Contacts of the helix formed by residues 263 - 273 (chain A) in PDB entry 3O9Z
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 LEU 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLN* 3.6 41.5 - - + +
130A LEU* 5.4 0.2 - - - -
132A VAL* 3.8 25.8 - - + +
133A HIS* 4.0 25.8 - - + -
134A PRO* 4.4 10.8 - - + -
259A GLY* 3.5 21.5 - - - +
260A PHE* 4.4 2.6 + - - +
261A THR 3.7 2.0 - - - -
262A ASP* 1.3 79.7 - - - +
264A HIS* 1.3 67.4 + - - +
265A THR 3.2 3.1 + - - -
266A GLU* 3.3 13.3 + - + +
267A VAL* 3.2 21.6 + - - +
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Residues in contact with HIS 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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13A ILE* 3.8 5.0 - - + +
16A ARG* 3.4 59.5 + - + +
17A HIS* 3.6 22.9 - + - -
20A ALA* 4.2 3.6 - - + -
100A GLU* 2.7 28.6 + - - -
127A VAL* 3.7 13.6 - - + +
129A GLN* 4.0 15.0 - - - +
260A PHE 5.5 0.2 + - - -
262A ASP 4.0 0.6 - - - -
263A LEU* 1.3 80.6 + - - +
265A THR* 1.3 64.4 + - - +
267A VAL* 3.3 7.9 + - - +
268A TYR* 3.1 28.2 + + + -
311A NAD 3.5 19.1 - - - -
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Residues in contact with THR 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG 5.0 0.5 + - - -
19A LYS* 4.3 5.0 - - - +
20A ALA* 3.4 24.6 + - - -
23A GLU* 2.8 44.5 + - + +
24A VAL* 4.3 11.9 - - + -
262A ASP 5.6 0.4 - - - -
263A LEU* 3.2 1.2 - - - +
264A HIS* 1.3 77.4 - - - +
266A GLU* 1.3 59.5 + - - +
268A TYR* 3.0 3.8 + - - +
269A ARG* 2.9 28.3 + - + +
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Residues in contact with GLU 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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132A VAL* 3.8 28.6 - - + +
263A LEU* 3.3 17.8 + - + +
264A HIS 3.2 0.6 - - - -
265A THR* 1.3 76.4 - - - +
267A VAL* 1.3 64.6 + - - +
269A ARG* 2.8 45.9 + - - +
270A LYS* 3.0 32.6 + - - +
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Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 4.7 3.1 - - + -
126A THR 3.9 8.7 - - - +
127A VAL* 3.8 37.7 - - + -
128A LEU 4.5 4.0 - - - +
129A GLN* 3.9 29.6 - - + +
132A VAL* 4.0 13.2 - - + -
263A LEU 3.2 15.8 + - - +
264A HIS* 3.3 8.5 + - - +
266A GLU* 1.3 74.7 - - - +
268A TYR* 1.3 58.6 + - + +
270A LYS* 3.4 6.6 + - - +
271A THR* 2.7 39.7 + - - +
277A PHE* 4.6 8.5 - - + -
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Residues in contact with TYR 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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4A PHE* 3.7 29.2 - + - -
17A HIS* 2.7 42.8 + + - +
20A ALA* 3.4 24.0 - - + -
21A ILE* 3.7 27.3 - - + +
24A VAL* 3.9 14.6 - - + -
75A SER* 2.8 19.8 + - - -
98A LEU* 3.7 20.8 - - + +
127A VAL* 5.0 2.9 - - + -
264A HIS* 3.1 24.5 + - + +
265A THR 3.0 9.4 + - - +
267A VAL* 1.3 76.8 - - + +
269A ARG* 1.3 63.9 + - - +
271A THR* 3.1 8.0 + - - -
272A LEU* 3.0 30.2 + - + +
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Residues in contact with ARG 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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24A VAL* 4.0 14.5 - - + +
265A THR* 2.9 16.5 + - + +
266A GLU* 2.8 41.2 + - - +
268A TYR* 1.3 77.9 - - - +
270A LYS* 1.3 77.2 + - - +
272A LEU* 3.2 6.1 + - - +
273A ALA* 2.9 39.1 + - + +
275A GLU* 4.5 11.3 + - - -
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Residues in contact with LYS 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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131A ARG 5.9 0.2 - - - -
132A VAL* 3.4 28.7 - - + -
266A GLU* 3.0 34.7 + - - +
267A VAL* 3.8 4.7 - - - +
269A ARG* 1.3 84.9 - - - +
271A THR* 1.3 57.7 + - - +
273A ALA* 3.2 7.9 + - - -
274A GLY 3.2 0.2 + - - -
275A GLU* 2.7 80.3 + - + +
276A GLY* 4.0 2.5 - - - -
277A PHE* 4.0 18.2 - - + -
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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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73A TYR* 3.8 24.2 + - + +
98A LEU* 4.1 21.1 - - + +
125A TYR* 3.8 41.5 - - + +
126A THR 5.1 0.7 + - - -
267A VAL* 2.7 25.7 + - - +
268A TYR* 3.1 7.8 + - - -
270A LYS* 1.3 76.6 - - - +
272A LEU* 1.3 65.5 + - + +
274A GLY* 3.1 13.9 + - - -
276A GLY* 3.8 16.7 + - - -
277A PHE* 5.0 0.7 + - - -
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Residues in contact with LEU 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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2A THR* 3.8 30.7 - - + +
4A PHE* 4.3 10.3 - - + -
24A VAL* 4.0 36.3 - - + +
73A TYR* 3.8 33.9 - - + -
268A TYR* 3.0 18.7 + - + +
269A ARG* 3.9 5.2 - - - +
271A THR* 1.3 79.4 - - + +
273A ALA* 1.3 59.6 + - - +
274A GLY 3.2 1.6 + - - -
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Residues in contact with ALA 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 ARG* 2.9 28.2 + - + +
270A LYS* 3.2 6.0 + - - +
271A THR 3.1 0.4 - - - -
272A LEU* 1.3 78.4 - - - +
274A GLY* 1.3 60.0 + - - +
275A GLU* 3.3 19.7 - - - +
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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