Contacts of the helix formed by residues 246 - 260 (chain H) in PDB entry 1O04
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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243H PHE* 3.7 0.9 - - - -
245H GLY* 1.3 75.4 - - - -
247H THR* 1.3 64.4 + - - +
248H GLU* 3.8 10.7 + - - +
249H ILE* 3.2 19.1 + - - +
250H GLY 3.0 18.0 + - - -
269H LEU* 3.6 3.5 - - - +
399H GLU* 5.5 0.2 - - - -
6508H NAD 2.8 52.2 + - - -
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Residues in contact with THR 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262G LEU* 3.9 14.6 - - + +
245H GLY 3.8 1.6 + - - -
246H SER* 1.3 71.1 - - - +
248H GLU* 1.3 63.8 + - - +
250H GLY* 3.1 10.0 + - - -
251H ARG* 3.2 20.5 + - - +
269H LEU* 3.3 9.0 - - - +
270H GLY* 3.3 10.5 + - - +
425H TYR* 3.3 29.9 + - + +
470H MET* 2.9 44.2 + - + +
6508H NAD 4.5 0.8 + - - -
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Residues in contact with GLU 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246H SER* 3.9 9.8 - - - +
247H THR* 1.3 81.6 - - - +
249H ILE* 1.3 75.7 + - + +
251H ARG* 3.5 23.3 + - - +
252H VAL* 3.6 10.7 + - + +
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Residues in contact with ILE 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243H PHE* 3.5 21.1 - - + -
246H SER* 3.2 15.6 + - - +
248H GLU* 1.3 92.2 - - + +
250H GLY* 1.3 65.0 + - - +
252H VAL* 2.9 14.6 + - + +
253H ILE* 2.9 22.2 + - + +
6508H NAD 3.4 76.1 - - + +
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Residues in contact with GLY 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262G LEU* 4.1 5.8 - - - -
243H PHE* 3.7 10.1 - - - -
246H SER 3.0 10.9 + - - -
247H THR 3.1 5.5 + - - -
249H ILE* 1.3 76.2 - - - +
251H ARG* 1.3 61.8 + - - +
253H ILE* 3.3 3.2 + - - +
254H GLN* 3.0 24.4 + - - +
267H LEU* 3.9 8.9 - - - +
269H LEU* 3.8 23.1 - - - -
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Residues in contact with ARG 251 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236G GLU* 5.0 4.0 + - - -
258G GLY 3.4 20.8 - - - +
259G SER* 3.7 14.3 + - - -
260G SER 3.0 27.9 + - - -
262G LEU* 3.8 18.3 - - + +
247H THR* 3.2 19.9 + - - +
248H GLU* 3.6 14.4 - - - +
249H ILE 3.2 0.4 - - - -
250H GLY* 1.3 74.4 - - - +
252H VAL* 1.3 64.8 + - + +
254H GLN* 3.3 1.7 + - - +
255H VAL* 3.0 29.8 + - + +
470H MET* 3.7 29.3 - - - +
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Residues in contact with VAL 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230H ALA* 6.1 2.0 - - + -
248H GLU* 3.8 14.6 - - + +
249H ILE* 2.9 22.0 + - + +
251H ARG* 1.3 79.2 - - + +
253H ILE* 1.3 56.8 + - + +
255H VAL* 3.4 6.0 + - - +
256H ALA* 2.9 31.0 + - + +
6508H NAD 4.0 27.1 - - - +
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Residues in contact with ILE 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H ILE* 3.9 7.4 - - + -
233H ALA* 3.8 18.0 - - + +
241H VAL* 3.9 26.9 - - + -
243H PHE* 3.7 34.8 - - + -
249H ILE* 2.9 18.6 + - + +
250H GLY 3.5 6.3 - - - +
252H VAL* 1.3 75.2 - - + +
254H GLN* 1.3 66.3 + - - +
256H ALA* 3.2 6.1 + - - +
257H ALA* 3.0 22.5 + - - +
265H VAL* 4.5 2.2 - - + -
267H LEU* 4.0 17.5 - - + -
6508H NAD 3.6 31.2 - - + +
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Residues in contact with GLN 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254G GLN* 3.9 17.0 - - + +
257G ALA* 3.3 22.1 - - - +
258G GLY* 3.6 24.0 - - - +
262G LEU* 3.2 35.1 + - + +
263G LYS 3.4 10.0 - - - +
265G VAL* 3.8 8.5 + - - +
250H GLY 3.0 15.3 + - - +
251H ARG 3.3 0.2 + - - -
253H ILE* 1.3 78.7 - - - +
255H VAL* 1.3 61.4 + - - +
257H ALA* 3.4 6.9 + - - +
258H GLY* 3.1 19.2 + - - -
265H VAL* 4.8 11.0 - - + +
267H LEU* 3.6 15.4 - - + +
473H SER* 5.5 2.2 + - - -
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Residues in contact with VAL 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255G VAL* 3.8 21.8 - - + +
258G GLY 3.8 1.8 - - - -
259G SER* 3.4 37.2 - - - +
251H ARG* 3.0 22.3 + - + +
252H VAL* 3.8 5.8 - - - +
254H GLN* 1.3 76.8 - - - +
256H ALA* 1.3 57.5 + - - +
258H GLY* 3.3 1.2 + - - -
259H SER* 2.8 44.1 + - - +
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Residues in contact with ALA 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230H ALA* 5.3 1.1 - - + +
233H ALA* 3.8 19.7 - - + -
234H SER* 3.5 23.7 + - - +
252H VAL* 2.9 21.0 + - + +
253H ILE 3.2 4.9 + - - +
255H VAL* 1.3 77.8 - - - +
257H ALA* 1.3 53.9 + - - +
259H SER* 3.4 5.6 + - - -
260H SER* 2.7 36.5 + - - -
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Residues in contact with ALA 257 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254G GLN* 3.4 19.3 - - - +
233H ALA 3.9 2.8 + - - +
241H VAL* 4.9 0.7 - - + -
253H ILE 3.0 12.3 + - - +
254H GLN 3.7 2.0 - - - +
255H VAL 3.3 0.2 - - - -
256H ALA* 1.3 74.6 - - - +
258H GLY* 1.3 62.7 + - - +
260H SER* 3.4 11.2 + - - -
262H LEU 3.0 26.7 + - - -
263H LYS* 3.5 21.5 - - + +
265H VAL* 3.4 24.9 - - + -
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Residues in contact with GLY 258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251G ARG* 3.3 29.6 + - - +
254G GLN* 3.7 32.7 - - - -
255G VAL* 3.8 11.9 - - - -
254H GLN 3.1 11.0 + - - -
255H VAL 3.8 2.2 - - - -
257H ALA* 1.3 78.1 - - - +
259H SER* 1.3 60.6 + - - +
260H SER 3.5 1.6 + - - +
262H LEU* 4.1 2.2 - - - +
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Residues in contact with SER 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251G ARG* 3.4 14.7 + - - +
255G VAL* 3.4 14.6 - - - +
255H VAL* 2.8 31.6 + - - +
256H ALA* 3.9 6.1 - - - -
258H GLY* 1.3 77.2 - - - +
260H SER* 1.3 57.1 + - - +
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Residues in contact with SER 260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251G ARG* 2.8 32.6 + - - -
233H ALA 3.7 0.7 + - - -
234H SER* 3.3 27.8 - - - -
236H GLU* 3.5 20.5 - - - +
256H ALA 2.7 20.4 + - - -
257H ALA 3.4 2.4 + - - -
258H GLY 3.3 1.4 - - - +
259H SER* 1.3 75.9 - - - +
261H ASN* 1.3 67.1 + - - -
262H LEU 3.6 2.4 + - - -
263H LYS* 3.1 20.8 + - - -
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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