Contacts of the helix formed by residues 242 - 264 (chain L) in PDB entry 6O85
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 GLU 242 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188L VAL* 5.4 0.8 - - - +
241L LEU* 1.3 80.3 - - + +
243L ARG* 1.3 60.0 + - - +
244L THR* 3.2 3.6 - - - -
245L GLU* 2.9 17.8 + - + +
246L GLY 2.8 21.7 + - - -
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Residues in contact with ARG 243 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188L VAL* 4.0 24.0 - - + +
190L ILE* 5.7 7.6 - - + -
240L THR 5.1 1.3 - - - -
241L LEU 3.6 1.7 - - - -
242L GLU* 1.3 71.9 - - - +
244L THR* 1.3 59.3 + - - +
245L GLU 3.2 0.2 - - - -
246L GLY* 3.5 5.6 - - - +
247L LEU* 2.9 31.2 + - - +
276L VAL* 5.3 10.8 - - + -
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Residues in contact with THR 244 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242L GLU* 3.2 1.4 - - - -
243L ARG* 1.3 79.0 - - - +
245L GLU* 1.3 59.2 + - - +
247L LEU* 4.2 3.6 + - - +
248L SER* 3.8 16.1 + - - -
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Residues in contact with GLU 245 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242L GLU* 2.9 19.6 + - + +
244L THR* 1.3 76.0 - - - +
246L GLY* 1.3 60.3 + - - +
247L LEU 3.3 0.7 - - - -
248L SER* 3.3 7.5 + - - -
249L VAL* 2.9 28.8 + - - +
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Residues in contact with GLY 246 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190L ILE* 4.5 11.5 - - - +
238L THR* 5.2 5.9 - - - -
240L THR* 6.1 4.7 - - - -
241L LEU 5.2 2.7 - - - -
242L GLU 2.8 13.8 + - - -
243L ARG* 3.3 6.2 + - - -
245L GLU* 1.3 74.6 - - - +
247L LEU* 1.3 58.2 + - - +
249L VAL* 3.3 7.1 + - - +
250L LEU* 2.9 29.6 + - - +
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Residues in contact with LEU 247 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190L ILE* 4.5 6.1 - - + +
243L ARG 2.9 17.4 + - - +
244L THR* 4.5 4.9 - - - +
246L GLY* 1.3 76.3 - - - +
248L SER* 1.3 57.9 + - - +
250L LEU* 3.4 1.0 + - - -
251L SER* 2.9 28.4 + - - -
274L PRO* 3.7 33.7 - - + +
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Residues in contact with SER 248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244L THR 3.8 11.9 + - - -
245L GLU* 3.3 11.7 + - - -
246L GLY 3.3 0.6 - - - -
247L LEU* 1.3 75.8 - - - +
249L VAL* 1.3 60.5 + - - +
251L SER* 3.4 6.3 + - - -
252L GLN* 2.9 29.7 + - - +
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Residues in contact with VAL 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217L CYS 5.7 0.7 - - - +
219L THR* 5.8 9.4 - - - +
222L MET* 5.7 8.5 - - + -
245L GLU 2.9 18.0 + - - +
246L GLY* 3.7 7.6 - - - +
247L LEU 3.3 0.2 - - - -
248L SER* 1.3 75.1 - - - +
250L LEU* 1.3 57.7 + - - +
252L GLN* 3.4 7.0 + - - +
253L ALA* 2.9 28.9 + - - +
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Residues in contact with LEU 250 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190L ILE* 5.0 12.6 - - + +
192L ALA* 5.2 9.0 - - + -
236L MET* 5.4 4.0 - - + +
238L THR* 5.2 7.6 - - - -
246L GLY 2.9 16.5 + - - +
247L LEU* 3.8 4.5 - - - +
248L SER 3.3 0.2 - - - -
249L VAL* 1.3 77.7 - - - +
251L SER* 1.3 57.6 + - - +
253L ALA* 3.4 6.6 + - - +
254L MET* 2.9 29.3 + - - +
274L PRO* 4.1 15.9 - - + -
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Residues in contact with SER 251 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247L LEU 2.9 18.3 + - - -
248L SER* 3.7 7.6 - - - -
250L LEU* 1.3 74.9 - - - +
252L GLN* 1.3 59.7 + - - +
254L MET* 3.4 6.0 + - - +
255L ALA* 2.9 29.8 + - - +
274L PRO* 4.8 5.8 - - - +
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Residues in contact with GLN 252 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217L CYS* 5.9 1.6 - - - -
248L SER 2.9 17.4 + - - +
249L VAL* 3.7 7.9 - - - +
250L LEU 3.3 0.2 - - - -
251L SER* 1.3 75.1 - - - +
253L ALA* 1.3 58.9 + - - +
255L ALA* 3.4 5.8 + - - +
256L VAL* 2.9 29.8 + - - +
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Residues in contact with ALA 253 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214L GLY* 4.3 22.6 - - - +
217L CYS* 4.9 13.0 - - + +
218L SER* 6.2 0.2 - - - -
224L ILE* 4.9 13.7 - - + -
249L VAL 2.9 17.2 + - - +
250L LEU* 3.7 7.2 - - - +
251L SER 3.3 0.2 - - - -
252L GLN* 1.3 76.3 - - - +
254L MET* 1.3 58.3 + - - +
256L VAL* 3.4 6.6 + - - +
257L ILE* 2.9 29.5 + - - +
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Residues in contact with MET 254 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194L ILE* 5.4 10.3 - - + -
250L LEU 2.9 18.7 + - - +
251L SER* 3.7 7.2 - - - +
253L ALA* 1.3 76.5 - - - +
255L ALA* 1.3 58.8 + - - +
257L ILE* 3.4 6.6 + - - +
258L LYS* 2.9 29.6 + - - +
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Residues in contact with ALA 255 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251L SER 2.9 18.5 + - - +
252L GLN* 3.7 7.2 - - - +
254L MET* 1.3 74.4 - - - +
256L VAL* 1.3 59.2 + - - +
258L LYS* 3.4 6.4 + - - +
259L GLU* 2.9 29.1 + - - +
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Residues in contact with VAL 256 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213L ALA* 5.1 9.8 - - + +
214L GLY* 5.5 1.6 - - - -
217L CYS* 4.9 13.5 - - + -
252L GLN 2.9 17.6 + - - +
253L ALA* 3.8 7.4 - - - +
254L MET 3.3 0.2 - - - -
255L ALA* 1.3 75.1 - - - +
257L ILE* 1.3 56.5 + - - +
259L GLU* 3.8 5.9 - - - +
260L LYS* 2.9 30.0 + - - +
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Residues in contact with ILE 257 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196L VAL* 5.3 7.8 - - + +
210L ALA* 4.2 22.6 - - + +
214L GLY* 4.9 7.1 - - - +
253L ALA 2.9 17.2 + - - +
254L MET* 3.8 7.9 - - - +
256L VAL* 1.3 76.4 - - - +
258L LYS* 1.3 57.5 + - - +
260L LYS* 3.4 6.2 + - - +
261L ILE* 2.9 29.6 + - - +
268L PHE* 5.2 1.1 - - - -
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Residues in contact with LYS 258 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254L MET 2.9 17.9 + - - +
255L ALA* 3.7 7.2 - - - +
257L ILE* 1.3 78.3 - - - +
259L GLU* 1.3 57.5 + - - +
261L ILE* 3.4 1.6 + - - +
262L GLU* 2.9 31.0 + - - +
268L PHE* 3.8 27.6 - - + +
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Residues in contact with GLU 259 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255L ALA 2.9 17.0 + - - +
256L VAL* 3.8 7.4 - - - +
258L LYS* 1.3 77.3 - - - +
260L LYS* 1.3 57.3 + - - +
262L GLU* 3.4 4.8 + - - +
263L GLU* 2.9 30.7 + - - +
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Residues in contact with LYS 260 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206L ALA 5.3 1.6 - - - +
209L GLU 5.2 0.7 - - - +
210L ALA* 4.1 24.6 - - + +
213L ALA* 4.4 13.9 - - + -
256L VAL 2.9 18.3 + - - +
257L ILE* 3.8 4.0 - - - +
259L GLU* 1.3 76.8 - - - +
261L ILE* 1.3 62.0 + - - +
263L GLU* 3.8 6.3 + - - +
264L LYS* 3.6 19.8 + - - +
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Residues in contact with ILE 261 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196L VAL* 4.7 9.0 - - + -
197L ALA 4.8 3.8 - - - +
198L CYS* 5.6 0.6 - - + +
206L ALA* 5.8 1.8 - - - -
210L ALA* 4.5 7.8 - - + +
257L ILE 2.9 18.1 + - - +
258L LYS 3.8 4.0 - - - +
259L GLU 3.3 0.2 - - - -
260L LYS* 1.3 78.1 - - - +
262L GLU* 1.3 60.4 + - - +
264L LYS* 3.4 10.2 + - - +
265L ARG 3.4 0.2 + - - -
266L GLY* 2.8 35.6 + - - +
267L VAL 4.2 5.6 - - - +
268L PHE* 3.9 16.4 - - + -
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Residues in contact with GLU 262 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258L LYS 2.9 17.7 + - - +
259L GLU* 4.0 5.2 - - - +
261L ILE* 1.3 74.3 - - - +
263L GLU* 1.3 64.2 + - - +
264L LYS 3.3 0.2 - - - -
265L ARG* 3.5 10.0 + - - +
266L GLY 3.6 11.4 + - - +
268L PHE* 6.3 0.2 - - + -
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Residues in contact with GLU 263 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259L GLU 2.9 18.5 + - - +
260L LYS* 4.1 7.4 - - - +
261L ILE 3.3 0.4 - - - -
262L GLU* 1.3 76.1 - - - +
264L LYS* 1.3 58.4 + - - +
265L ARG 3.3 2.5 + - - -
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Residues in contact with LYS 264 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198L CYS* 4.8 6.1 - - + +
206L ALA* 3.8 27.5 - - + +
260L LYS 3.6 12.9 + - - +
261L ILE* 3.4 4.7 + - - +
262L GLU 3.3 0.6 - - - -
263L GLU* 1.3 77.8 - - - +
265L ARG* 1.3 67.4 + - - +
266L GLY* 3.6 1.7 - - - -
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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