Contacts of the helix formed by residues 262 - 275 (chain A) in PDB entry 3LKB
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 THR 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A TYR* 3.6 29.5 - - - -
260A GLU 3.8 2.1 + - - -
261A ASP* 1.3 74.5 + - - +
263A PRO* 1.4 73.3 - - + +
264A GLY 2.8 15.5 - - - +
265A ILE* 3.3 17.9 - - + +
266A ARG* 3.0 33.6 + - - +
332A GLY* 2.5 38.8 - - - +
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Residues in contact with PRO 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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262A THR* 1.4 87.5 - - + +
264A GLY* 1.3 56.2 + - - +
266A ARG* 3.5 26.6 - - + +
267A LEU* 2.9 29.3 + - - +
330A LYS 5.9 0.9 - - - +
331A PRO 4.3 9.0 - - - +
332A GLY* 5.2 2.9 - - - -
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Residues in contact with GLY 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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262A THR* 2.8 9.5 - - - +
263A PRO* 1.3 76.9 - - - +
265A ILE* 1.3 55.2 + - - +
267A LEU* 3.1 6.0 + - - +
268A GLN 2.8 30.7 + - - -
331A PRO 3.4 19.1 + - - -
332A GLY 3.8 3.1 - - - -
333A PHE* 3.3 25.8 - - - -
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Residues in contact with ILE 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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256A TYR* 3.9 27.4 - - + +
257A MET 3.8 19.1 - - - +
258A ALA* 3.8 17.7 - - - +
260A GLU 4.1 10.1 - - - +
262A THR* 3.3 24.2 - - + +
264A GLY* 1.3 74.5 - - - +
266A ARG* 1.3 62.1 + - - +
268A GLN* 3.3 13.2 + - - +
269A LYS* 3.2 45.3 + - - +
288A THR* 3.9 26.5 - - + +
332A GLY 4.0 3.3 + - - +
333A PHE* 4.7 0.4 - - + +
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Residues in contact with ARG 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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261A ASP* 4.0 15.1 - - - +
262A THR* 3.0 40.8 + - - +
263A PRO* 3.5 30.4 - - + +
265A ILE* 1.3 76.7 - - - +
267A LEU* 1.3 57.0 + - - +
269A LYS* 3.2 9.9 + - - +
270A GLU* 3.0 27.9 + - - +
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Residues in contact with LEU 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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34A TYR* 4.1 14.4 - - + +
37A TRP* 3.5 50.9 - - + -
263A PRO 2.9 17.9 + - - +
264A GLY* 3.1 6.5 + - - +
266A ARG* 1.3 74.3 - - - +
268A GLN* 1.3 60.7 + - - +
270A GLU* 3.2 18.1 + - - +
271A ILE* 2.8 45.9 + - + +
291A MET* 4.9 0.4 - - - -
333A PHE* 4.8 11.4 - - + -
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Residues in contact with GLN 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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258A ALA* 5.6 2.5 - - - +
264A GLY 2.8 14.6 + - - +
265A ILE* 3.3 20.9 + - - +
267A LEU* 1.3 71.0 - - - +
269A LYS* 1.3 62.5 + - + +
271A ILE* 3.9 0.5 - - - +
272A GLY* 2.7 32.2 + - - -
282A ILE* 2.7 28.8 - - - +
283A GLU* 4.4 2.1 - - - -
284A SER 3.5 8.3 - - - +
287A TYR* 3.7 18.4 - - + -
288A THR* 2.6 50.2 + - - +
291A MET* 3.6 24.6 - - + -
333A PHE* 4.4 2.0 - - + -
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Residues in contact with LYS 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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258A ALA* 2.9 38.0 + - - +
265A ILE* 3.2 31.8 + - - +
266A ARG* 3.3 11.6 - - - +
267A LEU 3.2 0.2 - - - -
268A GLN* 1.3 81.2 - - + +
270A GLU* 1.3 59.4 + - - +
272A GLY* 3.2 1.2 + - - -
273A ARG* 2.9 33.9 + - - +
282A ILE* 3.4 34.0 - - + +
283A GLU* 5.4 1.3 - - - +
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Residues in contact with GLU 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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37A TRP* 4.6 12.2 + - - +
41A ARG* 6.0 0.2 - - - -
266A ARG 3.0 12.9 + - - +
267A LEU* 3.2 26.2 + - + +
269A LYS* 1.3 76.7 - - - +
271A ILE* 1.3 59.5 + - + +
273A ARG* 3.3 12.3 - - + +
274A LYS* 3.0 36.8 + - + +
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Residues in contact with ILE 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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33A ASP* 3.7 29.8 - - + +
34A TYR* 4.0 16.6 - - + -
37A TRP* 3.5 52.3 - - + +
267A LEU* 2.8 39.8 + - + +
268A GLN 3.9 2.2 - - - +
270A GLU* 1.3 69.4 - - - +
272A GLY* 1.3 68.6 + - - +
274A LYS* 3.2 8.3 + - - +
275A TYR* 3.2 32.2 + - + -
287A TYR* 3.9 4.0 - - - +
291A MET* 4.2 10.5 - - + -
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Residues in contact with GLY 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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268A GLN 2.7 20.2 + - - -
269A LYS 3.6 0.4 - - - -
271A ILE* 1.3 76.2 - - - +
273A ARG* 1.3 60.9 + - - +
275A TYR 3.5 0.7 + - - -
276A GLY 3.4 1.9 + - - -
277A ARG* 3.1 27.6 + - - +
282A ILE* 3.0 28.0 - - - -
287A TYR* 3.6 12.1 + - - -
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Residues in contact with ARG 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 LYS 2.9 19.1 + - - +
270A GLU* 3.3 18.4 - - - +
272A GLY* 1.3 69.4 - - - +
274A LYS* 1.3 86.0 + - - +
276A GLY* 2.8 17.7 + - - +
277A ARG 5.0 1.6 - - - +
279A GLU* 6.1 0.4 - - - +
282A ILE* 4.0 4.6 - - + +
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Residues in contact with LYS 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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37A TRP* 5.0 12.8 - - + +
40A GLU* 3.6 34.4 + - - -
41A ARG* 6.3 1.3 - - - +
270A GLU* 3.0 25.1 + - + +
271A ILE* 3.2 10.7 + - - +
273A ARG* 1.3 87.2 - - - +
275A TYR* 1.3 79.5 + - + +
276A GLY 3.5 1.6 + - - -
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Residues in contact with TYR 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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33A ASP* 3.5 50.5 - - - +
36A LYS* 3.4 21.4 - - + -
37A TRP* 3.2 27.2 + + + +
40A GLU* 3.2 34.3 - - - +
271A ILE* 3.2 32.2 + - + +
272A GLY 4.7 0.2 - - - +
273A ARG 3.2 0.6 - - - -
274A LYS* 1.3 97.0 - - + +
276A GLY* 1.3 61.6 + - - +
277A ARG* 3.4 10.2 + - + +
62B ASN* 3.8 18.0 + - - +
65B ARG* 5.0 17.3 + - - +
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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