Contacts of the helix formed by residues 263 - 273 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129C GLN* 3.8 41.7 - - + +
132C VAL* 3.9 22.7 - - + +
133C HIS* 3.9 28.7 - - + -
134C PRO* 4.5 10.1 - - + -
259C GLY* 3.3 22.4 - - - +
260C PHE* 4.4 2.0 + - - -
261C THR 3.7 1.8 - - - -
262C ASP* 1.3 80.6 - - - +
264C HIS* 1.3 68.3 + - - +
265C THR 3.3 2.5 - - - -
266C GLU* 3.2 14.8 + - + +
267C VAL* 3.0 24.5 + - - +
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Residues in contact with HIS 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ILE* 3.8 4.7 - - + +
16C ARG* 3.5 59.5 + - + +
17C HIS* 3.7 23.1 - + - -
19C LYS* 6.4 0.2 - - - -
20C ALA* 4.3 3.6 - - + -
100C GLU* 2.7 28.1 + - - -
127C VAL* 3.6 19.7 - - + +
129C GLN* 3.9 11.2 - - - +
262C ASP 3.7 1.2 - - - -
263C LEU* 1.3 80.9 + - - +
265C THR* 1.3 63.0 + - - +
267C VAL* 3.1 7.6 + - - +
268C TYR* 3.0 28.6 + + + -
311C NAD 3.5 19.5 + - - -
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Residues in contact with THR 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ARG 5.1 0.3 + - - -
19C LYS* 4.3 8.9 - - - +
20C ALA* 3.5 23.5 + - - +
23C GLU* 2.6 43.9 + - + +
24C VAL* 4.3 13.9 - - + -
262C ASP 5.4 1.2 + - - -
263C LEU 3.3 0.8 - - - +
264C HIS* 1.3 76.6 - - - +
266C GLU* 1.3 58.8 + - - +
268C TYR* 3.1 2.8 + - - +
269C ARG* 2.8 30.0 + - + +
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Residues in contact with GLU 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C VAL* 3.9 27.8 - - + +
262C ASP 5.8 0.4 - - - +
263C LEU* 3.2 19.1 + - + +
264C HIS 3.2 0.6 - - - -
265C THR* 1.3 79.3 - - - +
267C VAL* 1.3 57.4 + - - +
269C ARG* 2.6 47.4 + - - +
270C LYS* 2.9 35.5 + - - +
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Residues in contact with VAL 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LEU* 4.7 4.3 - - + -
126C THR 4.1 7.0 - - - +
127C VAL* 4.0 35.2 - - + -
128C LEU 4.5 3.1 - - - +
129C GLN* 3.9 22.9 - - + +
132C VAL* 3.8 23.6 - - + -
263C LEU 3.0 14.8 + - - +
264C HIS* 3.1 9.4 + - - +
266C GLU* 1.3 74.0 - - - +
268C TYR* 1.3 55.2 + - + +
270C LYS* 3.3 6.5 + - - +
271C THR* 2.7 44.8 + - - +
277C PHE* 4.5 8.7 - - + -
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Residues in contact with TYR 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C PHE* 3.6 35.0 - + - -
17C HIS* 2.7 45.3 + + - +
20C ALA* 3.4 24.7 - - + -
21C ILE* 3.7 17.2 - - + +
24C VAL* 4.0 15.9 - - + -
75C SER* 2.8 19.4 + - - -
98C LEU* 3.5 25.1 - - + +
127C VAL* 5.1 2.2 - - + -
264C HIS* 3.0 23.9 + + + +
265C THR 3.4 7.9 - - - +
267C VAL* 1.3 79.5 - - + +
269C ARG* 1.3 58.1 + - - +
271C THR* 3.2 6.4 + - - -
272C LEU* 2.8 36.5 + - + +
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Residues in contact with ARG 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C VAL* 4.0 13.6 - - + +
265C THR* 2.8 22.2 + - + +
266C GLU* 2.6 45.3 + - - +
268C TYR* 1.3 73.7 - - - +
270C LYS* 1.3 78.3 + - - +
272C LEU* 3.3 4.5 + - - +
273C ALA* 3.0 35.9 + - + +
275C GLU* 4.9 7.7 + - - -
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Residues in contact with LYS 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C ARG 5.8 0.9 - - - -
132C VAL* 3.4 27.1 - - + -
266C GLU* 2.9 25.8 + - - +
267C VAL* 3.8 5.8 - - - +
269C ARG* 1.3 96.6 - - - +
271C THR* 1.3 60.5 + - - +
273C ALA* 3.2 10.2 + - - -
275C GLU* 2.8 73.9 + - - +
276C GLY* 3.9 4.0 - - - +
277C PHE* 4.1 16.8 - - + -
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Residues in contact with THR 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C TYR* 3.7 24.4 + - + +
98C LEU* 4.0 20.6 - - + +
125C TYR* 3.6 42.1 - - + +
126C THR 5.1 0.7 + - - -
267C VAL* 2.7 26.3 + - - +
268C TYR* 3.2 7.6 + - - -
270C LYS* 1.3 76.3 - - - +
272C LEU* 1.3 63.8 + - + +
274C GLY* 3.1 13.5 + - - -
276C GLY* 3.8 16.9 + - - -
277C PHE* 5.0 1.0 + - - -
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Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C THR* 4.1 22.7 - - + +
4C PHE* 4.2 12.6 - - + -
24C VAL* 3.7 37.7 - - + +
73C TYR* 3.5 40.2 - - + +
98C LEU* 6.6 0.4 - - + -
268C TYR* 2.8 23.4 + - + +
269C ARG* 4.0 4.7 - - - +
271C THR* 1.3 75.1 - - + +
273C ALA* 1.3 58.4 + - - +
274C GLY 3.2 1.1 + - - -
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Residues in contact with ALA 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C ARG* 3.0 29.9 + - + +
270C LYS* 3.6 7.9 - - - +
271C THR 3.1 0.8 - - - -
272C LEU* 1.3 74.6 - - - +
274C GLY* 1.3 61.9 + - - +
275C GLU* 3.3 18.5 + - - +
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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