Contacts of the helix formed by residues 264 - 275 (chain B) in PDB entry 2E52
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 ARG 264 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A LYS 3.0 27.1 + - - -
261A ASN* 4.1 4.9 - - - +
262A PHE 3.0 32.6 + - - +
263A THR* 3.7 4.3 - - - +
264A ARG* 3.6 39.0 - - + +
267A ALA* 4.2 0.6 - - - +
263B THR* 1.3 72.8 - - - +
265B GLU* 1.3 88.5 + - - +
267B ALA* 3.3 3.6 + - - +
268B ILE* 3.0 44.5 + - + +
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Residues in contact with GLU 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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263B THR* 3.2 12.8 + - - +
264B ARG* 1.3 105.6 + - - +
266B GLU* 1.3 61.0 + - - +
268B ILE* 3.5 8.1 + - + +
269B GLU* 3.0 30.5 + - - +
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Residues in contact with GLU 266 (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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262B PHE* 3.5 44.7 - - + -
263B THR* 3.2 23.8 + - - +
265B GLU* 1.3 75.7 - - - +
267B ALA* 1.3 57.6 + - - +
269B GLU* 3.5 5.8 + - + +
270B ALA* 3.0 27.9 + - + +
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Residues in contact with ALA 267 (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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267A ALA* 3.7 27.5 - - + +
268A ILE* 4.0 20.2 - - + -
271A LEU* 4.2 6.4 - - + +
262B PHE* 3.6 19.2 - - + -
263B THR 3.0 16.4 + - - +
264B ARG* 3.7 1.1 - - - +
266B GLU* 1.3 74.2 - - - +
268B ILE* 1.3 61.1 + - - +
270B ALA* 3.4 2.8 + - - +
271B LEU* 2.9 30.1 + - - +
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Residues in contact with ILE 268 (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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259A ILE* 3.5 31.6 - - + +
260A LYS* 3.7 15.7 - - + +
262A PHE* 3.9 8.7 - - + +
267A ALA* 3.8 14.4 - - + -
264B ARG* 3.0 53.4 + - + +
265B GLU* 3.9 6.7 - - + +
267B ALA* 1.3 77.0 - - - +
269B GLU* 1.3 57.8 + - - +
271B LEU* 3.3 6.9 + - - +
272B LEU* 3.0 48.6 + - + +
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Residues in contact with GLU 269 (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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265B GLU 3.0 19.2 + - - +
266B GLU* 3.8 7.2 - - + +
268B ILE* 1.3 78.8 - - - +
270B ALA* 1.3 62.3 + - - +
272B LEU* 3.9 10.5 - - - +
273B LYS* 3.0 25.8 + - + +
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Residues in contact with ALA 270 (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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271A LEU* 3.7 25.1 - - + +
262B PHE* 4.0 10.3 - - + -
266B GLU* 3.0 18.4 + - + +
267B ALA 3.7 4.0 - - - +
269B GLU* 1.3 75.2 - - - +
271B LEU* 1.3 58.7 + - - +
273B LYS* 3.4 10.7 + - - +
274B ASP* 3.0 28.8 + - - +
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Residues in contact with LEU 271 (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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259A ILE* 3.8 25.6 - - + -
262A PHE* 3.8 11.4 - - + -
267A ALA* 4.6 4.0 - - - +
270A ALA* 3.7 28.3 - - + +
271A LEU* 4.0 29.8 - - + +
274A ASP* 3.8 23.8 - - + +
267B ALA 2.9 18.2 + - - +
268B ILE* 3.7 5.6 - - - +
269B GLU 3.3 0.2 - - - -
270B ALA* 1.3 76.5 - - - +
272B LEU* 1.3 58.0 + - - +
274B ASP* 3.0 5.3 + - + +
275B ILE* 3.0 45.9 + - + +
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Residues in contact with LEU 272 (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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256A ILE* 4.2 15.0 - - + -
259A ILE* 3.8 24.9 - - + -
260A LYS* 4.2 24.2 - - + -
268B ILE* 3.0 37.6 + - + +
269B GLU* 4.0 11.9 - - - +
271B LEU* 1.3 72.7 - - - +
273B LYS* 1.3 65.8 + - - +
275B ILE* 4.0 3.9 - - + +
276B ASN* 3.0 22.7 + - - -
277B MET* 3.9 29.3 + - + +
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Residues in contact with LYS 273 (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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54B LYS* 5.5 11.9 - - - +
269B GLU* 3.0 20.6 + - + +
270B ALA* 3.5 9.4 - - - +
272B LEU* 1.3 78.3 - - - +
274B ASP* 1.3 63.1 - - - +
276B ASN* 3.6 13.7 + - - +
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Residues in contact with ASP 274 (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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271A LEU* 5.0 2.9 - - + -
274A ASP* 3.6 28.1 - - + +
275A ILE* 3.7 31.3 - - + +
54B LYS* 5.0 9.9 + - - -
270B ALA 3.0 15.3 + - - +
271B LEU* 3.0 9.1 + - + +
273B LYS* 1.3 78.5 - - - +
275B ILE* 1.3 64.5 + - + +
276B ASN* 4.2 2.8 - - - +
9E T 5.8 0.2 + - - -
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Residues in contact with ILE 275 (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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252A TRP* 3.9 32.5 - - + -
259A ILE* 3.6 29.8 - - + -
274A ASP* 4.1 17.0 - - - +
271B LEU* 3.0 36.6 + - + +
272B LEU* 4.0 6.3 - - - +
274B ASP* 1.3 78.9 - - - +
276B ASN* 1.3 66.6 + - - +
277B MET* 3.9 18.8 - - + +
280B LYS* 3.6 22.1 + - - +
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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