Contacts of the helix formed by residues 254 - 265 (chain A) in PDB entry 1V0O
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 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A LYS* 5.3 4.5 + - - -
252A GLY 4.3 0.4 - - - -
253A LEU* 1.3 76.7 - - - +
255A GLU* 1.3 71.3 + - - +
256A SER* 3.7 7.8 + - - -
257A GLY* 3.1 31.0 + - - -
258A ILE* 3.1 12.0 + - - +
283A TYR* 4.0 14.5 - - - -
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Residues in contact with GLU 255 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A ASP* 1.3 76.5 - - - +
256A SER* 1.3 57.4 + - - +
258A ILE* 3.4 9.8 + - - +
259A ASP* 3.1 27.7 + - - +
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Residues in contact with SER 256 (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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254A ASP* 3.2 9.4 + - - -
255A GLU* 1.3 76.5 - - - +
257A GLY* 1.3 60.5 + - - +
259A ASP* 3.5 3.5 + - - -
260A LEU* 3.1 24.1 + - - +
281A HIS* 3.2 16.3 - - - -
282A ALA* 4.4 10.8 + - - +
283A TYR* 4.0 27.9 + - - +
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Residues in contact with GLY 257 (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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191A PHE* 3.5 7.7 - - - -
253A LEU* 3.4 18.0 - - - +
254A ASP* 3.1 14.9 + - - -
256A SER* 1.3 74.9 - - - +
258A ILE* 1.3 58.5 + - - +
260A LEU* 3.7 0.6 + - - +
261A LEU* 3.1 28.2 + - - +
283A TYR* 3.5 26.4 - - - -
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Residues in contact with ILE 258 (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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246A TRP* 3.5 45.4 - - + +
247A GLU* 4.4 25.1 - - + +
250A LEU* 4.7 7.0 - - + +
253A LEU* 3.8 34.1 - - + +
254A ASP 3.1 14.4 + - - +
255A GLU* 3.7 11.0 - - - +
256A SER 3.3 0.2 - - - -
257A GLY* 1.3 75.2 - - - +
259A ASP* 1.3 60.6 + - - +
261A LEU* 3.4 4.0 + - - +
262A SER* 2.9 28.9 + - - -
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Residues in contact with ASP 259 (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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255A GLU 3.1 16.8 + - - +
256A SER* 3.7 7.0 - - - +
258A ILE* 1.3 77.9 - - - +
260A LEU* 1.3 59.7 + - - +
262A SER* 2.8 23.1 + - - -
263A LYS* 3.1 41.2 + - - +
281A HIS* 2.8 25.3 + - + +
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Residues in contact with LEU 260 (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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106A LEU* 3.8 28.3 - - + -
110A LEU* 4.8 0.2 - - + -
191A PHE* 4.1 2.9 - - + -
256A SER 3.1 16.1 + - - +
257A GLY 4.0 4.0 - - - +
259A ASP* 1.3 75.8 - - - +
261A LEU* 1.3 63.1 + - - +
263A LYS* 3.1 13.1 + - - +
264A MET* 3.3 24.8 + - + +
273A ILE* 4.0 15.9 - - + -
278A ALA* 3.9 25.1 - - + -
281A HIS* 3.7 23.9 + - + +
283A TYR* 3.9 19.7 - - + -
284A PHE* 3.9 13.7 - - + -
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Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A GLY* 3.4 33.4 - - - +
191A PHE* 3.7 24.2 - - + -
192A ALA* 4.3 7.4 - - + +
246A TRP* 4.6 8.0 - - + -
249A PHE* 5.6 0.4 - - + -
250A LEU* 3.4 45.1 - - + -
253A LEU* 4.1 10.1 - - + -
257A GLY 3.1 16.3 + - - +
258A ILE 3.7 3.6 - - - +
260A LEU* 1.3 81.4 - - - +
262A SER* 1.3 62.0 + - - +
264A MET* 3.2 4.9 + - - +
265A LEU* 3.1 33.3 + - + +
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Residues in contact with SER 262 (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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246A TRP* 3.4 43.8 - - - -
258A ILE* 2.9 15.1 + - - -
259A ASP* 2.8 25.5 + - - -
261A LEU* 1.3 76.0 - - - +
263A LYS* 1.3 63.8 + - - +
265A LEU 3.8 2.4 - - - +
266A LYS* 3.5 31.5 + - - +
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Residues in contact with LYS 263 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A ASP* 3.1 41.6 + - - +
260A LEU 3.1 10.1 + - - +
262A SER* 1.3 81.7 + - - +
264A MET* 1.3 59.1 + - - +
266A LYS* 3.7 23.0 - - - +
271A GLN 5.7 0.2 - - - +
272A ARG* 3.4 8.3 - - - -
273A ILE* 2.9 54.6 + - + +
281A HIS* 4.8 7.3 + - + -
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Residues in contact with MET 264 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A LEU* 4.3 3.8 - - + -
110A LEU* 3.8 28.7 - - + -
184A ILE* 3.9 18.9 - - + +
185A TRP* 4.1 9.0 - - - -
187A VAL* 3.6 26.2 - - + -
188A GLY* 3.9 27.6 - - - -
191A PHE* 4.2 17.3 - - - -
260A LEU* 3.5 30.7 - - + +
261A LEU* 3.2 6.8 + - - +
263A LYS* 1.3 78.1 - - - +
265A LEU* 1.3 58.9 + - - +
266A LYS 3.3 2.2 - - - -
272A ARG* 3.3 25.6 + - - +
273A ILE* 3.8 11.7 - - + -
278A ALA* 4.3 3.4 - - + -
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Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A TRP* 3.5 50.9 - - + +
188A GLY* 3.8 11.0 - - - +
189A CYS* 3.8 11.7 - - - +
200A LEU* 3.8 29.2 - - + -
201A PHE* 4.5 3.8 - - + -
217A LEU* 3.9 23.6 - - + +
246A TRP* 4.4 22.6 - - + -
261A LEU* 3.1 31.8 + - + +
262A SER 3.8 6.3 - - - +
264A MET* 1.3 75.8 - - - +
266A LYS* 1.3 60.7 + - - +
267A LEU* 3.7 3.8 + - - +
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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