Contacts of the helix formed by residues 285 - 294 (chain A) in PDB entry 3L6D
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 ASP 285 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A GLU* 5.7 1.4 - - - +
226A ALA* 5.4 0.7 - - - -
229A ARG* 3.5 46.5 + - - +
235A PHE* 2.8 19.0 + - + +
236A LYS 3.7 5.6 - - - +
237A GLY* 3.9 3.0 - - - -
239A GLN* 5.2 0.7 - - - +
240A ALA* 3.6 27.9 + - - +
242A LEU* 4.4 1.4 - - - +
284A GLN* 1.3 75.2 - - - +
286A ILE* 1.3 61.4 + - - +
287A ALA* 2.7 34.7 + - - +
288A ALA* 2.8 32.6 + - - +
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Residues in contact with ILE 286 (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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226A ALA* 6.3 0.7 - - + -
240A ALA* 3.0 30.9 + - + +
242A LEU* 4.1 16.4 - - + +
245A HIS* 3.7 41.3 - - + +
249A PHE* 4.9 3.8 - - + -
273A VAL* 4.5 14.1 - - + -
284A GLN 3.5 0.4 + - - -
285A ASP* 1.3 75.9 - - - +
287A ALA* 1.3 62.3 + - + +
288A ALA 3.1 0.2 - - - -
289A THR* 2.6 39.8 + - - +
130B TYR* 4.7 0.7 - - - +
187B MSE 3.9 23.6 - - + -
188B VAL* 5.6 1.8 - - + -
191B PHE* 3.6 16.8 - - + -
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Residues in contact with ALA 287 (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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226A ALA* 4.1 35.0 - - + +
229A ARG* 4.7 4.7 - - + -
230A LEU* 3.9 8.6 - - + +
235A PHE* 3.8 10.7 - - + -
285A ASP* 2.7 23.3 + - - +
286A ILE* 1.3 69.8 - - + +
288A ALA* 1.3 59.7 + - - +
289A THR 2.9 6.5 + - - -
290A THR* 3.0 24.8 + - - -
191B PHE* 3.9 12.8 - - + -
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Residues in contact with ALA 288 (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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235A PHE* 3.7 18.1 - - + -
242A LEU* 4.7 2.9 - - + -
281A TYR* 4.2 17.8 - - + -
284A GLN* 3.5 33.7 - - + +
285A ASP 2.8 21.8 + - - +
287A ALA* 1.3 67.3 - - - +
289A THR* 1.3 64.9 + - - +
290A THR 3.0 2.7 - - - -
291A LYS* 2.9 25.0 + - + +
292A SER 3.7 2.1 + - - -
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Residues in contact with THR 289 (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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242A LEU* 3.3 20.0 - - - +
272A VAL* 3.6 30.5 - - + -
273A VAL* 4.4 10.2 - - + +
276A ALA* 4.6 7.4 - - + -
286A ILE* 2.6 30.0 + - - +
288A ALA* 1.3 77.2 - - - +
290A THR* 1.3 63.2 + - - +
292A SER* 2.9 27.7 + - - +
293A PHE* 3.4 6.2 - - + -
188B VAL* 4.9 2.5 - - + -
191B PHE* 3.7 24.3 - - + -
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Residues in contact with THR 290 (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 LEU* 3.8 13.4 - - + +
287A ALA 3.0 16.9 + - - -
289A THR* 1.3 77.8 - - - +
291A LYS* 1.3 65.2 + - + +
293A PHE* 3.3 19.7 + - - +
294A ALA* 4.2 2.1 + - - +
191B PHE* 3.6 34.4 - - - +
194B VAL* 3.9 12.9 - - + +
195B GLY* 3.9 9.1 - - - +
204B VAL* 3.8 36.7 - - + +
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Residues in contact with LYS 291 (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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233A GLN* 5.5 1.1 - - - -
235A PHE* 3.5 44.2 - - + -
281A TYR* 3.5 35.0 + - + +
284A GLN* 2.8 29.7 + - - +
288A ALA* 2.9 20.0 + - - +
290A THR* 1.3 71.9 - - + +
292A SER* 1.3 57.4 + - - +
293A PHE 3.0 5.4 - - - -
294A ALA* 2.9 31.7 + - + +
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Residues in contact with SER 292 (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 VAL* 4.6 5.4 + - - +
275A ARG* 3.7 21.4 + - - -
276A ALA* 4.2 19.0 - - - +
279A MSE 3.8 30.1 - - - +
281A TYR* 4.1 12.0 - - - -
288A ALA 3.7 1.6 + - - -
289A THR* 2.9 20.3 + - - +
291A LYS* 1.3 77.0 - - - +
293A PHE* 1.3 69.4 + - - +
294A ALA 3.4 2.2 + - - -
262B TRP* 4.9 6.4 - - - -
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Residues in contact with PHE 293 (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 VAL* 3.5 31.9 - - + -
289A THR* 3.4 23.1 - - + -
290A THR 3.7 11.4 - - - +
291A LYS 3.0 1.2 + - - -
292A SER* 1.3 80.2 - - - +
294A ALA* 1.3 56.5 + - - +
188B VAL* 5.2 0.9 - - + -
191B PHE 3.9 13.0 - - - -
192B GLU* 3.6 48.7 - - + -
195B GLY* 3.9 19.0 - - - +
196B ALA* 4.6 0.7 - - - +
199B ARG* 2.7 37.5 + - - +
262B TRP* 3.3 51.1 - + + -
264B PRO* 4.4 0.2 - - + -
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Residues in contact with ALA 294 (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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290A THR 4.2 1.7 + - - +
291A LYS* 2.9 22.1 + - + +
292A SER 3.4 2.2 - - - -
293A PHE* 1.3 75.5 - - - +
195B GLY* 5.3 0.6 - - - -
198B ASP* 3.9 26.9 - - + +
199B ARG* 3.0 31.5 + - - +
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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