Contacts of the helix formed by residues 263 - 273 (chain E) in PDB entry 3U3F
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 ALA 263 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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921A ILE* 3.5 24.9 - - + -
925A ASP* 3.6 12.8 + - - +
943A GLN* 4.1 24.7 - - + +
944A LYS* 5.8 0.7 - - - +
947A ASN* 3.2 27.2 + - - +
262E SER* 1.3 78.2 - - - +
264E THR* 1.3 64.3 + - - +
265E ARG 3.2 0.7 + - - -
266E GLU* 3.4 4.6 + - - +
267E LEU* 3.4 3.8 + - - +
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Residues in contact with THR 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918A ARG* 4.5 25.8 - - + +
921A ILE* 4.0 14.3 - - + +
922A GLY* 4.2 17.5 - - - +
925A ASP* 3.9 13.1 + - + +
262E SER 3.8 8.5 + - - -
263E ALA* 1.3 73.6 - - - +
265E ARG* 1.3 57.0 + - - +
267E LEU* 2.8 15.6 + - - +
268E ASP* 2.7 45.3 + - - +
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Residues in contact with ARG 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E SER* 2.6 24.2 + - - +
264E THR* 1.3 76.6 + - - +
266E GLU* 1.3 63.1 + - - +
267E LEU 2.9 1.2 + - - -
268E ASP* 3.1 10.1 + - - +
269E GLU* 3.1 20.5 + - - +
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Residues in contact with GLU 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947A ASN* 3.9 16.8 - - + +
262E SER 3.9 1.6 + - - +
263E ALA* 3.4 5.7 + - - +
265E ARG* 1.3 78.0 - - - +
267E LEU* 1.3 55.5 + - - +
269E GLU* 3.5 8.7 - - - +
270E LEU* 3.0 27.9 + - - +
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Residues in contact with LEU 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914A GLY 4.5 2.2 - - - +
917A LEU* 4.1 11.7 - - + -
918A ARG* 3.5 48.7 - - + +
921A ILE* 4.5 7.0 - - + -
947A ASN* 3.0 31.6 - - - +
950A LEU* 3.6 31.2 - - + -
263E ALA 3.4 7.6 + - - +
264E THR* 2.8 14.8 + - - +
266E GLU* 1.3 75.2 - - - +
268E ASP* 1.3 50.3 + - - +
269E GLU 3.0 1.6 - - - -
270E LEU* 2.8 9.0 + - + +
271E MET* 2.6 41.3 + - - +
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Residues in contact with ASP 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918A ARG* 2.7 41.0 + - - -
886C GLU* 5.1 2.4 - - - +
919C LYS* 4.4 5.2 + - - -
264E THR* 2.7 36.2 + - - +
265E ARG* 3.6 9.2 + - - +
267E LEU* 1.3 71.6 - - - +
269E GLU* 1.3 56.9 + - - +
271E MET* 3.1 12.2 - - - +
272E ALA* 2.9 27.9 + - - +
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Residues in contact with GLU 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E ARG 3.1 12.0 + - - +
266E GLU* 3.5 13.5 - - - +
267E LEU 3.0 0.2 - - - -
268E ASP* 1.3 74.5 - - - +
270E LEU* 1.3 66.6 + - - +
271E MET 3.1 0.9 + - - -
272E ALA* 3.3 18.7 + - - +
273E SER* 3.6 6.1 + - - -
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Residues in contact with LEU 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947A ASN* 3.2 42.6 - - + +
950A LEU* 4.5 9.9 - - + -
951A ALA* 3.7 23.3 - - + +
954A ILE* 3.7 28.5 - - + +
266E GLU 3.0 15.6 + - - +
267E LEU* 2.8 16.4 + - + +
269E GLU* 1.3 75.6 - - - +
271E MET* 1.3 56.4 + - - +
273E SER* 2.9 28.1 + - - +
274E LEU 4.3 0.5 + - - -
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Residues in contact with MET 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910A VAL 4.5 0.2 - - - +
911A LYS* 3.5 20.2 - - + +
914A GLY* 3.3 42.0 - - - +
915A LEU* 3.8 13.7 - - + +
918A ARG* 5.7 3.6 - - - -
950A LEU* 4.5 11.7 - - + -
954A ILE* 5.6 0.2 - - - -
919C LYS* 6.2 1.6 - - - +
267E LEU* 2.6 22.4 + - - +
268E ASP* 3.1 17.3 - - - +
270E LEU* 1.3 71.3 - - - +
272E ALA* 1.3 67.1 + - - +
274E LEU* 2.9 48.7 + - + +
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Residues in contact with ALA 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E ASP 2.9 12.0 + - - +
269E GLU* 3.3 12.1 + - - +
271E MET* 1.3 76.7 - - - +
273E SER* 1.3 54.8 + - - +
274E LEU 2.6 21.8 + - - +
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Residues in contact with SER 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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954A ILE* 4.9 10.7 - - - +
958A ARG* 3.7 12.5 + - - -
269E GLU 3.6 6.3 + - - -
270E LEU* 2.9 25.5 + - - +
271E MET 3.2 0.6 - - - -
272E ALA* 1.3 77.2 - - - +
274E LEU* 1.3 61.3 + - - +
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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