Contacts of the helix formed by residues 239 - 260 (chain B) in PDB entry 3CUQ
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 THR 239 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS* 4.1 9.6 - - - +
218B LYS* 4.3 12.3 + - - +
219B SER* 4.7 15.9 - - - +
222B LEU* 3.6 17.5 - - + +
238B GLY* 1.3 75.2 - - - -
240B GLN* 1.3 78.8 + - + +
241B TYR* 3.3 20.9 - - + +
242B HIS* 3.1 37.1 + - - +
243B MET* 3.2 20.6 + - - +
293B MET* 4.0 5.8 - - - +
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Residues in contact with GLN 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ILE* 3.4 53.9 - - + +
218B LYS* 5.6 0.7 - - - +
219B SER* 6.0 0.7 - - - -
238B GLY 4.4 3.7 + - - +
239B THR* 1.3 82.7 - - + +
241B TYR* 1.3 60.3 + - - +
243B MET* 3.2 21.8 - - + +
244B GLN* 2.8 34.5 + - + +
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Residues in contact with TYR 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A SER* 4.6 0.7 - - - -
83A GLY* 5.0 2.6 - - - -
84A LYS* 3.7 56.8 + - + +
222B LEU* 4.0 6.3 - - + -
239B THR* 3.3 7.3 - - + +
240B GLN* 1.3 74.6 - - - +
242B HIS* 1.3 78.9 + + - +
244B GLN* 3.0 14.5 + - + +
245B LEU* 2.9 43.0 + - + +
277B ARG* 5.8 0.5 + - - -
281B LEU 5.2 1.9 + - - -
282B LEU* 4.1 6.2 - - - +
286B ASP* 3.3 32.8 + - - -
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Residues in contact with HIS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LEU* 3.7 26.8 - - + +
232B ARG* 5.9 2.0 + - - -
238B GLY* 4.4 3.4 - - - -
239B THR* 3.1 44.7 + - - +
241B TYR* 1.3 86.9 - + - +
243B MET* 1.3 57.8 + - - +
245B LEU* 3.1 9.8 + - - +
246B ALA* 2.9 25.5 + - - +
285B GLU* 6.4 0.2 - - + -
286B ASP* 4.1 25.7 + - - -
289B ASN* 3.9 35.3 + - + +
290B ALA* 3.5 17.0 - - - +
293B MET* 4.0 15.0 - - + -
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Residues in contact with MET 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B THR 3.2 5.7 + - - +
240B GLN* 3.2 30.3 - - - +
241B TYR 3.1 0.4 - - - -
242B HIS* 1.3 79.0 - - - +
244B GLN* 1.3 72.5 + - - +
245B LEU 3.0 1.0 + - - -
246B ALA* 3.0 15.1 + - - +
247B LYS* 3.5 45.2 - - - +
293B MET* 3.8 14.3 - - - -
297B LEU* 3.8 29.6 - - + -
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Residues in contact with GLN 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B GLN* 2.8 23.8 + - + +
241B TYR* 3.0 13.7 + - + +
243B MET* 1.3 79.0 - - - +
245B LEU* 1.3 59.5 + - - +
247B LYS* 3.8 26.0 + - - +
248B GLN* 3.5 21.2 + - - +
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Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B TYR* 2.9 37.3 + - + +
242B HIS* 3.3 11.7 - - - +
244B GLN* 1.3 76.1 - - - +
246B ALA* 1.3 64.7 + - - +
247B LYS 3.2 2.2 - - - -
248B GLN* 3.0 41.8 - - + +
249B LEU* 3.2 23.2 + - + +
277B ARG* 4.7 7.4 - - - +
282B LEU* 3.5 39.7 - - + -
286B ASP* 4.7 7.4 - - + +
290B ALA* 4.1 16.2 - - + -
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Residues in contact with ALA 246 (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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242B HIS 2.9 12.7 + - - +
243B MET* 3.0 10.7 + - - +
245B LEU* 1.3 77.1 - - - +
247B LYS* 1.3 59.9 + - - +
249B LEU* 3.4 5.1 + - - +
250B ALA 3.3 16.1 + - - -
290B ALA* 3.7 26.9 - - - +
293B MET* 4.5 0.4 - - + -
294B LEU* 3.5 24.2 - - + +
297B LEU* 3.7 22.0 - - + -
299B LEU* 3.7 3.1 - - - +
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Residues in contact with LYS 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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243B MET* 3.5 44.0 - - - +
244B GLN* 4.1 21.8 + - - +
245B LEU 3.2 0.2 - - - -
246B ALA* 1.3 75.8 - - + +
248B GLN* 1.3 68.2 - - - +
249B LEU 3.4 0.2 + - - -
250B ALA* 3.4 9.9 + - - +
251B GLY* 3.6 7.1 + - - -
297B LEU* 4.7 10.9 - - + +
299B LEU* 3.7 25.4 - - + -
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Residues in contact with GLN 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B GLN 3.5 17.6 + - - +
245B LEU* 3.0 26.8 + - + +
247B LYS* 1.3 80.3 - - - +
249B LEU* 1.3 60.8 + - + +
251B GLY* 3.3 2.6 + - - -
252B ILE* 3.1 35.0 + - + +
277B ARG* 4.3 16.5 + - - -
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 3.2 22.8 + - + +
246B ALA* 3.4 8.0 + - - +
247B LYS 3.2 0.2 - - - -
248B GLN* 1.3 78.8 - - + +
250B ALA* 1.3 66.2 - - - +
252B ILE* 3.9 9.6 - - + -
253B LEU* 2.9 41.3 + - + +
273B VAL* 4.3 33.2 - - + -
282B LEU* 4.4 12.1 - - + -
287B LEU* 4.3 18.8 - - + -
290B ALA* 4.1 21.3 - - + -
291B CYS* 4.3 14.6 - - - +
294B LEU* 5.3 3.8 - - + -
301B LEU* 3.7 3.8 - - + +
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Residues in contact with ALA 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ALA 3.3 11.7 + - - +
247B LYS 3.7 9.0 - - - +
248B GLN 3.3 0.2 - - - -
249B LEU* 1.3 78.6 - - - +
251B GLY* 1.3 61.8 + - - +
254B GLN* 3.4 23.9 + - - +
294B LEU* 5.3 0.2 - - + -
299B LEU* 4.1 30.7 - - + -
300B PRO* 4.6 7.2 - - + -
301B LEU* 3.5 23.1 - - + +
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Residues in contact with GLY 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LYS 3.6 4.5 + - - -
248B GLN 3.3 6.7 + - - -
249B LEU 3.2 0.2 - - - -
250B ALA* 1.3 79.8 - - - +
252B ILE* 1.3 65.2 + - - +
253B LEU 3.3 0.5 + - - -
254B GLN* 3.7 11.3 + - - +
255B VAL 5.0 0.9 + - - -
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Residues in contact with ILE 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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248B GLN* 3.1 27.0 + - + +
249B LEU* 3.1 13.9 + - + +
251B GLY* 1.3 77.0 - - - +
253B LEU* 1.3 76.1 + - + +
256B PRO* 3.4 19.8 - - - +
272B LEU* 4.5 8.3 - - + -
273B VAL* 4.3 20.6 - - + -
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Residues in contact with LEU 253 (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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249B LEU* 2.9 27.9 + - + +
252B ILE* 1.3 89.8 - - + +
254B GLN* 1.3 67.3 + - - +
255B VAL 3.4 2.2 - - - -
256B PRO* 3.3 5.3 - - + +
257B LEU* 2.8 39.7 + - + +
264B MET* 5.1 5.4 - - - -
269B VAL* 3.9 42.2 - - + -
272B LEU* 4.1 14.6 - - + -
273B VAL* 4.1 7.6 - - + -
291B CYS* 6.2 0.2 - - - -
301B LEU* 3.8 21.3 - - + -
313B ILE* 4.6 13.0 - - + -
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Residues in contact with GLN 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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250B ALA 3.4 16.1 + - - +
251B GLY* 3.7 8.3 + - - +
252B ILE 3.5 1.4 - - - -
253B LEU* 1.3 79.5 - - - +
255B VAL* 1.3 65.5 + - + +
257B LEU* 3.4 3.5 + - - +
258B GLU* 3.2 45.5 + - - +
300B PRO* 4.3 15.9 - - - +
301B LEU* 4.0 9.9 - - - +
315B LEU* 3.5 30.2 - - - +
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Residues in contact with VAL 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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251B GLY 5.0 0.8 + - - -
252B ILE 4.9 0.2 + - - -
254B GLN* 1.3 76.9 - - + +
256B PRO* 1.3 76.1 - - + +
257B LEU 3.0 1.6 - - - -
258B GLU* 2.9 24.0 + - + +
259B GLU* 2.9 43.1 + - + +
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Residues in contact with PRO 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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252B ILE 3.4 22.9 - - - +
253B LEU* 3.3 10.8 - - + +
255B VAL* 1.3 95.2 - - + +
257B LEU* 1.3 60.4 + - - +
259B GLU* 3.2 16.0 + - - +
260B ARG* 2.6 42.2 + - - +
264B MET* 4.8 7.2 - - - -
272B LEU* 4.1 27.6 - - + -
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Residues in contact with LEU 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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253B LEU* 2.8 32.4 + - + +
254B GLN 3.5 4.5 - - - +
256B PRO* 1.3 68.7 - - - +
258B GLU* 1.3 68.4 + - - +
260B ARG* 2.8 11.0 + - - +
261B GLY 3.1 0.2 + - - -
262B GLY* 2.8 25.4 + - - +
263B ILE* 3.5 21.1 - - - +
264B MET* 3.4 35.9 - - + +
269B VAL* 5.8 0.2 - - + -
301B LEU* 3.6 31.9 - - + -
313B ILE* 3.8 21.8 - - + +
315B LEU* 3.8 19.5 - - + +
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Residues in contact with GLU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B GLN* 3.2 31.6 + - - +
255B VAL* 2.9 30.8 + - + +
257B LEU* 1.3 78.2 - - - +
259B GLU* 1.3 63.8 + - + +
260B ARG 3.1 1.0 + - - -
261B GLY* 3.3 9.5 + - - -
262B GLY 4.5 3.1 - - - +
315B LEU* 4.2 15.7 - - + -
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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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255B VAL* 2.9 37.6 + - + +
256B PRO* 3.4 18.2 - - - +
257B LEU 3.1 0.4 - - - -
258B GLU* 1.3 78.1 - - + +
260B ARG* 1.3 69.0 + - + +
261B GLY 3.4 1.0 + - - -
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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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252A GLU* 5.5 4.2 + - - -
256B PRO* 2.6 46.4 + - - +
257B LEU 2.8 4.8 + - - +
259B GLU* 1.3 94.2 + - - +
261B GLY* 1.3 62.0 + - - +
262B GLY 3.4 1.3 - - - -
263B ILE* 3.5 21.3 - - - +
264B MET* 3.8 32.1 - - + +
268B GLU* 3.9 14.9 + - - +
272B LEU* 4.3 22.0 - - - +
348B MET* 6.0 1.6 - - - +
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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
------------------------------------------------------------
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