Contacts of the helix formed by residues 261 - 270 (chain A) in PDB entry 5U03
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 GLY 261 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A GLU* 4.4 7.0 - - - +
257A LEU 2.7 10.0 + - - -
258A GLU* 2.9 14.3 + - - -
259A GLU 4.4 0.7 - - - -
260A GLN* 1.3 75.8 - - - +
262A VAL* 1.3 64.8 + - - +
263A VAL* 3.0 4.9 + - - -
264A ASP* 3.2 24.6 + - - +
265A TYR* 3.3 9.0 + - - +
279A ARG* 5.1 7.0 - - - -
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Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 5.6 1.8 - - + -
26A ILE* 5.2 2.5 - - + -
213A LEU* 4.6 3.4 - - + -
239A GLU* 6.0 0.7 - - - +
242A ILE* 3.7 30.5 - - + -
257A LEU* 3.4 39.4 + - + +
260A GLN* 3.6 24.0 - - + +
261A GLY* 1.3 75.2 - - - +
263A VAL* 1.3 70.2 + - + +
265A TYR* 3.2 12.4 + - - +
266A PHE* 2.9 49.2 + - + -
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Residues in contact with VAL 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 3.6 29.6 - - + -
27A LEU* 6.2 1.6 - - + -
30A CYS* 4.0 23.8 - - - -
257A LEU 5.4 1.8 - - - +
258A GLU* 5.5 2.5 - - - -
261A GLY* 3.0 1.1 - - - -
262A VAL* 1.3 85.0 - - + +
264A ASP* 1.3 62.2 + - - +
266A PHE* 2.9 14.8 + - + +
267A LEU* 2.8 41.7 + - + +
274A ILE* 4.6 0.9 - - + -
279A ARG* 3.7 30.1 - - + -
280A LYS* 4.5 10.5 - - + -
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Residues in contact with ASP 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLU* 5.7 0.2 - - - +
261A GLY* 3.2 12.6 + - - +
263A VAL* 1.3 79.4 - - - +
265A TYR* 1.3 62.9 + - - +
267A LEU* 3.1 20.6 + - - +
268A ARG* 3.0 41.7 + - - +
279A ARG* 2.9 44.9 + - - +
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Residues in contact with TYR 265 (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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212A ASP* 2.9 21.3 + - + +
213A LEU* 3.6 33.9 - - + -
239A GLU* 3.8 28.5 - - + +
240A GLN* 2.9 39.2 + - + -
261A GLY 3.3 3.7 + - - +
262A VAL* 3.2 15.9 + - - +
263A VAL 3.1 0.4 - - - -
264A ASP* 1.3 79.3 - - - +
266A PHE* 1.3 57.0 + + - +
268A ARG* 2.9 20.4 + - + +
269A ARG* 2.7 68.3 + - + +
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Residues in contact with PHE 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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4A ILE* 4.7 8.7 - - + -
23A VAL* 4.2 31.2 - - + -
26A ILE* 6.4 0.4 - - + -
27A LEU* 5.1 14.6 - - + -
176A CYS* 3.6 30.1 - - - -
178A ILE* 4.0 11.7 - - + -
213A LEU* 3.6 21.5 - - + -
262A VAL* 2.9 43.5 + - + -
263A VAL* 2.9 14.3 + - + +
265A TYR* 1.3 78.9 - + - +
267A LEU* 1.3 59.9 + - + +
269A ARG* 4.2 2.5 - - + +
270A LEU* 2.7 55.2 + - + +
272A LEU* 4.7 3.3 - - + +
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Residues in contact with LEU 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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30A CYS* 5.6 3.1 - - + -
263A VAL* 2.8 26.1 + - + +
264A ASP* 3.1 28.2 + - - +
266A PHE* 1.3 77.5 - - + +
268A ARG* 1.3 58.6 + - + +
271A ASP* 3.1 8.5 + - - -
272A LEU* 3.0 54.7 + - + +
273A PRO 3.9 4.9 - - - +
274A ILE* 3.5 45.5 - - + -
279A ARG* 5.7 0.7 - - - -
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Residues in contact with ARG 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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172A ARG* 5.5 1.6 + - - -
239A GLU* 2.7 38.6 + - - -
264A ASP* 3.0 35.1 + - + +
265A TYR* 2.9 20.1 + - + +
267A LEU* 1.3 80.6 - - + +
269A ARG* 1.3 58.7 + - - +
271A ASP* 3.1 20.5 - - - +
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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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172A ARG* 2.9 63.1 + - - +
173A GLU* 3.5 11.0 - - - +
175A PHE* 3.1 22.3 + - - -
176A CYS* 4.8 5.8 - - - -
212A ASP* 2.8 35.8 + - + -
265A TYR* 2.7 51.0 + - + +
266A PHE* 3.9 3.4 - - - +
268A ARG* 1.3 76.7 - - - +
270A LEU* 1.3 68.4 + - + +
271A ASP* 3.3 3.1 + - - +
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Residues in contact with LEU 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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2A LYS* 2.8 42.8 + - + -
4A ILE* 4.2 20.0 - - + -
27A LEU* 5.8 2.0 - - + -
142A VAL* 5.4 0.9 - - + -
173A GLU* 3.1 24.9 - - - +
175A PHE 4.3 8.7 - - - +
176A CYS* 4.1 20.6 - - + -
266A PHE* 2.7 40.7 + - + +
269A ARG* 1.3 78.3 - - + +
271A ASP* 1.3 70.4 + - - +
272A LEU* 3.7 27.1 - - + -
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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