Contacts of the helix formed by residues 266 - 278 (chain A) in PDB entry 4LBD
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 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A LEU 3.0 16.4 + - - +
263A LEU 3.7 0.2 - - - -
265A ALA* 1.3 75.5 - - - +
267A CYS* 1.3 64.3 + - - +
268A LEU 3.4 2.2 - - - -
269A ASP* 3.3 11.0 + - + +
270A ILE* 3.1 29.1 + - + +
335A CYS 3.5 27.4 - - - +
336A LEU* 3.9 16.4 - - + +
341A ARG* 3.6 9.0 - - - +
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Residues in contact with CYS 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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238A ILE* 3.7 35.2 - - - -
241A ILE* 3.9 24.9 - - + +
242A VAL* 5.9 0.2 - - - -
263A LEU* 2.8 21.8 + - - +
264A LYS* 4.0 1.0 + - - -
265A ALA 3.6 1.0 - - - -
266A ALA* 1.3 74.4 - - - +
268A LEU* 1.3 60.9 + - - +
270A ILE* 3.3 9.2 + - - +
271A LEU* 2.9 28.3 + - - +
415A MET* 3.7 27.1 - - + -
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Residues in contact with LEU 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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1A 961 4.1 30.7 - - + -
264A LYS 5.1 0.6 + - - -
265A ALA 5.1 1.6 + - - +
266A ALA 3.4 0.2 - - - -
267A CYS* 1.3 78.3 - - - +
269A ASP* 1.3 54.0 + - - +
271A LEU* 3.1 6.7 + - + +
272A MET* 2.8 59.3 + - + +
390A SER* 3.2 37.5 - - - +
393A GLY* 4.0 5.2 - - - +
394A ALA* 3.7 20.9 - - + +
415A MET* 3.7 23.6 - - + +
416A LEU* 4.8 5.8 - - + -
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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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265A ALA 4.0 10.8 - - - +
266A ALA* 3.3 18.6 + - + +
267A CYS 3.2 0.4 - - - -
268A LEU* 1.3 78.4 - - - +
270A ILE* 1.3 64.0 + - + +
272A MET* 3.2 0.6 + - - -
273A LEU* 3.0 18.7 + - - +
335A CYS* 4.9 8.8 - - + -
341A ARG* 5.0 7.9 + - - -
383A ILE* 4.5 2.9 - - - +
386A LEU* 3.4 25.4 - - + +
387A ARG* 3.3 32.0 + - - +
390A SER* 2.8 32.9 + - - -
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Residues in contact with ILE 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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241A ILE* 3.6 37.7 - - + -
244A PHE* 5.4 8.1 - - + -
266A ALA* 3.1 18.5 + - + +
267A CYS 3.8 3.1 - - - +
269A ASP* 1.3 75.5 - - - +
271A LEU* 1.3 53.8 + - - +
273A LEU* 3.2 7.3 + - - +
274A ARG* 2.7 53.5 + - + +
332A SER* 3.9 41.5 - - - +
335A CYS* 4.7 7.9 - - + -
336A LEU* 4.0 27.8 - - + -
386A LEU* 5.6 0.2 - - - -
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Residues in contact with LEU 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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1A 961 3.1 58.3 + - + +
234A ALA* 4.5 3.8 - - + +
237A CYS* 3.5 33.2 - - + -
238A ILE* 3.9 13.9 - - + -
241A ILE* 3.5 21.3 - - + -
267A CYS 2.9 10.6 + - - +
268A LEU* 3.2 11.7 - - + +
270A ILE* 1.3 77.4 - - - +
272A MET* 1.3 60.3 + - - +
274A ARG* 3.4 2.0 + - - -
275A ILE* 3.2 14.6 + - - +
415A MET* 3.6 33.4 - - + -
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Residues in contact with MET 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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1A 961 2.9 42.0 - - + +
268A LEU* 2.8 34.8 + - + +
269A ASP 3.5 4.9 - - - +
271A LEU* 1.3 71.4 - - - +
273A LEU* 1.3 63.7 + - - +
275A ILE* 3.6 2.7 - - - +
276A CYS* 3.2 31.4 + - - -
307A LEU* 4.2 7.0 - - + -
311A VAL* 4.4 15.5 - - + -
314A PHE* 5.7 0.2 - - + -
386A LEU* 3.9 13.2 - - + -
389A ILE* 3.6 36.6 - - + +
390A SER* 4.0 11.9 - - - +
393A GLY* 3.9 18.8 - - - -
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Residues in contact with LEU 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 3.0 12.7 + - - +
270A ILE* 3.6 7.9 - - - +
272A MET* 1.3 76.5 - - - +
274A ARG* 1.3 63.4 + - + +
276A CYS* 3.3 4.5 + - - +
277A THR* 3.1 38.7 + - + +
314A PHE* 5.0 2.5 - - + -
318A LEU* 4.3 23.8 - - + -
323A MET* 5.5 5.2 - - + -
328A THR* 4.2 18.4 - - + +
331A LEU* 3.8 30.5 - - + -
332A SER* 3.3 28.5 - - - +
335A CYS* 5.5 0.9 - - - -
382A LYS* 6.4 1.1 - - + -
386A LEU* 3.6 21.5 - - + +
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Residues in contact with ARG 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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1A 961 4.0 5.6 - - + -
197A HIS* 4.1 16.0 + - + -
200A THR* 2.9 46.7 + - - -
201A PHE* 3.1 53.9 - - + +
237A CYS* 3.7 20.9 - - - -
240A LYS* 3.8 15.2 + - - +
241A ILE* 3.9 12.5 - - - +
244A PHE* 4.2 15.0 - - - +
270A ILE* 2.7 39.3 + - + +
271A LEU 3.6 5.4 - - - +
272A MET 3.2 0.4 - - - -
273A LEU* 1.3 70.3 - - + +
275A ILE* 1.3 65.5 + - - +
277A THR* 2.8 23.6 + - - -
278A ARG* 3.6 2.8 - - - +
328A THR* 5.9 2.2 - - + -
332A SER* 5.4 2.6 + - - +
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Residues in contact with ILE 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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1A 961 3.5 47.5 - - + +
271A LEU 3.2 2.9 + - - +
272A MET* 3.6 11.2 - - - +
274A ARG* 1.3 79.3 - - - +
276A CYS* 1.3 70.3 + - - +
278A ARG* 3.1 17.7 + - + +
286A MET* 3.7 31.9 - - + +
287A THR 3.6 26.0 - - - +
288A PHE* 3.6 32.3 - - + -
299A MET* 4.3 6.3 - - + -
304A PHE* 5.0 2.0 - - + -
311A VAL* 4.8 6.5 - - + -
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Residues in contact with CYS 276 (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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272A MET* 3.2 25.2 + - - +
273A LEU 3.7 4.3 - - - +
274A ARG 3.1 0.8 - - - -
275A ILE* 1.3 76.0 - - - +
277A THR* 1.3 59.6 + - - +
278A ARG 3.0 6.3 + - - -
279A TYR* 3.4 17.8 + - - +
286A MET* 4.6 0.7 - - - -
311A VAL* 3.9 24.7 - - - -
314A PHE* 3.6 26.7 - - + -
315A ALA* 3.6 31.8 - - + +
318A LEU* 4.0 15.7 - - + +
319A LEU* 5.9 1.0 - - - +
389A ILE* 6.5 0.7 - - - -
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Residues in contact with THR 277 (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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201A PHE* 3.3 19.8 - - - -
204A LEU* 4.2 13.2 - - - +
273A LEU* 3.1 19.5 + - + +
274A ARG 2.8 17.7 + - - -
276A CYS* 1.3 76.7 - - - +
278A ARG* 1.3 57.2 + - - +
279A TYR 3.4 4.5 + - - +
318A LEU* 4.1 16.6 - - + -
323A MET* 6.5 0.7 - - - -
328A THR* 4.1 29.6 - - + +
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Residues in contact with ARG 278 (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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1A 961 3.0 22.6 + - - -
201A PHE* 3.4 22.5 - - + -
202A PRO* 2.7 36.8 + - - +
204A LEU* 3.8 38.1 - - - +
207A LEU* 3.8 13.2 - - - +
274A ARG 3.6 13.7 - - - +
275A ILE* 3.1 15.7 + - - +
276A CYS 3.0 1.0 - - - -
277A THR* 1.3 78.8 - - - +
279A TYR* 1.3 60.3 + - - +
280A THR* 3.8 2.3 + - - -
286A MET* 3.4 2.5 - - - -
287A THR 2.9 52.1 + - - +
288A PHE 3.4 6.7 - - - -
289A SER* 2.8 23.0 + - - +
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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