Contacts of the helix formed by residues 246 - 260 (chain J) in PDB entry 2ONM
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 SER 246 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243J PHE* 3.5 1.7 - - - -
245J GLY* 1.3 73.5 - - - -
247J THR* 1.3 59.3 + - - +
248J GLU* 3.9 10.7 - - - +
249J ILE* 3.3 17.7 + - - +
250J GLY 3.0 22.7 + - - -
269J LEU* 3.4 7.3 - - - +
270J GLY 5.2 0.9 - - - +
510J ADP 2.6 41.0 + - - -
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Residues in contact with THR 247 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262I LEU* 4.6 5.8 - - + -
245J GLY 3.9 1.0 + - - -
246J SER* 1.3 73.0 - - - +
248J GLU* 1.3 62.8 + - - +
250J GLY* 3.2 6.6 + - - -
251J ARG* 3.0 30.3 + - + +
269J LEU* 3.7 19.9 - - + +
270J GLY* 4.7 2.0 + - - +
424J THR* 5.8 1.3 - - + -
425J TYR* 2.9 35.4 + - + -
470J MET* 3.6 37.2 - - + +
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Residues in contact with GLU 248 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246J SER* 3.9 11.6 - - - +
247J THR* 1.3 81.0 - - - +
249J ILE* 1.3 72.9 + - + +
251J ARG* 3.5 18.6 + - - +
252J VAL* 3.6 13.3 - - + +
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Residues in contact with ILE 249 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243J PHE* 3.6 17.3 - - + -
246J SER* 3.3 15.9 + - - +
248J GLU* 1.3 85.8 - - + +
250J GLY* 1.3 65.5 + - - +
251J ARG 3.1 2.7 - - - -
252J VAL* 3.0 11.5 + - + +
253J ILE* 3.0 22.6 + - + +
510J ADP 3.3 84.4 - - + +
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Residues in contact with GLY 250 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262I LEU* 4.5 1.3 - - - -
243J PHE* 3.7 15.0 - - - -
246J SER 3.0 15.1 + - - -
247J THR 3.2 6.1 + - - -
249J ILE* 1.3 78.0 - - - +
251J ARG* 1.3 58.7 + - - +
253J ILE* 3.6 0.8 + - - -
254J GLN* 3.3 16.3 + - - +
267J LEU* 3.5 28.3 - - - +
269J LEU* 3.9 10.8 - - - -
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Residues in contact with ARG 251 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236I GLU* 5.1 0.4 + - - -
258I GLY 4.1 15.0 + - - +
259I SER 4.5 6.4 + - - -
260I SER 2.5 31.3 + - - -
261I ASN* 4.5 0.2 - - - +
262I LEU* 3.9 22.7 - - + +
247J THR* 3.0 24.1 - - - +
248J GLU* 3.7 11.0 - - - +
249J ILE 3.1 0.4 - - - -
250J GLY* 1.3 74.8 - - - +
252J VAL* 1.3 67.2 + - + +
254J GLN* 3.4 2.1 + - - +
255J VAL* 3.1 30.8 + - + +
470J MET* 3.8 26.7 - - - +
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Residues in contact with VAL 252 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230J ALA* 5.9 3.4 - - + -
248J GLU* 3.6 17.0 - - + +
249J ILE* 3.0 19.5 + - + +
251J ARG* 1.3 78.9 - - + +
253J ILE* 1.3 56.5 + - - +
255J VAL* 3.4 5.5 + - - +
256J ALA* 2.9 32.6 + - + +
510J ADP 4.1 24.9 - - - +
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Residues in contact with ILE 253 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165J ILE* 3.8 12.8 - - + -
233J ALA* 3.7 17.6 - - + +
241J VAL* 3.9 31.9 - - + -
243J PHE* 4.0 25.8 - - + -
249J ILE* 3.0 15.1 + - + +
250J GLY 3.7 6.5 - - - +
252J VAL* 1.3 76.8 - - + +
254J GLN* 1.3 57.3 + - - +
256J ALA* 3.3 6.4 + - - +
257J ALA* 3.0 28.1 + - - +
265J VAL* 4.3 9.0 - - + -
267J LEU* 4.3 2.7 - - + -
510J ADP 3.3 34.8 - - + +
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Residues in contact with GLN 254 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254I GLN* 3.0 37.4 + - - +
258I GLY* 3.4 25.7 - - - +
262I LEU* 3.8 15.9 - - + +
263I LYS 4.9 11.3 + - - +
265I VAL* 5.0 3.2 - - - +
250J GLY 3.3 12.2 + - - +
251J ARG 3.4 8.2 + - - +
253J ILE* 1.3 79.2 - - - +
255J VAL* 1.3 61.0 + - - +
257J ALA* 3.4 7.1 + - - +
258J GLY* 3.1 18.4 + - - -
265J VAL* 4.1 22.7 + - - +
267J LEU* 3.7 19.0 - - + +
473J SER* 5.1 3.6 + - - -
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Residues in contact with VAL 255 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255I VAL* 4.6 20.6 - - + +
258I GLY* 3.9 25.4 - - - +
259I SER* 4.1 12.6 - - - +
251J ARG* 3.1 17.8 + - + +
252J VAL* 3.8 5.6 - - - +
254J GLN* 1.3 73.4 - - - +
256J ALA* 1.3 62.3 + - - +
258J GLY* 3.2 1.7 + - - -
259J SER* 2.9 44.6 + - - +
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Residues in contact with ALA 256 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230J ALA* 6.1 1.6 - - + -
233J ALA* 3.7 17.8 - - + +
234J SER* 3.5 24.7 + - - +
252J VAL* 2.9 23.0 + - + +
253J ILE 3.3 4.9 + - - +
255J VAL* 1.3 76.0 - - - +
257J ALA* 1.3 51.1 + - - +
259J SER* 3.7 6.3 + - - -
260J SER* 2.8 33.6 + - - -
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Residues in contact with ALA 257 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254I GLN* 4.9 2.9 - - + -
233J ALA 4.0 4.7 - - - +
241J VAL* 4.8 0.9 - - + -
253J ILE 3.0 13.1 + - - +
254J GLN 3.5 4.3 - - - +
255J VAL 3.1 0.2 - - - -
256J ALA* 1.3 76.2 - - - +
258J GLY* 1.3 61.8 + - - +
259J SER 3.2 0.2 - - - -
260J SER* 3.1 12.2 + - - -
262J LEU* 3.1 27.7 + - - -
263J LYS* 3.7 18.9 + - + +
265J VAL* 3.4 33.2 - - + -
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Residues in contact with GLY 258 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251I ARG* 4.1 25.3 + - - +
254I GLN* 3.4 30.9 - - - +
255I VAL* 4.0 12.1 - - - +
254J GLN 3.1 9.2 + - - -
255J VAL 3.2 2.9 + - - -
257J ALA* 1.3 79.5 - - - +
259J SER* 1.3 59.3 + - - +
260J SER 3.6 1.0 + - - -
262J LEU* 4.1 8.9 - - - +
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Residues in contact with SER 259 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251I ARG* 3.9 8.7 + - - +
255I VAL* 4.0 14.2 - - - +
236J GLU* 4.8 0.5 - - - +
255J VAL* 2.9 27.1 + - - +
256J ALA* 4.1 7.2 - - - -
258J GLY* 1.3 77.7 - - - +
260J SER* 1.3 60.7 + - - +
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Residues in contact with SER 260 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251I ARG* 2.6 29.5 + - - -
470I MET* 4.5 0.7 - - - +
234J SER* 3.4 26.5 - - - -
235J HIS 4.5 0.2 - - - -
236J GLU* 3.5 23.9 - - - +
256J ALA 2.8 22.1 + - - -
257J ALA 3.1 5.5 + - - -
258J GLY 3.3 1.9 - - - -
259J SER* 1.3 77.3 - - - +
261J ASN* 1.3 66.6 + - - -
262J LEU 3.7 1.6 - - - -
263J LYS* 3.1 17.2 + - - -
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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