Contacts of the helix formed by residues 246 - 260 (chain G) in PDB entry 2JG7
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243G PHE* 3.8 0.3 - - - -
245G GLY* 1.3 75.7 - - - +
247G THR* 1.3 60.1 + - - +
248G HIS* 3.3 22.4 + - - -
249G VAL* 3.1 21.8 + - - +
250G GLY* 2.9 26.5 + - - -
268G LEU* 3.9 0.5 - - - +
1510G NAD 2.7 53.4 + - - -
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Residues in contact with THR 247 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245G GLY 3.7 1.6 + - - -
246G SER* 1.3 73.6 - - - +
248G HIS* 1.3 64.4 + - + +
251G LYS* 3.2 22.9 + - - +
268G LEU* 3.8 9.4 - - - -
269G GLY* 3.8 22.5 - - - +
398G GLU* 4.7 8.1 - - + +
424G GLN* 5.2 13.5 - - + +
472G HIS* 3.4 43.8 + - + +
261H PHE* 4.0 7.1 - - - -
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Residues in contact with HIS 248 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246G SER* 3.3 26.0 + - - -
247G THR* 1.3 83.1 - - + +
249G VAL* 1.3 80.0 + - + +
251G LYS* 3.7 7.1 + - - +
252G MET* 3.7 23.0 + - - +
1510G NAD 5.5 1.8 + - - -
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Residues in contact with VAL 249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243G PHE* 3.4 20.4 - - + -
246G SER* 3.1 20.9 + - - +
248G HIS* 1.3 87.2 - - + +
250G GLY* 1.3 67.5 + - - +
252G MET* 3.0 23.8 + - - +
253G VAL* 3.1 10.7 + - + +
1510G NAD 3.4 65.5 - - + +
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Residues in contact with GLY 250 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243G PHE* 3.6 19.9 - - - -
246G SER 2.9 18.0 + - - -
247G THR 4.1 0.9 - - - -
249G VAL* 1.3 76.4 - - - +
251G LYS* 1.3 50.5 + - - +
253G VAL* 3.2 4.3 + - - +
254G ALA* 2.7 38.6 + - - +
266G LEU* 4.4 2.8 - - - +
268G LEU* 3.7 18.6 - - - -
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Residues in contact with LYS 251 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247G THR 3.2 16.9 + - - +
248G HIS* 3.7 8.3 - - - +
249G VAL 3.2 0.4 - - - -
250G GLY* 1.3 72.9 - - - +
252G MET* 1.3 67.0 + - + +
254G ALA* 3.2 4.1 + - + +
255G MET* 2.9 38.3 + - + +
258H GLN 5.2 2.9 - - - +
259H GLU* 3.0 54.6 + - - +
261H PHE* 3.7 28.4 - - + -
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Residues in contact with MET 252 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248G HIS* 3.7 15.9 + - - +
249G VAL* 3.0 16.2 + - - +
251G LYS* 1.3 79.0 - - + +
253G VAL* 1.3 62.9 + - + +
255G MET* 3.5 6.3 + - - +
256G MET* 3.1 41.6 + - + +
1510G NAD 3.5 26.7 - - - +
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Residues in contact with VAL 253 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162G ILE* 5.3 0.2 - - + -
229G GLY 4.9 0.2 - - - +
233G ALA* 4.1 9.4 - - + -
241G LEU* 3.5 31.0 - - + -
243G PHE* 4.0 30.3 - - + -
249G VAL* 3.1 10.2 + - + +
250G GLY* 3.5 8.3 - - - +
252G MET* 1.3 77.2 - - + +
254G ALA* 1.3 67.6 + - - +
256G MET* 3.2 9.5 + - + +
257G VAL* 2.9 25.2 + - + +
264G LYS* 6.3 0.4 - - + -
266G LEU* 5.1 3.8 - - + -
1510G NAD 3.6 34.5 - - + +
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Residues in contact with ALA 254 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250G GLY 2.7 20.8 + - - +
251G LYS* 3.5 8.5 - - + +
253G VAL* 1.3 74.3 - - - +
255G MET* 1.3 52.1 + - - +
257G VAL* 3.1 3.8 + - - +
258G GLN* 2.8 36.2 + - - +
264G LYS* 4.0 12.3 - - + +
266G LEU* 3.7 18.6 - - + +
258H GLN* 3.3 31.5 - - - +
261H PHE* 4.9 0.2 - - + -
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Residues in contact with MET 255 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251G LYS* 2.9 33.6 + - + +
252G MET* 3.7 6.3 - - - +
254G ALA* 1.3 75.7 - - - +
256G MET* 1.3 57.3 + - + +
258G GLN* 4.4 0.7 - - - -
259G GLU* 3.0 28.4 + - - +
255H MET* 3.4 51.0 - - + +
258H GLN* 3.7 12.1 - - + -
259H GLU* 3.4 44.2 - - + -
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Residues in contact with MET 256 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230G THR* 3.7 35.9 - - + +
233G ALA* 3.8 22.4 - - + +
234G LYS* 3.8 28.0 - - + +
252G MET* 3.1 46.4 + - + +
253G VAL* 3.2 17.9 + - + +
255G MET* 1.3 74.8 - - + +
257G VAL* 1.3 65.3 + - - +
259G GLU* 3.3 18.9 - - - +
260G ARG* 3.6 10.9 - - - +
1510G NAD 4.7 2.9 - - - +
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Residues in contact with VAL 257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233G ALA* 3.4 17.7 - - - +
241G LEU* 3.8 28.3 - - + -
253G VAL* 2.9 22.3 + - + +
254G ALA 3.7 4.0 - - - +
256G MET* 1.3 72.4 - - - +
258G GLN* 1.3 67.4 + - - +
260G ARG* 3.2 18.4 + - - +
262G GLY* 3.0 53.5 + - - +
263G ARG 3.7 11.9 - - - +
264G LYS* 3.9 18.4 - - + +
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Residues in contact with GLN 258 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254G ALA 2.8 20.6 + - - +
255G MET 3.8 4.3 - - - +
257G VAL* 1.3 72.6 - - - +
259G GLU* 1.3 63.5 + - - +
261G PHE* 3.0 33.8 + - - +
262G GLY 5.2 0.9 - - - -
264G LYS* 2.9 23.4 + - - +
251H LYS* 5.3 2.1 - - - +
254H ALA* 3.3 27.8 - - + +
255H MET* 3.8 16.3 - - - +
258H GLN* 4.0 21.5 - - + -
264H LYS* 2.9 28.9 + - - -
266H LEU* 4.1 6.3 - - - +
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Residues in contact with GLU 259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255G MET 3.0 13.2 + - - +
256G MET* 3.3 15.3 - - - +
258G GLN* 1.3 77.0 - - - +
260G ARG* 1.3 59.9 + - - +
261G PHE* 3.7 4.5 + - - -
251H LYS* 3.1 46.4 + - - +
255H MET* 3.5 27.1 - - + -
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Residues in contact with ARG 260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232G MET 3.6 9.5 + - - -
233G ALA 2.9 23.8 + - - -
234G LYS* 3.3 22.7 - - - +
235G ASP 2.9 24.0 + - - -
236G GLU* 3.8 34.7 + - + +
238G VAL* 3.0 31.5 + - - +
241G LEU* 4.8 2.6 - - - +
256G MET 3.6 8.3 - - - +
257G VAL* 3.3 26.2 - - - +
259G GLU* 1.3 80.3 - - + +
261G PHE* 1.3 71.3 + - - +
262G GLY* 3.2 21.0 + - - -
263G ARG 5.3 1.0 + - - -
472H HIS* 4.6 7.5 - - - -
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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