Contacts of the helix formed by residues 260 - 275 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A VAL 3.1 10.3 + - - -
257A VAL 4.0 8.7 - - - -
258A ILE 3.2 1.6 - - - -
259A THR* 1.3 82.2 - - - +
261A TRP* 1.3 66.7 + - - -
262A GLY 3.2 3.5 + - - -
263A ALA 4.0 0.4 + - - -
264A LEU* 3.2 28.3 + - - +
258H ILE 4.5 0.2 - - - -
260H GLY* 3.6 17.5 - - - -
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Residues in contact with TRP 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 3.8 17.9 - - + -
102A PRO* 3.8 19.5 - - + +
105A LEU* 3.4 32.2 - - + +
260A GLY* 1.3 74.5 - - - -
262A GLY* 1.3 64.1 + - - +
263A ALA 3.4 0.6 + - - -
264A LEU* 3.9 10.9 + - + +
265A ARG 4.8 1.9 + - - -
288A PHE* 6.6 0.2 - + - -
301A LEU* 4.2 19.7 - - + -
304A LEU* 3.8 31.4 - - + -
305A TYR* 3.5 45.8 - + - -
308A ILE* 3.9 18.8 - - + -
233H ASP* 4.3 6.2 - - - +
257H VAL 5.4 1.3 - - - -
258H ILE* 3.3 33.0 + - + +
284H MET* 4.6 15.0 - - + +
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Residues in contact with GLY 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A PRO* 4.8 3.4 - - - -
260A GLY 3.2 0.2 - - - -
261A TRP* 1.3 81.0 - - - +
263A ALA* 1.3 58.0 + - - +
265A ARG* 5.4 0.9 + - - +
232H ALA 4.5 4.5 - - - -
233H ASP* 3.6 4.2 - - - +
234H LEU* 2.9 30.1 + - - -
237H MET* 3.9 9.8 - - - +
258H ILE 3.7 0.4 + - - -
259H THR* 2.9 35.8 + - - -
263H ALA* 5.0 0.9 - - - -
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Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A LEU* 4.2 17.5 - - + -
237A MET* 5.5 0.2 - - + -
259A THR* 4.8 7.5 + - + +
260A GLY 4.0 2.0 + - - -
262A GLY* 1.3 75.0 - - - +
264A LEU* 1.3 59.9 + - - +
265A ARG 3.3 2.5 - - - -
266A TYR* 3.3 4.6 + - - +
267A ILE* 3.0 33.8 + - + +
234H LEU* 4.3 14.1 - - + +
259H THR 4.3 1.8 + - - -
262H GLY 5.1 0.7 - - - -
263H ALA* 3.3 32.5 - - + +
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A VAL* 4.5 8.1 - - + -
256A VAL* 4.0 26.7 - - + +
259A THR* 4.1 18.6 - - + +
260A GLY 3.2 18.8 + - - +
261A TRP* 3.9 10.5 + - + +
262A GLY 3.7 1.4 - - - -
263A ALA* 1.3 78.4 - - - +
265A ARG* 1.3 57.5 + - - +
267A ILE* 3.3 8.9 + - + +
268A ARG* 2.9 30.2 + - + +
305A TYR* 3.3 39.0 - - + -
308A ILE* 3.8 23.1 - - + -
310A ILE* 4.7 8.3 - - + -
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Residues in contact with ARG 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ALA* 5.2 12.3 + - - +
135A GLU 2.9 30.3 + - - -
136A PHE* 3.3 34.1 - - - +
137A ASP* 3.9 20.1 + - - +
261A TRP 4.8 2.9 + - - +
262A GLY 6.0 0.4 - - - +
263A ALA* 3.3 1.0 - - - -
264A LEU* 1.3 77.1 - - - +
266A TYR* 1.3 57.7 + - - +
268A ARG* 3.3 7.6 + - + +
269A ASP* 2.8 51.8 + - - +
308A ILE* 4.4 18.9 - - + +
233H ASP* 3.9 35.1 + - + +
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Residues in contact with TYR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A LEU* 3.9 17.9 - - + -
238A GLU* 2.5 39.5 + - + -
263A ALA 3.3 8.8 + - - +
265A ARG* 1.3 79.5 - - - +
267A ILE* 1.3 61.4 + - + +
269A ASP* 3.2 8.8 + - + +
270A LEU* 2.8 51.4 + - + +
234H LEU* 3.6 34.0 - - + +
235H LEU* 4.1 29.4 - - + -
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Residues in contact with ILE 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ILE* 4.3 9.4 - - + -
234A LEU* 4.1 16.4 - - + -
237A MET* 4.0 40.6 - - + -
238A GLU* 5.4 0.9 - - + +
241A LEU* 4.3 12.9 - - + +
254A VAL* 4.0 29.8 - - + -
259A THR* 4.7 5.2 - - + -
263A ALA* 3.0 22.9 + - + +
264A LEU* 3.5 12.3 - - + +
266A TYR* 1.3 80.2 - - + +
268A ARG* 1.3 59.5 + - - +
270A LEU* 3.4 5.0 + - + +
271A ALA* 2.9 30.6 + - + +
278A ILE* 5.6 2.7 - - + -
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Residues in contact with ARG 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ASP* 3.4 26.0 + - - +
138A GLY 3.0 24.5 + - - -
140A ALA* 4.1 16.3 - - - +
264A LEU* 2.9 17.2 + - + +
265A ARG* 3.6 5.2 - - - +
267A ILE* 1.3 78.0 - - - +
269A ASP* 1.3 80.7 + - - +
271A ALA* 3.4 2.1 + - - +
272A ALA* 2.9 48.8 + - - +
278A ILE* 3.6 26.3 - - + +
308A ILE* 3.2 37.0 + - + +
309A GLY* 4.0 10.8 + - - +
310A ILE* 5.3 2.9 - - + -
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Residues in contact with ASP 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ASP* 4.7 6.2 - - - +
265A ARG* 2.8 42.4 + - - +
266A TYR* 3.6 9.0 - - + +
268A ARG* 1.3 101.1 + - - +
270A LEU* 1.3 57.0 + - - +
272A ALA* 3.2 2.3 + - - +
273A ASP* 2.9 38.8 + - - +
235H LEU* 5.9 2.8 - - - +
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Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A GLU* 4.2 28.3 - - + +
241A LEU* 3.6 21.1 - - + -
266A TYR* 2.8 43.2 + - + +
267A ILE* 3.7 5.6 - - + +
269A ASP* 1.3 74.2 - - - +
271A ALA* 1.3 62.2 + - - +
273A ASP* 3.2 16.1 + - + +
274A TYR* 3.0 59.5 + - + +
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Residues in contact with ALA 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A LEU* 4.3 19.0 - - + +
252A ALA* 4.9 2.0 - - + -
267A ILE* 2.9 19.1 + - + +
268A ARG 3.8 3.6 - - - +
270A LEU* 1.3 75.8 - - - +
272A ALA* 1.3 62.3 + - - +
274A TYR* 3.1 10.5 + - - +
275A GLY 3.0 4.9 + - - -
276A LEU* 2.9 37.6 + - + +
278A ILE* 3.9 24.2 - - + -
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ALA* 4.5 14.6 - - + -
141A PHE* 6.0 1.1 - - - -
268A ARG* 2.9 46.6 + - - +
269A ASP 3.5 4.3 - - - +
271A ALA* 1.3 76.4 - - - +
273A ASP* 1.3 65.5 + - - +
275A GLY* 3.1 13.2 + - - -
276A LEU 4.5 5.6 + - - +
278A ILE* 5.3 0.8 - - + +
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Residues in contact with ASP 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ASP* 2.9 23.0 + - - +
270A LEU* 3.2 18.0 + - + +
272A ALA* 1.3 81.2 - - - +
274A TYR* 1.3 62.4 + - + +
275A GLY* 3.1 1.1 + - - -
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Residues in contact with TYR 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A GLU 4.8 1.6 + - - -
241A LEU* 3.9 25.6 - - + -
242A GLU* 3.8 29.1 + - + +
245A ALA* 3.2 32.6 - - + +
246A ASP* 5.9 0.7 - - - -
270A LEU* 3.0 54.6 + - + +
271A ALA* 3.1 8.7 + - - +
273A ASP* 1.3 77.4 - - + +
275A GLY* 1.3 60.7 + - - +
276A LEU* 3.8 17.4 - - + +
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Residues in contact with GLY 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A PHE* 3.5 23.5 - - - -
249A LEU 4.9 2.8 - - - +
250A LYS* 4.6 4.2 - - - +
271A ALA 3.0 2.4 + - - -
272A ALA 3.1 14.0 + - - -
273A ASP 3.1 1.2 - - - -
274A TYR* 1.3 80.8 - - - +
276A LEU* 1.3 63.9 + - - +
277A 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