Contacts of the helix formed by residues 254 - 265 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B LYS* 5.2 5.0 + - - -
252B GLY 4.3 0.6 + - - -
253B LEU* 1.3 79.9 - - - +
255B GLU* 1.3 66.2 + - - +
256B SER* 4.2 9.6 + - - -
257B GLY* 3.3 18.4 + - - -
258B ILE* 3.0 17.5 + - - +
283B TYR* 4.1 11.4 - - - -
286B GLU* 4.6 7.4 - - - +
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Residues in contact with GLU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ASP* 1.3 74.7 - - - +
256B SER* 1.3 58.9 + - - +
258B ILE* 3.4 8.6 + - - +
259B ASP* 3.1 26.3 + - - +
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Residues in contact with SER 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ASP* 3.4 6.7 + - - -
255B GLU* 1.3 75.6 - - - +
257B GLY* 1.3 60.6 + - - +
259B ASP* 3.2 6.2 + - - -
260B LEU* 3.0 24.9 + - - +
281B HIS* 3.3 14.4 - - - -
282B ALA* 3.5 4.1 - - - +
283B TYR* 2.8 33.2 + - - +
286B GLU* 3.4 25.8 - - - -
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Residues in contact with GLY 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B PHE* 3.6 7.9 - - - -
253B LEU* 3.9 12.1 - - - -
254B ASP* 3.2 14.8 + - - -
256B SER* 1.3 75.1 - - - +
258B ILE* 1.3 60.2 + - - +
260B LEU* 3.5 1.0 + - - +
261B LEU* 3.0 30.3 + - - +
283B TYR* 3.4 28.8 - - - -
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Residues in contact with ILE 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B TRP* 3.7 30.1 - - + +
247B GLU* 4.0 44.0 - - + +
250B LEU* 4.3 14.4 - - + +
253B LEU* 3.5 29.1 - - + +
254B ASP 3.0 17.7 + - - +
255B GLU* 3.7 11.0 - - - +
257B GLY* 1.3 75.4 - - - +
259B ASP* 1.3 59.1 + - - +
261B LEU* 3.4 3.4 + - - +
262B SER* 3.0 29.3 + - - -
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Residues in contact with ASP 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B GLU 3.1 14.9 + - - +
256B SER* 3.4 10.5 - - - +
258B ILE* 1.3 74.7 - - - +
260B LEU* 1.3 64.7 + - - +
262B SER* 2.9 22.8 + - - -
263B LYS* 2.8 46.2 + - - +
281B HIS* 2.8 26.3 + - + +
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Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 4.1 9.2 - - + -
191B PHE* 4.5 3.4 - - + -
256B SER 3.0 15.0 + - - +
257B GLY 3.8 4.5 - - - +
259B ASP* 1.3 76.1 - - - +
261B LEU* 1.3 64.4 + - - +
263B LYS* 3.1 14.0 + - - +
264B MET* 3.2 26.4 + - + +
273B ILE* 4.3 7.6 - - + -
278B ALA* 3.7 28.7 - - + +
281B HIS* 3.6 25.9 + - + +
283B TYR* 3.6 31.0 - - + -
284B PHE* 3.7 22.4 - - + -
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Residues in contact with LEU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B GLY* 3.3 35.9 - - - +
191B PHE* 3.7 27.1 - - + -
192B ALA* 3.9 13.2 - - + +
195B VAL* 4.5 0.4 - - + -
246B TRP* 4.8 1.1 - - + -
250B LEU* 3.7 40.4 - - + -
253B LEU* 4.1 8.1 - - + -
257B GLY 3.0 17.7 + - - +
258B ILE* 3.8 5.6 - - - +
259B ASP 3.3 0.2 - - - -
260B LEU* 1.3 75.9 - - - +
262B SER* 1.3 62.6 + - - +
264B MET* 3.1 4.6 + - - +
265B LEU* 3.1 33.6 + - + +
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Residues in contact with SER 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B TRP* 3.4 46.9 - - - -
258B ILE* 3.0 15.9 + - - -
259B ASP* 2.9 22.0 + - - -
261B LEU* 1.3 76.7 - - - +
263B LYS* 1.3 64.2 + - - +
264B MET 3.3 0.2 - - - -
265B LEU 3.6 3.5 - - - +
266B LYS* 3.6 28.6 + - - +
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Residues in contact with LYS 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B ASP* 2.8 47.1 + - - +
260B LEU 3.1 9.7 + - - +
262B SER* 1.3 79.8 + - - +
264B MET* 1.3 62.5 + - - +
266B LYS* 3.7 23.2 - - + +
271B GLN 5.8 0.7 - - - +
272B ARG* 3.5 7.1 - - - -
273B ILE* 3.0 53.8 + - + +
281B HIS* 4.7 5.8 - - + +
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Residues in contact with MET 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 4.4 4.9 - - + -
110B LEU* 3.9 26.9 - - + -
184B ILE* 3.9 20.8 - - + +
185B TRP* 4.1 5.9 - - - -
187B VAL* 3.9 20.4 - - + -
188B GLY* 3.8 31.4 - - - -
191B PHE* 4.3 13.9 - - - -
260B LEU* 3.2 34.9 + - + +
261B LEU* 3.1 7.9 + - - +
263B LYS* 1.3 77.2 - - - +
265B LEU* 1.3 58.2 + - - +
266B LYS 3.3 1.8 - - - -
272B ARG* 3.2 27.4 + - - +
273B ILE* 3.7 14.4 - - + -
278B ALA* 4.1 2.9 - - + -
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Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B TRP* 3.4 55.6 - - + +
188B GLY* 3.9 7.0 - - - -
189B CYS* 3.9 9.0 - - - +
200B LEU* 4.0 27.6 - - + -
201B PHE* 4.5 5.4 - - + -
217B LEU* 3.9 21.5 - - + +
246B TRP* 4.3 21.4 - - + -
261B LEU* 3.1 35.4 + - + +
262B SER 3.6 7.1 + - - +
264B MET* 1.3 77.3 - - - +
266B LYS* 1.3 61.1 + - - +
267B LEU* 3.6 3.6 + - - +
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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