Contacts of the helix formed by residues 266 - 276 (chain A) in PDB entry 4OE4
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 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A GLN* 3.5 9.1 + - - +
97A ALA 5.1 2.6 + - - -
237A GLN* 4.8 1.6 - - - +
265A GLY* 1.3 68.0 - - - -
267A PRO* 1.3 77.7 - - - +
268A VAL* 3.3 10.4 + - - +
269A GLN* 2.9 57.2 + - + +
270A VAL* 2.9 29.0 + - - +
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Residues in contact with PRO 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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234A LYS* 3.7 14.1 - - + +
237A GLN* 4.9 14.1 - - + +
265A GLY 3.2 6.5 - - - +
266A ASP* 1.3 93.6 - - - +
268A VAL* 1.3 56.6 + - + +
271A THR* 2.7 36.6 + - - -
1000A NAD 3.5 55.0 - - + +
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Residues in contact with VAL 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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266A ASP* 3.3 9.3 + - - +
267A PRO* 1.3 75.9 - - + +
269A GLN* 1.3 63.4 + - + +
271A THR* 3.8 3.1 - - - -
272A ASP* 2.9 49.6 + - - +
298A LYS* 4.0 14.8 - - - +
1000A NAD 3.8 26.0 - - + +
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Residues in contact with GLN 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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97A ALA 5.6 3.7 - - - +
99A GLU 5.9 0.3 + - - -
266A ASP* 2.9 40.9 + - + +
268A VAL* 1.3 75.3 - - + +
270A VAL* 1.3 63.8 - - + +
272A ASP* 3.9 5.7 - - - +
273A GLN* 3.1 23.4 + - - +
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Residues in contact with VAL 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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97A ALA* 4.2 15.7 - - + +
102A VAL* 4.1 20.4 - - + +
206A TYR* 3.8 13.2 - - - +
234A LYS* 3.9 16.6 - - + -
263A ILE* 3.8 29.6 - - + +
265A GLY* 4.0 23.3 - - - +
266A ASP 2.9 20.8 + - - +
269A GLN* 1.3 75.4 - - + +
271A THR* 1.3 64.8 + - - +
273A GLN* 3.1 3.6 + - - +
274A VAL* 3.0 29.4 + - + +
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Residues in contact with THR 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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206A TYR* 2.7 29.3 + - + -
208A VAL* 5.0 0.2 - - - +
234A LYS* 4.8 0.3 - - - -
267A PRO 2.7 22.6 + - - -
268A VAL* 3.8 4.0 - - - -
270A VAL* 1.3 76.0 - - - +
272A ASP* 1.3 69.7 + - - +
274A VAL* 3.8 0.5 - - - +
275A LEU* 3.0 40.8 + - + +
295A LEU* 3.4 27.0 - - + +
298A LYS* 4.6 6.5 - - + +
1000A NAD 3.3 18.2 + - + -
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Residues in contact with ASP 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 VAL* 2.9 32.0 + - - +
269A GLN* 3.9 6.8 - - - +
271A THR* 1.3 76.5 - - - +
273A GLN* 1.3 62.2 + - - +
275A LEU* 4.0 5.0 - - - +
276A ALA* 3.2 21.0 + - - +
298A LYS* 2.8 37.6 + - - +
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Residues in contact with GLN 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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99A GLU* 3.2 47.8 + - + +
102A VAL* 3.7 22.6 - - + +
103A MET* 3.3 27.1 - - + +
106A VAL* 5.4 1.0 - - - +
269A GLN 3.1 14.1 + - - +
270A VAL 3.1 4.9 + - - +
272A ASP* 1.3 76.3 - - - +
274A VAL* 1.3 67.1 + - - +
276A ALA* 3.2 27.6 + - - +
277A ASP* 3.8 4.2 + - - +
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Residues in contact with VAL 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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102A VAL* 3.5 20.4 - - + -
106A VAL* 4.6 6.1 - - + -
204A PHE* 3.7 28.8 - - + -
206A TYR* 3.5 49.6 - - + -
232A VAL* 4.0 12.6 - - + -
270A VAL* 3.0 25.1 + - + +
271A THR 3.8 3.6 - - - +
273A GLN* 1.3 76.7 - - - +
275A LEU* 1.3 57.8 + - - +
277A ASP* 3.1 25.3 + - - +
280A PHE* 4.5 4.6 - - + +
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Residues in contact with LEU 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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206A TYR* 4.6 8.7 - - + -
271A THR* 3.0 40.7 + - + +
272A ASP* 4.0 4.9 - - - +
274A VAL* 1.3 73.1 - - + +
276A ALA* 1.3 62.6 + - - +
277A ASP 3.1 2.2 - - - -
280A PHE* 3.7 42.4 - - + -
295A LEU* 4.7 4.9 - - + +
298A LYS* 3.7 32.3 - - + +
299A ILE* 3.9 16.2 - - + -
307A LYS* 4.4 4.0 - - - +
308A TYR* 2.7 35.6 + - - +
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Residues in contact with ALA 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 ASP 3.2 13.6 + - - +
273A GLN* 3.2 27.7 + - - +
274A VAL 3.1 1.0 - - - -
275A LEU* 1.3 76.8 - - - +
277A ASP* 1.3 59.3 + - - +
278A LYS* 3.6 2.4 + - - -
307A LYS* 4.9 14.9 - - - +
308A TYR* 5.0 0.7 - - - -
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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