Contacts of the helix formed by residues 263 - 275 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A LEU* 4.2 22.4 - - + -
259A THR 4.3 0.8 + - - -
262A GLY 5.0 1.6 - - - -
263A ALA* 3.3 33.3 - - + +
234H LEU* 4.2 10.8 - - + -
237H MET* 5.5 0.2 - - + -
259H THR* 4.8 7.5 + - + +
260H GLY 4.3 2.4 + - - -
262H GLY* 1.3 74.9 - - - +
264H LEU* 1.3 65.2 + - - +
265H ARG 3.3 2.5 - - - -
266H TYR* 3.3 4.4 + - - +
267H ILE* 3.0 27.0 + - + +
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Residues in contact with LEU 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254H VAL* 4.4 10.3 - - + -
256H VAL* 4.2 24.5 - - + +
259H THR* 4.1 20.1 - - + +
260H GLY 3.2 20.6 + - - +
261H TRP* 3.7 9.4 + - + +
262H GLY 3.6 1.4 - - - -
263H ALA* 1.3 77.9 - - - +
265H ARG* 1.3 58.3 + - - +
267H ILE* 3.2 9.6 + - + +
268H ARG* 2.9 28.7 + - + +
305H TYR* 3.6 34.1 - - + -
308H ILE* 3.8 26.7 - - + -
310H ILE* 4.6 7.6 - - + -
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Residues in contact with ARG 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ASP* 3.9 36.6 + - + +
99H ALA* 5.6 9.8 + - - +
135H GLU 3.1 27.6 + - - -
136H PHE* 3.5 32.5 - - - +
137H ASP* 3.7 21.8 + - - +
261H TRP 4.7 2.8 + - - +
262H GLY 5.9 0.2 - - - +
263H ALA 3.3 0.6 - - - -
264H LEU* 1.3 78.9 - - - +
266H TYR* 1.3 58.1 + - - +
268H ARG* 3.2 6.9 + - - +
269H ASP* 2.8 52.6 + - - +
308H ILE* 4.1 21.9 - - + +
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Residues in contact with TYR 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ASP* 6.2 0.6 - - - +
234A LEU* 3.5 39.7 - - + +
235A LEU* 3.8 33.4 - - + -
234H LEU* 4.0 12.3 - - + -
238H GLU* 2.4 41.2 + - + +
263H ALA* 3.3 8.1 + - - +
264H LEU 3.3 0.6 - - - -
265H ARG* 1.3 74.3 - - - +
267H ILE* 1.3 64.6 + - + +
269H ASP* 3.5 8.9 + - + +
270H LEU* 2.8 48.3 + - + +
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Residues in contact with ILE 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230H ILE* 4.3 13.7 - - + -
234H LEU* 3.9 25.4 - - + -
237H MET* 4.0 33.7 - - + -
238H GLU* 5.3 0.4 - - + -
241H LEU* 4.1 21.4 - - + +
254H VAL* 4.3 17.5 - - + -
259H THR* 4.9 3.6 - - + -
263H ALA 3.0 17.5 + - - +
264H LEU* 3.2 13.0 + - + +
266H TYR* 1.3 80.4 - - + +
268H ARG* 1.3 60.4 + - - +
270H LEU* 3.5 5.5 - - + +
271H ALA* 2.9 30.1 + - + +
278H ILE* 5.5 2.7 - - + -
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Residues in contact with ARG 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H ASP* 3.7 27.7 + - - +
138H GLY 2.8 25.8 + - - -
140H ALA* 3.8 22.8 - - - +
264H LEU* 2.9 14.8 + - + +
265H ARG* 3.2 9.8 + - - +
267H ILE* 1.3 77.6 - - - +
269H ASP* 1.3 79.6 + - - +
271H ALA* 3.4 1.7 + - - +
272H ALA* 2.9 43.9 + - - +
278H ILE* 3.6 24.8 - - + +
308H ILE* 3.3 32.8 + - + +
309H GLY* 3.9 13.5 + - - +
310H ILE* 5.4 2.2 - - + -
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Residues in contact with ASP 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A LEU* 6.0 2.1 - - - +
137H ASP* 4.4 6.0 - - - +
265H ARG* 2.8 41.6 + - - +
266H TYR* 3.9 8.7 - - + +
268H ARG* 1.3 101.8 + - - +
270H LEU* 1.3 57.8 + - - +
272H ALA* 3.3 5.6 - - - +
273H ASP* 3.0 38.9 + - - +
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Residues in contact with LEU 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238H GLU* 3.8 31.2 - - + +
241H LEU* 3.4 25.4 - - + -
266H TYR* 2.8 39.2 + - + +
267H ILE* 3.5 7.0 - - + +
268H ARG 3.2 0.2 - - - -
269H ASP* 1.3 73.6 - - - +
271H ALA* 1.3 65.9 + - - +
273H ASP* 3.1 23.4 + - + +
274H TYR* 3.2 45.3 + - + +
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Residues in contact with ALA 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241H LEU* 4.4 16.0 - - + +
252H ALA* 4.9 1.8 - - + -
267H ILE* 2.9 20.6 + - + +
270H LEU* 1.3 72.2 - - - +
272H ALA* 1.3 62.7 + - - +
274H TYR* 3.1 9.4 + - - +
275H GLY 3.0 5.5 + - - -
276H LEU* 2.9 48.5 + - + +
278H ILE* 3.8 22.2 - - + -
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Residues in contact with ALA 272 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140H ALA* 4.6 14.8 - - + -
141H PHE* 5.9 1.2 - - - -
268H ARG* 2.9 39.2 + - - +
269H ASP* 3.3 11.4 - - - +
270H LEU 3.2 0.2 - - - -
271H ALA* 1.3 77.3 - - - +
273H ASP* 1.3 65.8 - - - +
275H GLY* 3.0 13.7 + - - -
276H LEU 4.8 3.6 - - - +
278H ILE* 5.4 0.2 - - - +
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Residues in contact with ASP 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269H ASP* 3.0 21.8 + - - +
270H LEU* 3.1 16.6 + - + +
272H ALA* 1.3 79.3 - - - +
274H TYR* 1.3 65.2 + - + +
275H GLY* 3.4 0.5 + - - -
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Residues in contact with TYR 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238H GLU 4.9 1.8 + - - -
241H LEU* 3.9 28.7 - - + -
242H GLU* 4.0 25.8 + - + +
245H ALA* 3.3 29.7 - - + +
270H LEU* 3.2 47.9 + - + +
271H ALA 3.1 7.4 + - - +
273H ASP* 1.3 80.7 - - + +
275H GLY* 1.3 61.4 + - - +
276H LEU* 3.8 20.1 - - + +
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Residues in contact with GLY 275 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H PHE* 3.5 25.1 - - - -
249H LEU 4.9 1.9 - - - +
250H LYS* 4.3 4.5 - - - +
271H ALA 3.0 3.2 + - - -
272H ALA 3.0 13.3 + - - -
273H ASP 3.2 1.0 + - - -
274H TYR* 1.3 79.4 - - - +
276H LEU* 1.3 63.4 + - - +
277H ALA 4.1 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