Contacts of the helix formed by residues 246 - 260 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243B PHE* 3.8 0.5 - - - -
245B GLY* 1.3 74.0 - - - -
247B THR* 1.3 59.2 + - - +
248B HIS* 3.7 8.4 + - - +
249B VAL* 3.1 21.3 + - - +
250B GLY* 2.9 26.7 + - - -
268B LEU* 3.9 0.7 - - - +
398B GLU* 5.6 0.2 - - - -
1510B NAD 2.8 54.2 + - - -
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Residues in contact with THR 247 (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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261A PHE* 4.1 7.3 - - - -
245B GLY 3.7 1.2 + - - -
246B SER* 1.3 73.6 - - - +
248B HIS* 1.3 62.0 + - - +
251B LYS* 3.2 23.2 + - - +
268B LEU* 3.8 9.2 - - - -
269B GLY* 3.8 22.7 - - - +
398B GLU* 4.8 7.9 - - + +
424B GLN* 5.2 13.7 - - + +
472B HIS* 3.5 42.9 + - + +
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Residues in contact with HIS 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B SER* 3.9 8.7 - - - +
247B THR* 1.3 80.4 - - - +
249B VAL* 1.3 77.7 + - + +
251B LYS* 3.7 9.7 + - - +
252B MET* 3.7 28.2 + - - +
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B PHE* 3.4 20.0 - - + -
246B SER* 3.1 19.5 + - - +
248B HIS* 1.3 90.9 - - + +
250B GLY* 1.3 67.0 + - - +
252B MET* 3.1 19.2 + - - +
253B VAL* 3.1 12.0 + - + +
1510B NAD 3.3 64.6 - - + +
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Residues in contact with GLY 250 (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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243B PHE* 3.7 20.1 - - - -
246B SER 2.9 17.5 + - - -
247B THR 4.0 1.1 - - - -
248B HIS 3.4 0.2 - - - -
249B VAL* 1.3 77.0 - - - +
251B LYS* 1.3 51.3 + - - +
253B VAL* 3.3 3.7 + - - +
254B ALA* 2.7 37.5 + - - +
266B LEU* 4.3 3.3 - - - +
268B LEU* 3.7 18.4 - - - -
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Residues in contact with LYS 251 (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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258A GLN 5.3 2.5 - - - +
259A GLU* 3.1 53.0 + - - +
261A PHE* 3.7 28.8 - - + -
247B THR 3.2 18.4 + - - +
248B HIS* 3.7 7.2 - - - +
249B VAL 3.2 0.4 - - - -
250B GLY* 1.3 73.4 - - - +
252B MET* 1.3 65.1 + - + +
254B ALA* 3.3 4.1 + - + +
255B MET* 2.9 39.7 + - + +
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Residues in contact with MET 252 (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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230B THR* 5.8 0.2 - - - +
248B HIS* 3.7 33.1 + - - +
249B VAL* 3.1 12.2 + - - +
251B LYS* 1.3 79.1 - - + +
253B VAL* 1.3 63.4 + - + +
255B MET* 3.4 6.8 + - - +
256B MET* 3.1 41.3 + - + +
1510B NAD 3.5 26.7 - - - +
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Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B GLY 5.1 0.4 - - - +
233B ALA* 4.1 8.3 - - + -
241B LEU* 3.5 31.2 - - + -
243B PHE* 4.0 30.5 - - + -
249B VAL* 3.1 11.1 + - + +
250B GLY 3.5 8.7 - - - +
252B MET* 1.3 77.0 - - + +
254B ALA* 1.3 60.8 + - - +
256B MET* 3.2 10.8 + - + +
257B VAL* 2.9 30.0 + - + +
264B LYS* 6.3 0.7 - - + -
266B LEU* 5.0 3.4 - - + -
1510B NAD 3.6 34.3 - - + +
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Residues in contact with ALA 254 (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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258A GLN* 3.3 30.8 - - + +
261A PHE* 5.0 0.7 - - + -
250B GLY 2.7 21.0 + - - +
251B LYS* 3.3 8.7 + - + +
253B VAL* 1.3 73.8 - - - +
255B MET* 1.3 53.5 + - - +
257B VAL* 3.2 4.0 + - - +
258B GLN* 2.8 35.9 + - - +
264B LYS* 4.0 11.8 - - + +
266B LEU* 3.7 18.8 - - + -
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Residues in contact with MET 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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255A MET* 3.4 50.0 - - + +
258A GLN* 3.7 13.9 - - + -
259A GLU* 3.5 42.0 - - + -
251B LYS* 2.9 33.6 + - + +
252B MET* 3.6 7.0 - - - +
254B ALA* 1.3 74.7 - - - +
256B MET* 1.3 58.0 + - + +
258B GLN* 4.4 0.4 - - - -
259B GLU* 3.1 27.7 + - - +
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Residues in contact with MET 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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230B THR* 3.7 36.6 - - + +
233B ALA* 3.8 21.2 - - + +
234B LYS* 3.8 27.5 - - + +
252B MET* 3.1 45.6 + - + +
253B VAL* 3.2 18.1 + - + +
255B MET* 1.3 76.6 - - + +
257B VAL* 1.3 61.4 + - - +
259B GLU* 3.3 18.8 - - - +
260B ARG* 3.6 10.7 + - - +
1510B NAD 4.7 2.5 - - - +
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Residues in contact with VAL 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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233B ALA* 3.4 18.6 - - - +
241B LEU* 3.9 28.3 - - + -
253B VAL* 2.9 21.9 + - + +
254B ALA 3.7 3.8 - - - +
256B MET* 1.3 74.2 - - - +
258B GLN* 1.3 64.2 + - - +
260B ARG* 3.3 14.8 + - - +
261B PHE 3.3 2.9 + - - -
262B GLY* 3.0 53.7 + - - +
263B ARG 3.7 11.9 - - - +
264B LYS* 3.9 17.7 - - + +
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Residues in contact with GLN 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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251A LYS* 5.3 2.1 - - - +
254A ALA* 3.4 26.3 - - + +
255A MET* 3.8 16.2 - - + +
258A GLN* 4.0 22.2 - - + -
264A LYS* 3.0 23.4 - - - -
266A LEU* 4.2 5.5 - - - +
254B ALA 2.8 20.8 + - - +
255B MET 3.8 4.5 - - - +
257B VAL* 1.3 72.6 - - - +
259B GLU* 1.3 64.2 + - - +
261B PHE* 3.0 35.6 + - - +
262B GLY 5.1 0.9 + - - +
264B LYS* 3.0 26.9 + - - +
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Residues in contact with GLU 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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251A LYS* 3.0 45.3 + - - +
255A MET* 3.5 25.3 - - + -
255B MET 3.1 13.2 + - - +
256B MET* 3.3 15.9 - - - +
257B VAL 3.3 0.2 - - - -
258B GLN* 1.3 77.4 - - - +
260B ARG* 1.3 60.8 + - - +
261B PHE* 3.7 4.5 + - - -
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Residues in contact with ARG 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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472A HIS* 4.5 7.0 - - - -
232B MET 3.5 9.1 + - - -
233B ALA 2.9 25.0 + - - -
234B LYS* 3.3 22.5 - - - +
235B ASP 2.9 24.0 + - - -
236B GLU* 3.8 33.7 + - + +
238B VAL* 3.0 32.5 + - - +
241B LEU* 4.8 3.0 - - - +
256B MET 3.6 8.5 - - - +
257B VAL* 3.4 25.9 - - - +
259B GLU* 1.3 81.5 - - - +
261B PHE* 1.3 70.8 + - - +
262B GLY* 3.2 21.6 + - - -
263B ARG 5.4 0.4 + - - -
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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