Contacts of the helix formed by residues 256 - 269 (chain M) in PDB entry 6CET
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 ARG 256 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180M MET 4.4 11.2 + - - -
181M ALA* 5.2 1.8 - - - +
182M ASP* 2.5 46.3 + - - +
183M GLY* 5.8 0.9 - - - -
252M LEU* 3.2 11.0 - - + +
254M ALA 4.2 0.8 + - - -
255M ILE* 1.3 90.7 - - + +
257M PRO* 1.3 68.7 - - - +
258M TYR 3.6 1.8 - - - -
259M HIS* 3.1 39.8 + - + +
260M ALA 4.5 0.2 + - - -
282M LEU* 5.4 10.3 - - + +
301M ASP* 5.3 4.2 + - - +
305M ALA* 4.7 17.0 - - - +
420M GLU* 4.4 7.5 + - - -
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Residues in contact with PRO 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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249M GLU* 5.7 3.8 - - + -
252M LEU* 3.3 31.6 - - + +
253M LYS* 4.1 28.9 - - + +
255M ILE 3.7 1.1 - - - +
256M ARG* 1.3 90.1 - - - +
258M TYR* 1.3 65.0 + - + +
259M HIS 3.5 0.4 - - - -
260M ALA* 3.2 8.3 + - - +
261M LEU* 3.1 23.5 + - - +
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Residues in contact with TYR 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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256M ARG 3.6 0.4 - - - -
257M PRO* 1.3 84.8 - - + +
259M HIS* 1.3 61.8 + - - +
261M LEU* 3.6 32.3 - - + +
262M LEU* 2.9 58.7 + - + +
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Residues in contact with HIS 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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181M ALA* 3.8 34.6 - - + +
182M ASP 4.9 4.9 + - - -
183M GLY* 5.4 4.2 - - - -
252M LEU* 5.1 1.4 - - + +
256M ARG* 3.1 54.3 + - + +
258M TYR* 1.3 76.8 - - - +
260M ALA* 1.3 68.0 + - + +
262M LEU* 3.3 16.5 + - + +
263M LEU* 2.9 39.7 + - + +
278M CYS* 5.8 3.9 - - - +
281M ALA* 5.4 5.2 - - + -
282M LEU* 3.8 31.9 - - + -
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Residues in contact with ALA 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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208M TYR* 5.4 2.1 - - + -
248M ILE* 6.0 6.1 - - + -
252M LEU* 4.5 15.7 - - + -
257M PRO 3.2 11.6 + - - +
258M TYR 3.2 0.2 - - - -
259M HIS* 1.3 93.2 - - + +
261M LEU* 1.3 59.9 + - - +
263M LEU* 3.2 13.1 + - + +
264M LEU* 2.9 27.2 + - - +
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Residues in contact with LEU 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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243M ILE 4.8 6.5 - - - +
244M PRO* 5.4 9.4 - - + -
245M PRO* 5.5 2.9 - - + -
257M PRO 3.1 13.7 + - - +
258M TYR* 3.2 36.3 + - + +
260M ALA* 1.3 74.4 - - - +
262M LEU* 1.3 58.3 + - - +
264M LEU* 3.3 29.7 + - + +
265M SER* 3.0 26.9 + - - -
268M LYS* 5.7 1.6 - - - +
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Residues in contact with LEU 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 TYR* 2.9 49.7 + - + +
259M HIS* 3.4 13.7 - - - +
261M LEU* 1.3 76.6 - - - +
263M LEU* 1.3 57.0 + - + +
265M SER* 2.5 26.6 + - - +
266M ASP* 2.8 28.3 + - - +
277M ASP 4.9 5.4 - - - +
281M ALA* 3.9 27.1 - - + -
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Residues in contact with LEU 263 (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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181M ALA* 5.4 7.2 - - + +
205M LYS* 5.6 5.4 - - + -
208M TYR* 3.2 45.2 + - + +
259M HIS* 2.9 32.3 + - + +
260M ALA* 3.2 17.0 + - + +
262M LEU* 1.3 72.8 - - + +
264M LEU* 1.3 61.3 + - - +
266M ASP* 3.6 5.1 - - + +
267M GLU* 2.9 34.0 + - - +
274M LEU* 3.7 31.0 - - + -
278M CYS* 5.1 13.0 - - + -
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Residues in contact with LEU 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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208M TYR* 4.9 4.4 - - - -
212M CYS* 4.9 12.3 - - + -
213M THR* 4.8 21.1 - - + -
243M ILE* 4.0 28.7 - - + +
245M PRO* 4.7 13.7 - - + -
248M ILE* 6.1 0.7 - - + -
260M ALA 2.9 13.1 + - - +
261M LEU* 3.3 24.2 + - + +
263M LEU* 1.3 75.2 - - - +
265M SER* 1.3 56.5 + - - +
267M GLU* 3.4 3.4 + - - +
268M LYS* 2.9 71.7 + - + +
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Residues in contact with SER 265 (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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261M LEU 3.0 10.6 + - - -
262M LEU* 2.5 34.4 + - - +
264M LEU* 1.3 76.5 - - - +
266M ASP* 1.3 58.2 + - - +
268M LYS* 3.4 21.5 - - - +
269M SER* 2.4 44.8 + - - -
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Residues in contact with ASP 266 (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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262M LEU* 2.8 30.6 + - - +
263M LEU* 3.3 8.4 + - - +
265M SER* 1.3 81.8 + - - +
267M GLU* 1.3 68.9 + - - +
269M SER* 4.0 6.0 + - - -
270M LEU* 2.8 25.6 - - - +
271M LEU* 4.9 0.9 - - - -
273M GLU 5.9 1.6 - - - -
274M LEU* 4.5 23.2 - - + +
277M ASP* 4.6 18.4 - - - +
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Residues in contact with GLU 267 (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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205M LYS* 6.1 3.7 - - + +
208M TYR* 4.2 18.6 - - + +
209M ASP* 4.3 25.5 - - + +
217M VAL* 5.6 1.2 - - - +
219M LEU* 3.4 59.6 + - - +
221M ILE* 4.4 17.8 - - - +
263M LEU 2.9 17.3 + - - +
264M LEU* 3.7 3.1 - - - +
266M ASP* 1.3 84.4 - - + +
268M LYS* 1.3 56.6 + - - +
269M SER 3.6 0.7 - - - -
270M LEU 5.3 0.2 - - - +
271M LEU* 5.6 2.8 - - - +
274M LEU* 5.8 5.5 - - + +
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Residues in contact with LYS 268 (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 THR* 6.1 6.1 - - + -
219M LEU* 4.9 4.9 - - - -
243M ILE 5.1 10.5 - - - +
261M LEU* 5.2 1.6 + - - +
264M LEU* 2.9 40.9 + - + +
265M SER* 3.4 27.9 - - - +
267M GLU* 1.3 79.3 - - - +
269M SER* 1.3 61.6 + - - +
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Residues in contact with SER 269 (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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219M LEU* 4.5 6.2 - - - +
265M SER* 2.4 27.9 + - - -
266M ASP* 4.0 4.9 + - - -
267M GLU 3.6 0.4 - - - -
268M LYS* 1.3 83.5 - - - +
270M LEU* 1.3 70.5 + - - +
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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
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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