Contacts of the helix formed by residues 286 - 297 (chain A) in PDB entry 4WTH
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 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A LYS* 6.0 4.0 - - - +
281A GLU 4.3 2.9 - - - +
282A ASN* 3.8 26.2 + - - +
283A TYR* 2.9 19.9 + - - -
284A LEU 2.7 5.1 + - - +
285A LEU* 1.3 78.8 - - - +
287A ASP* 1.3 67.5 + - - +
288A GLU* 4.1 5.1 + - - +
289A GLY 3.2 10.2 + - - -
290A LEU* 2.9 23.4 + - - +
304A LEU* 3.6 8.7 - - - -
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Residues in contact with ASP 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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286A THR* 1.3 70.9 - - - +
288A GLU* 1.3 55.6 + - + +
290A LEU* 3.7 0.3 - - - -
291A GLU* 2.8 37.2 + - - +
304A LEU* 3.8 0.8 - - - +
306A SER* 2.9 30.7 + - - -
307A TYR* 3.4 31.5 + - + +
310A GLU* 2.5 29.9 - - - +
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Residues in contact with GLU 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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23A VAL* 4.9 0.3 - - - +
26A LYS* 4.4 17.9 + - - +
286A THR* 3.3 5.0 + - - +
287A ASP* 1.3 78.7 - - + +
289A GLY* 1.3 65.3 + - - +
291A GLU* 3.6 19.3 + - - +
292A ALA* 3.2 21.7 + - - +
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Residues in contact with GLY 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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23A VAL* 3.6 19.8 - - - +
283A TYR 3.4 22.2 - - - -
284A LEU* 3.6 9.6 - - - -
286A THR* 3.2 11.5 + - - -
288A GLU* 1.3 76.7 - - - +
290A LEU* 1.3 61.2 + - - +
292A ALA* 3.3 13.3 + - - +
293A VAL* 3.4 12.5 + - - +
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Residues in contact with LEU 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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108A ILE* 4.0 27.1 - - + +
284A LEU* 3.5 31.2 - - + +
285A LEU* 4.3 11.4 - - + -
286A THR 2.9 12.9 + - - +
289A GLY* 1.3 72.4 - - - +
291A GLU* 1.3 55.9 + - - +
293A VAL* 3.4 4.6 + - + +
294A ASN* 2.7 38.3 + - - +
299A LEU* 4.1 10.1 - - + +
302A VAL* 4.3 13.7 - - + -
304A LEU* 3.7 37.0 - - + -
307A TYR* 3.6 24.9 - - + -
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Residues in contact with GLU 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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287A ASP 2.8 18.6 + - - +
288A GLU* 3.7 22.9 - - - +
289A GLY 3.3 0.2 - - - -
290A LEU* 1.3 76.5 - - - +
292A ALA* 1.3 56.2 + - - +
295A LYS* 2.9 70.6 + - + +
307A TYR* 3.2 27.2 - - + +
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Residues in contact with ALA 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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19A GLY* 3.5 18.3 - - - +
22A GLU* 4.0 18.5 - - + +
23A VAL* 3.7 20.0 - - + -
288A GLU 3.2 9.5 + - - +
289A GLY 3.5 9.4 - - - +
290A LEU 3.2 0.2 - - - -
291A GLU* 1.3 82.1 - - - +
293A VAL* 1.3 62.9 + - - +
295A LYS* 3.6 3.6 + - - +
296A ASP* 3.4 12.0 + - - +
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Residues in contact with VAL 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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11A ILE* 5.6 6.1 - - + -
15A LYS* 6.1 0.7 - - + -
16A GLY* 3.7 21.5 - - - +
19A GLY* 4.0 7.6 - - - +
20A LEU* 3.7 27.4 - - + +
23A VAL* 4.7 0.2 - - + -
108A ILE* 6.3 0.4 - - + -
284A LEU* 3.8 21.3 - - + -
289A GLY 3.4 12.5 + - - +
290A LEU* 3.4 7.2 + - + +
292A ALA* 1.3 76.0 - - - +
294A ASN* 1.3 58.0 + - - +
296A ASP* 2.9 18.9 + - - +
297A LYS 3.0 15.2 + - - +
299A LEU* 4.0 28.0 - - + -
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Residues in contact with ASN 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 LEU 2.7 22.4 + - - +
291A GLU 4.0 0.2 - - - +
293A VAL* 1.3 73.2 - - - +
295A LYS* 1.3 64.1 + - - +
296A ASP 3.4 0.5 + - - -
297A LYS 3.7 5.2 - - - -
298A PRO* 3.4 29.5 - - - +
299A LEU* 2.9 37.3 + - + +
300A GLY 4.4 1.9 + - - +
302A VAL* 4.8 0.3 - - - +
307A TYR* 3.8 23.9 + - + +
311A LEU* 4.0 27.4 - - - +
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Residues in contact with LYS 295 (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 SER* 5.0 0.5 + - - -
291A GLU* 2.9 54.0 + - + +
292A ALA* 4.1 4.3 - - - +
294A ASN* 1.3 77.2 - - - +
296A ASP* 1.3 63.0 + - - +
307A TYR* 5.2 4.0 - - - +
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Residues in contact with ASP 296 (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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15A LYS 4.7 0.2 - - - +
16A GLY* 3.1 16.3 - - - -
17A TYR* 3.5 0.5 + - - -
18A ASN* 2.9 48.8 + - - +
19A GLY* 3.8 15.0 - - - +
233A SER* 2.6 27.5 + - - -
292A ALA 3.4 6.8 + - - +
293A VAL 2.9 10.4 + - - +
294A ASN 4.1 0.2 - - - -
295A LYS* 1.3 81.5 - - - +
297A LYS* 1.3 62.8 + - - +
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Residues in contact with LYS 297 (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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13A GLY 5.4 2.0 - - - -
14A ASP* 3.6 18.8 - - - +
15A LYS* 3.6 9.4 - - - +
16A GLY* 3.3 29.7 + - - +
17A TYR* 6.4 1.1 - - - -
230A TRP* 3.1 28.0 - - + +
233A SER* 3.9 13.6 - - - +
234A ASN* 3.7 29.5 + - - +
293A VAL* 3.0 15.8 + - - +
294A ASN* 3.5 4.4 - - - +
296A ASP* 1.3 86.4 + - - +
298A PRO* 1.3 73.0 - - - +
299A LEU* 3.3 6.4 + - - +
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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