Contacts of the helix formed by residues 242 - 264 (chain M) in PDB entry 6O81
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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188M VAL* 5.3 0.8 - - - +
241M LEU* 1.3 79.3 - - + +
243M ARG* 1.3 59.7 + - - +
244M THR* 3.2 4.0 - - - -
245M GLU* 3.0 17.7 + - + +
246M GLY 2.8 22.0 + - - -
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Residues in contact with ARG 243 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188M VAL* 4.0 24.4 - - + +
190M ILE* 5.4 7.9 - - + +
240M THR 5.1 1.3 - - - -
241M LEU 3.6 2.3 - - - -
242M GLU* 1.3 71.0 - - - +
244M THR* 1.3 60.3 + - - +
245M GLU 3.2 0.2 - - - -
246M GLY* 3.5 6.3 - - - +
247M LEU* 2.9 31.4 + - - +
276M VAL* 5.3 11.2 - - + -
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Residues in contact with THR 244 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242M GLU* 3.2 1.3 - - - -
243M ARG* 1.3 77.4 - - - +
245M GLU* 1.3 59.0 + - - +
247M LEU* 4.5 3.6 - - - +
248M SER* 3.8 15.6 + - - -
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Residues in contact with GLU 245 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242M GLU* 3.0 18.9 + - + +
244M THR* 1.3 76.9 - - - +
246M GLY* 1.3 60.6 + - - +
247M LEU 3.3 0.7 - - - -
248M SER* 3.3 7.0 + - - -
249M VAL* 2.9 28.2 + - - +
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Residues in contact with GLY 246 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190M ILE* 4.5 11.0 - - - +
238M THR* 5.3 6.3 - - - -
240M THR* 6.1 4.0 - - - -
241M LEU 5.2 2.9 - - - -
242M GLU 2.8 13.9 + - - -
243M ARG* 3.3 6.0 + - - -
245M GLU* 1.3 75.6 - - - +
247M LEU* 1.3 59.5 + - - +
249M VAL* 3.7 7.1 - - - +
250M LEU* 2.9 29.1 + - - +
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Residues in contact with LEU 247 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190M ILE* 4.5 6.6 - - + +
243M ARG 2.9 17.4 + - - +
244M THR* 4.5 4.7 - - - +
246M GLY* 1.3 75.7 - - - +
248M SER* 1.3 57.5 + - - +
250M LEU* 3.4 1.2 + - - -
251M SER* 2.9 29.2 + - - -
274M PRO* 3.7 33.4 - - + +
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Residues in contact with SER 248 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244M THR 3.8 11.3 + - - -
245M GLU* 3.3 11.3 + - - -
246M GLY 3.3 0.4 - - - -
247M LEU* 1.3 77.6 - - - +
249M VAL* 1.3 59.5 + - - +
251M SER* 3.4 6.4 + - - -
252M GLN* 2.9 29.5 + - - +
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Residues in contact with VAL 249 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217M CYS 5.7 0.7 - - - +
219M THR* 5.8 9.2 - - - +
222M MET* 5.7 8.5 - - + -
245M GLU 2.9 17.6 + - - +
246M GLY* 3.7 7.9 - - - +
247M LEU 3.3 0.2 - - - -
248M SER* 1.3 76.5 - - - +
250M LEU* 1.3 57.8 + - - +
252M GLN* 3.4 6.4 + - - +
253M ALA* 2.9 29.5 + - - +
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Residues in contact with LEU 250 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190M ILE* 5.0 12.1 - - + +
192M ALA* 5.2 9.6 - - + -
224M ILE* 6.2 3.1 - - - -
236M MET* 5.5 3.6 - - + +
238M THR* 5.2 7.4 - - - -
246M GLY 2.9 17.6 + - - +
247M LEU* 3.7 4.9 - - - +
248M SER 3.3 0.2 - - - -
249M VAL* 1.3 77.5 - - - +
251M SER* 1.3 56.3 + - - +
253M ALA* 3.4 6.4 + - - +
254M MET* 2.9 28.8 + - - +
274M PRO* 4.2 15.0 - - + -
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Residues in contact with SER 251 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247M LEU 2.9 17.9 + - - -
248M SER* 3.7 7.6 - - - -
250M LEU* 1.3 73.8 - - - +
252M GLN* 1.3 59.1 + - - +
254M MET* 3.4 6.8 + - - +
255M ALA* 2.9 29.3 + - - +
274M PRO* 4.8 6.2 - - - +
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Residues in contact with GLN 252 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217M CYS* 5.9 1.6 - - - -
248M SER 2.9 17.6 + - - +
249M VAL* 3.7 7.6 - - - +
250M LEU 3.3 0.2 - - - -
251M SER* 1.3 74.8 - - - +
253M ALA* 1.3 59.3 + - - +
255M ALA* 3.4 7.0 + - - +
256M VAL* 2.9 28.6 + - - +
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Residues in contact with ALA 253 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214M GLY* 4.3 22.1 - - - +
217M CYS* 4.9 14.3 - - + +
218M SER* 6.2 0.2 - - - -
224M ILE* 4.9 13.9 - - + -
249M VAL 2.9 18.2 + - - +
250M LEU* 3.7 7.0 - - - +
252M GLN* 1.3 76.3 - - - +
254M MET* 1.3 58.2 + - - +
256M VAL* 3.4 6.2 + - - +
257M ILE* 2.9 29.5 + - - +
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Residues in contact with MET 254 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194M ILE* 5.5 11.0 - - + -
250M LEU 2.9 17.6 + - - +
251M SER* 3.7 7.9 - - - +
253M ALA* 1.3 75.5 - - - +
255M ALA* 1.3 58.5 + - - +
257M ILE* 3.4 7.0 + - - +
258M LYS* 2.9 29.8 + - - +
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Residues in contact with ALA 255 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251M SER 2.9 17.8 + - - +
252M GLN* 3.7 7.9 - - - +
253M ALA 3.3 0.2 - - - -
254M MET* 1.3 75.0 - - - +
256M VAL* 1.3 59.3 + - - +
258M LYS* 3.4 6.8 + - - +
259M GLU* 2.9 28.8 + - - +
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Residues in contact with VAL 256 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213M ALA* 5.1 10.1 - - + +
214M GLY* 5.5 1.6 - - - -
217M CYS* 4.9 13.2 - - + -
252M GLN 2.9 17.9 + - - +
253M ALA* 3.8 6.5 - - - +
255M ALA* 1.3 76.9 - - - +
257M ILE* 1.3 58.4 + - - +
259M GLU* 3.4 6.2 + - - +
260M LYS* 2.9 29.5 + - - +
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Residues in contact with ILE 257 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196M VAL* 5.4 7.9 - - + +
210M ALA* 4.2 22.6 - - + +
214M GLY* 4.9 6.7 - - - +
253M ALA 2.9 18.5 + - - +
254M MET* 3.8 7.4 - - - +
255M ALA 3.3 0.2 - - - -
256M VAL* 1.3 76.7 - - - +
258M LYS* 1.3 58.4 + - - +
260M LYS* 3.4 6.0 + - - +
261M ILE* 2.9 30.0 + - - +
268M PHE* 5.2 0.9 - - - -
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Residues in contact with LYS 258 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254M MET 2.9 17.8 + - - +
255M ALA* 3.7 7.6 - - - +
256M VAL 3.3 0.2 - - - -
257M ILE* 1.3 78.1 - - - +
259M GLU* 1.3 56.1 + - - +
261M ILE* 3.3 1.6 + - - +
262M GLU* 2.9 31.1 + - - +
268M PHE* 3.8 28.0 - - + +
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Residues in contact with GLU 259 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255M ALA 2.9 18.2 + - - +
256M VAL* 3.7 7.4 - - - +
258M LYS* 1.3 77.5 - - - +
260M LYS* 1.3 57.5 + - - +
262M GLU* 3.8 4.7 - - - +
263M GLU* 2.9 30.5 + - - +
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Residues in contact with LYS 260 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206M ALA* 5.3 1.2 - - - +
209M GLU 5.2 0.9 - - - +
210M ALA* 4.1 24.2 - - + +
213M ALA* 4.4 14.1 - - + -
256M VAL 2.9 17.9 + - - +
257M ILE* 3.8 4.5 - - - +
258M LYS 3.3 0.2 - - - -
259M GLU* 1.3 77.2 - - - +
261M ILE* 1.3 61.4 + - - +
263M GLU* 3.7 6.2 + - - +
264M LYS* 3.6 20.4 + - - +
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Residues in contact with ILE 261 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196M VAL* 4.8 9.2 - - + -
197M ALA 4.8 3.8 - - - +
198M CYS* 5.7 0.3 - - - +
206M ALA* 5.8 1.8 - - - -
210M ALA* 4.5 8.4 - - + +
257M ILE 2.9 17.9 + - - +
258M LYS 3.8 3.8 - - - +
260M LYS* 1.3 77.1 - - - +
262M GLU* 1.3 61.0 + - - +
264M LYS* 3.4 9.8 + - - +
265M ARG 3.4 0.2 + - - -
266M GLY* 2.8 35.6 + - - +
267M VAL 4.2 4.9 - - - +
268M PHE* 3.9 16.6 - - + -
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Residues in contact with GLU 262 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258M LYS 2.9 18.1 + - - +
259M GLU* 4.0 5.2 - - - +
261M ILE* 1.3 74.7 - - - +
263M GLU* 1.3 63.5 + - - +
264M LYS 3.3 0.2 - - - -
265M ARG* 3.5 9.4 + - - -
266M GLY 3.6 10.7 + - - +
268M PHE* 6.3 0.4 - - + -
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Residues in contact with GLU 263 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259M GLU 2.9 18.2 + - - +
260M LYS* 4.1 7.6 - - - +
261M ILE 3.3 0.6 - - - -
262M GLU* 1.3 77.7 - - - +
264M LYS* 1.3 55.5 + - - +
265M ARG 3.3 2.6 + - - -
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Residues in contact with LYS 264 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198M CYS* 4.8 5.4 - - - +
206M ALA* 3.8 26.7 - - + +
260M LYS 3.6 12.6 + - - +
261M ILE* 3.4 4.7 + - - +
262M GLU 3.3 0.2 - - - -
263M GLU* 1.3 78.0 - - - +
265M ARG* 1.3 68.8 + - - +
266M 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
------------------------------------------------------------
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