Contacts of the helix formed by residues 243 - 260 (chain B) in PDB entry 2JGZ
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 MET 243 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B VAL* 3.6 12.1 - - + -
240B PRO* 2.5 42.3 + - + +
242B LYS* 1.3 94.2 - - + +
244B LEU* 1.3 60.3 + - - -
245B GLN 3.5 1.1 - - - -
246B LEU* 3.3 20.3 + - + +
247B VAL* 3.2 22.5 + - - +
277B TYR* 4.0 21.3 - - + -
281B GLN* 4.6 12.6 - - - +
285B MET* 4.9 8.3 - - + -
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B VAL* 4.0 28.5 - - + -
201B MET* 4.1 29.2 - - + +
202B ARG* 4.8 2.2 - - - +
205B LEU* 3.8 22.0 - - + +
234B MET* 3.9 26.0 - - + -
239B VAL* 3.9 22.0 - - + -
240B PRO 3.3 2.3 + - - +
241B LYS* 3.1 18.9 + - - +
242B LYS 3.3 0.2 - - - -
243B MET* 1.3 72.7 - - - +
245B GLN* 1.3 67.1 + - - +
246B LEU 3.1 1.6 - - - -
247B VAL* 3.2 7.0 + - + +
248B GLY 3.1 18.5 + - - -
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Residues in contact with GLN 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 4.0 9.6 - - + +
208B TRP* 3.5 51.4 - - + +
241B LYS 4.7 0.2 + - - -
242B LYS 4.4 0.8 + - - +
243B MET 3.5 0.2 - - - -
244B LEU* 1.3 79.1 - - - +
246B LEU* 1.3 62.0 + - - +
248B GLY* 3.5 0.7 + - - -
249B VAL* 3.2 25.1 + - - +
273B THR* 3.5 28.7 - - + +
276B THR* 4.1 4.5 + - - +
277B TYR* 3.6 17.8 + - + +
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Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B MET* 3.3 23.5 + - - +
244B LEU 3.1 0.2 - - - -
245B GLN* 1.3 79.1 - - - +
247B VAL* 1.3 59.6 + - - +
249B VAL* 3.6 3.4 - - + +
250B THR* 2.9 33.8 + - - +
277B TYR* 3.5 46.8 + - + -
281B GLN* 4.0 14.8 - - + +
282B ILE* 3.7 33.9 - - + +
285B MET* 3.8 33.9 - - + -
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Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 5.8 0.9 - - + -
230B ILE* 4.5 23.3 - - + +
233B PHE* 4.1 27.8 - - + -
234B MET* 5.2 7.9 - - + -
239B VAL* 3.9 15.9 - - + -
243B MET 3.2 12.3 + - - +
244B LEU* 3.2 11.5 + - + +
246B LEU* 1.3 73.3 - - - +
248B GLY* 1.3 67.9 + - - +
250B THR* 4.0 0.6 - - - -
251B ALA* 2.9 24.1 + - + +
285B MET* 3.7 31.2 - - + -
289B ILE* 4.5 6.6 - - + +
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Residues in contact with GLY 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 4.1 7.1 - - - +
209B LEU* 3.9 28.7 - - - +
226B THR* 4.1 1.6 - - - +
230B ILE* 4.0 9.6 - - - -
244B LEU 3.1 13.2 + - - -
245B GLN 3.5 3.6 + - - -
247B VAL* 1.3 78.3 - - - +
249B VAL* 1.3 62.2 + - - +
251B ALA* 3.3 3.1 + - - +
252B MET* 3.0 21.3 + - - +
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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
----------------------------------------------------------
208B TRP* 3.7 22.7 - - + -
209B LEU* 4.5 4.5 - - + -
212B VAL* 5.6 0.7 - - + -
245B GLN 3.2 14.1 + - - +
246B LEU* 3.6 11.9 - - + +
248B GLY* 1.3 74.4 - - - +
250B THR* 1.3 55.8 + - - +
252B MET* 3.1 7.4 + - - +
253B PHE* 2.6 36.9 + - - +
269B PHE* 3.9 26.1 - - + +
272B VAL* 4.4 4.3 - - + -
273B THR* 3.6 32.1 - - + -
277B TYR* 5.2 0.2 - - + -
282B ILE* 4.2 20.4 - - + -
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Residues in contact with THR 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B LEU* 2.9 23.0 + - - +
247B VAL 4.0 2.2 - - - -
248B GLY 3.3 0.2 - - - -
249B VAL* 1.3 73.2 - - - +
251B ALA* 1.3 67.5 + - - +
253B PHE* 3.0 10.5 + - + +
254B ILE* 2.8 25.8 + - + +
282B ILE* 3.4 22.5 - - + +
285B MET* 3.6 19.5 - - - +
286B GLU* 3.4 40.8 - - + +
289B ILE* 4.0 6.7 - - + -
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B THR* 3.9 9.6 - - + +
229B ILE* 3.8 28.7 - - + +
230B ILE* 3.6 24.7 - - + -
247B VAL* 2.9 19.0 + - + +
248B GLY 3.4 4.5 - - - +
250B THR* 1.3 77.5 - - - +
252B MET* 1.3 58.0 + - - +
254B ILE* 3.2 7.1 + - - +
255B ALA* 2.9 27.9 + - - +
289B ILE* 4.4 3.7 - - + +
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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
----------------------------------------------------------
209B LEU* 3.6 41.3 - - + +
212B VAL* 3.7 18.4 - - - -
213B GLN* 4.2 6.7 - - + +
218B LEU* 3.8 19.5 - - + -
222B THR* 4.6 4.3 - - + -
223B MET* 4.0 20.0 - - - -
226B THR* 3.1 24.7 + - + +
248B GLY 3.0 13.7 + - - +
249B VAL* 3.6 7.6 - - - +
251B ALA* 1.3 76.3 - - - +
253B PHE* 1.3 53.5 + - - +
255B ALA 3.2 1.2 + - - -
256B SER* 2.7 37.9 + - - -
269B PHE* 3.6 23.3 - - + -
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Residues in contact with PHE 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 3.2 34.5 - - - -
249B VAL 2.6 17.9 + - - +
250B THR* 3.2 13.5 - - + +
252B MET* 1.3 72.5 - - - +
254B ILE* 1.3 61.1 + - - +
256B SER* 3.1 14.8 + - - -
257B LYS* 3.1 40.4 + - + +
263B PRO* 6.3 0.2 - - + -
264B PRO 4.2 8.5 - - - -
266B ILE* 3.7 45.1 - - + -
269B PHE* 3.4 29.9 - + + -
282B ILE* 4.1 18.6 - - + -
283B ARG* 5.7 0.9 - - + -
286B GLU* 4.2 13.2 - - + -
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Residues in contact with ILE 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 4.6 6.2 - - + +
225B MET* 5.8 0.2 - - - -
229B ILE* 3.7 17.9 - - + -
250B THR* 2.8 30.6 + - + +
251B ALA* 3.5 8.3 - - - +
253B PHE* 1.3 69.4 - - + +
255B ALA* 1.3 68.5 + - - +
257B LYS* 2.9 19.9 + - - +
258B TYR* 2.9 12.4 + - + +
286B GLU* 4.1 28.9 - - + +
289B ILE* 4.0 24.0 - - + -
290B LEU* 4.0 22.4 - - + -
297B LEU* 3.8 26.7 - - + -
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Residues in contact with ALA 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B THR* 3.7 16.4 - - + +
225B MET* 3.7 32.1 - - + -
226B THR* 3.6 20.4 - - - +
229B ILE* 4.4 0.9 - - + -
251B ALA 2.9 16.0 + - - +
252B MET 3.6 1.1 - - - +
254B ILE* 1.3 77.4 - - - +
256B SER* 1.3 58.0 + - - +
258B TYR* 3.4 1.6 + - - +
259B GLU* 2.9 33.6 + - - +
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Residues in contact with SER 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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218B LEU* 4.9 3.4 - - - -
222B THR* 3.6 9.4 - - - +
252B MET 2.7 25.3 + - - -
253B PHE* 3.1 15.4 + - - -
255B ALA* 1.3 70.9 - - - +
257B LYS* 1.3 58.9 + - - +
260B GLU* 2.9 52.2 + - - +
263B PRO* 3.5 16.1 - - - +
264B PRO* 4.2 8.9 - - - +
269B PHE* 3.5 13.7 - - - -
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Residues in contact with LYS 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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42A GLU* 2.7 33.7 + - + +
44A VAL 2.8 24.0 + - - +
45A PRO* 5.3 0.2 - - + -
46A SER* 3.4 35.0 - - - +
49A ILE* 3.5 18.2 - - + -
50A ARG* 3.8 10.0 + - - -
253B PHE* 3.1 41.3 + - + +
254B ILE 2.9 8.2 + - - +
256B SER* 1.3 75.6 - - - +
258B TYR* 1.3 62.9 + - - +
260B GLU 4.5 2.4 - - - +
263B PRO* 4.5 16.1 - - + +
286B GLU* 2.8 23.5 + - - -
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Residues in contact with TYR 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 3.9 23.3 - - + +
50A ARG* 2.9 47.3 + - + +
53A SER* 4.1 22.6 + - - -
54A LEU* 4.3 10.2 - - + +
122A ARG* 4.6 1.9 + - - -
150A ARG* 4.7 2.6 + - - +
151A ALA* 3.5 29.6 - - + +
225B MET* 3.4 38.6 - - + -
254B ILE 2.9 15.3 + - - +
255B ALA 3.7 3.6 - - - +
257B LYS* 1.3 79.1 - - - +
259B GLU* 1.3 67.3 - - + +
297B LEU* 4.2 17.7 - - + -
298B GLY* 4.0 15.2 - - - -
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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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50A ARG* 4.2 0.2 - - - -
150A ARG* 3.0 13.0 + - - +
151A ALA* 5.5 2.5 - - - +
157A ARG* 2.7 66.8 + - - +
219B LEU* 3.7 4.5 - - + +
221B GLU* 4.1 17.6 - - + +
222B THR* 3.7 17.0 - - - +
225B MET* 3.4 34.8 - - + +
255B ALA 2.9 14.7 + - - +
258B TYR* 1.3 87.1 - - + +
260B GLU* 1.3 58.5 + - - +
261B MET 3.9 0.5 + - - -
301B LEU* 4.6 3.5 - - - +
304B HIS* 4.8 6.9 + - - -
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Residues in contact with GLU 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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50A ARG* 3.8 11.6 + - - -
160A TPO 4.1 0.3 + - - -
217B ARG 4.7 2.4 - - - +
218B LEU* 3.5 20.4 - - + +
219B LEU* 3.1 36.1 + - - +
222B THR* 2.6 22.5 + - - +
256B SER* 2.9 43.0 + - - +
257B LYS 4.5 3.1 - - - +
259B GLU* 1.3 74.2 - - - +
261B MET* 1.3 63.6 + - - +
262B TYR 4.1 5.5 + - - +
263B PRO* 3.4 26.5 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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