* 3.3 25.1 + - - +
305B TYR* 6.4 0.2 - - - -
257G VAL 5.7 0.2 - - - -
258G ILE 4.6 0.7 - - - -
260G GLY* 3.7 16.2 - - - -
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Residues in contact with TRP 261 (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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101B LEU* 4.0 9.9 - - + -
102B PRO* 4.1 18.8 - - + +
105B LEU* 3.5 26.3 - - + +
260B GLY* 1.3 73.3 - - - -
262B GLY* 1.3 66.8 + - - +
263B ALA 3.1 1.0 + - - -
264B LEU* 3.6 11.8 + - + +
265B ARG 4.6 1.4 + - - -
288B PHE* 6.4 0.2 - + - -
296B ILE* 6.6 0.2 - - + -
301B LEU* 3.7 24.2 - - + -
304B LEU* 3.6 40.4 - - + -
305B TYR* 3.6 42.8 - + - -
308B ILE* 3.9 21.6 - - + +
233G ASP* 4.3 6.9 - - - +
257G VAL 5.3 1.1 - - - -
258G ILE* 3.4 33.6 + - + +
284G MET* 4.4 14.9 - - + +
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Residues in contact with GLY 262 (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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102B PRO* 4.6 2.9 - - - -
261B TRP* 1.3 78.9 - - - +
263B ALA* 1.3 58.8 + - - +
265B ARG 5.5 0.3 + - - -
232G ALA 3.8 6.2 - - - +
233G ASP* 3.6 4.9 - - - +
234G LEU* 3.0 29.1 + - - -
237G MET* 3.9 8.7 - - - +
258G ILE 3.6 1.0 + - - -
259G THR* 2.7 37.1 + - - -
263G ALA* 4.7 0.7 - - - -
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Residues in contact with ALA 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 4.3 9.6 - - + -
237B MET* 5.4 0.4 - - + -
259B THR* 4.8 8.2 + - + +
260B GLY 3.8 2.8 + - - -
262B GLY* 1.3 75.0 - - - +
264B LEU* 1.3 66.4 + - - +
265B ARG 3.3 2.9 - - - -
266B TYR* 3.3 4.3 + - - +
267B ILE* 3.1 27.2 + - + +
234G LEU* 4.2 21.3 - - + -
259G THR 4.2 1.6 + - - -
262G GLY 5.1 0.9 - - - -
263G ALA* 3.3 30.7 - - + +
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B VAL* 4.6 7.4 - - + -
256B VAL* 4.0 25.8 - - + +
259B THR* 4.3 15.9 - - + +
260B GLY 3.3 18.8 + - - +
261B TRP* 3.6 9.8 + - + +
263B ALA* 1.3 78.1 - - - +
265B ARG* 1.3 57.2 + - - +
267B ILE* 3.4 7.9 + - + +
268B ARG* 3.0 27.4 + - - +
305B TYR* 3.4 32.5 - - + -
308B ILE* 3.3 37.9 - - + -
310B ILE* 4.3 8.7 - - + -
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Residues in contact with ARG 265 (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 ALA* 5.5 9.2 + - - +
101B LEU* 6.2 0.4 - - - +
135B GLU 2.8 25.5 + - - -
136B PHE* 3.3 41.6 - - - +
137B ASP* 4.1 16.6 + - - +
261B TRP 4.6 2.2 + - - +
262B GLY 5.5 0.6 + - - +
263B ALA 3.3 0.8 - - - -
264B LEU* 1.3 76.7 - - - +
266B TYR* 1.3 60.0 + - - +
268B ARG* 3.3 6.5 + - - +
269B ASP* 2.8 50.3 + - - +
308B ILE* 4.3 21.6 + - + +
233G ASP* 3.8 38.0 + - + +
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Residues in contact with TYR 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 4.0 15.9 - - + -
238B GLU* 2.5 39.7 + - + +
263B ALA* 3.3 7.9 + - - +
264B LEU 3.3 0.4 - - - -
265B ARG* 1.3 76.7 - - - +
267B ILE* 1.3 64.1 + - + +
269B ASP* 3.2 9.1 + - + +
270B LEU* 2.8 52.8 + - + +
234G LEU* 3.9 36.0 - - + +
235G LEU* 4.2 36.1 - - + -
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Residues in contact with ILE 267 (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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230B ILE* 4.1 22.9 - - + -
234B LEU* 3.8 18.8 - - + +
237B MET* 3.6 41.5 - - + -
238B GLU* 5.2 1.1 - - + -
241B LEU* 4.2 14.1 - - + +
254B VAL* 4.2 16.8 - - + -
259B THR* 4.9 3.1 - - + -
263B ALA 3.1 16.1 + - - +
264B LEU* 3.7 13.2 - - + +
266B TYR* 1.3 83.3 - - + +
268B ARG* 1.3 58.3 + - - +
270B LEU* 3.4 5.3 + - + +
271B ALA* 2.8 30.5 + - + +
278B ILE* 5.8 2.2 - - + -
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Residues in contact with ARG 268 (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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137B ASP* 3.3 28.8 + - - +
138B GLY 2.9 24.0 + - - -
139B PRO 4.5 0.2 - - - -
140B ALA* 4.1 17.7 - - - +
264B LEU* 3.0 18.6 + - + +
265B ARG* 3.5 6.1 - - - +
267B ILE* 1.3 77.3 - - - +
269B ASP* 1.3 87.5 + - - +
271B ALA* 3.3 2.8 + - - +
272B ALA* 3.0 44.9 + - - +
278B ILE* 3.6 26.6 - - + +
308B ILE* 3.3 36.1 + - + +
309B GLY* 4.2 7.1 + - - +
310B ILE* 5.2 2.9 - - + -
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Residues in contact with ASP 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ASP* 4.4 7.1 - - - +
265B ARG* 2.8 37.0 + - - +
266B TYR* 3.6 9.0 - - + +
268B ARG* 1.3 104.4 + - - +
270B LEU* 1.3 65.4 + - - +
272B ALA* 3.1 3.3 + - - +
273B ASP* 2.9 32.5 + - - +
235G LEU* 5.8 3.6 - - - +
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Residues in contact with LEU 270 (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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238B GLU* 4.0 29.8 - - + +
241B LEU* 3.5 22.7 - - + -
266B TYR* 2.8 43.0 + - + +
267B ILE* 3.6 6.3 - - + +
269B ASP* 1.3 73.3 - - - +
271B ALA* 1.3 62.6 + - - +
273B ASP* 3.4 11.8 + - + +
274B TYR* 3.1 60.5 + - + +
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Residues in contact with ALA 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 4.4 21.0 - - + +
252B ALA* 5.2 1.6 - - + -
267B ILE* 2.8 20.6 + - + +
268B ARG 3.5 5.2 - - - +
269B ASP 3.2 0.2 - - - -
270B LEU* 1.3 76.6 - - - +
272B ALA* 1.3 61.2 + - - +
274B TYR* 3.2 4.7 + - - +
275B GLY 3.1 3.5 + - - -
276B LEU* 2.8 38.1 + - + +
278B ILE* 3.8 27.4 - - + -
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Residues in contact with ALA 272 (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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140B ALA* 4.2 22.2 - - + -
141B PHE* 5.4 1.1 - - - -
268B ARG* 3.0 32.8 + - - +
269B ASP 3.5 7.6 - - - +
271B ALA* 1.3 72.8 - - - +
273B ASP* 1.3 60.8 + - - +
275B GLY* 2.6 26.5 + - - +
276B LEU 4.3 6.5 + - - +
278B ILE* 5.4 0.2 - - - +
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Residues in contact with ASP 273 (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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269B ASP* 2.9 19.4 + - - +
270B LEU* 3.6 16.7 - - + +
272B ALA* 1.3 77.8 - - - +
274B TYR* 1.3 65.7 + - + +
275B GLY* 3.2 1.0 + - - -
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Residues in contact with TYR 274 (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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238B GLU 5.0 1.3 + - - -
241B LEU* 3.9 28.7 - - + -
242B GLU* 3.9 29.2 - - + +
245B ALA* 3.4 31.9 - - + +
246B ASP* 6.0 0.9 - - - -
270B LEU* 3.1 51.3 + - + +
271B ALA* 3.6 7.6 - - - +
272B ALA 3.1 0.2 - - - -
273B ASP* 1.3 77.5 - - + +
275B GLY* 1.3 61.9 + - - +
276B LEU* 4.0 14.4 - - + +
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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