Contacts of the helix formed by residues 221 - 239 (chain E) in PDB entry 6CAJ
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 GLY 221 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E VAL 3.8 0.2 - - - -
220E SER* 1.3 79.7 - - - +
222E SER* 1.3 65.2 + - - -
223E ASN 3.3 2.9 - - - -
224E ALA* 3.8 14.1 - - - +
225E ARG* 3.1 28.6 + - - +
338E CYS* 5.3 13.0 - - - -
339E SER* 6.4 0.9 - - - -
406E HIS* 6.1 0.2 - - - -
417E ARG* 5.2 0.9 - - - -
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Residues in contact with SER 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220E SER 3.8 1.6 + - - -
221E GLY* 1.3 73.0 - - - -
223E ASN* 1.3 61.9 + - - +
225E ARG* 4.0 8.0 + - - +
226E CYS* 3.8 9.5 + - - +
270E SER* 4.5 9.4 + - - -
272E SER* 3.4 24.0 + - - -
338E CYS 5.8 0.6 + - - -
406E HIS* 3.7 41.6 + - - +
442E LYS* 3.5 26.8 - - - -
489E TYR* 6.0 0.4 - - - -
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Residues in contact with ASN 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221E GLY* 4.4 0.2 - - - -
222E SER* 1.3 76.4 - - - +
224E ALA* 1.3 60.0 + - - +
225E ARG 3.3 0.7 - - - -
226E CYS* 3.3 3.7 + - - +
227E ILE* 2.9 37.1 + - + +
312E ILE* 4.6 13.0 - - + +
340E SER* 3.5 26.6 + - - +
341E LEU* 4.6 16.0 - - - +
439E GLU* 4.9 8.8 + - - +
441E TYR* 2.5 31.4 + - - +
442E LYS* 4.1 19.8 - - - +
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Residues in contact with ALA 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E VAL* 3.7 18.1 - - + +
220E SER 5.3 0.2 - - - +
221E GLY* 3.4 15.5 + - - +
223E ASN* 1.3 75.9 - - - +
225E ARG* 1.3 60.8 + - - +
227E ILE* 3.9 9.6 - - - +
228E ALA* 2.9 31.4 + - - +
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Residues in contact with ARG 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214E TYR* 2.6 42.4 + - + +
219E VAL* 3.7 25.4 - - + +
220E SER 4.8 4.3 - - - -
221E GLY 3.1 18.8 + - - +
222E SER* 4.2 6.5 - - - +
224E ALA* 1.3 77.0 - - - +
226E CYS* 1.3 56.1 + - - +
229E LEU* 2.9 17.7 + - - +
267E ARG* 3.0 39.2 + - - +
268E PRO 3.1 22.8 + - - -
269E LEU* 3.4 13.9 - - - +
270E SER* 3.3 28.6 - - - +
273E MET* 3.4 34.2 - - + +
456E GLU* 5.0 0.4 + - - -
489E TYR* 4.4 6.7 + - - -
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Residues in contact with CYS 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222E SER 3.8 11.4 + - - +
223E ASN 3.3 8.1 + - - +
225E ARG* 1.3 77.4 - - - +
227E ILE* 1.3 61.2 + - + +
229E LEU* 3.5 4.9 - - - +
230E LEU* 2.9 54.3 + - - +
272E SER* 4.1 13.9 - - - +
273E MET* 4.3 6.0 - - + +
276E ALA* 4.2 14.6 - - - -
307E TYR* 5.3 4.5 - - - -
308E VAL* 6.2 1.3 - - - -
312E ILE* 5.5 5.2 - - + -
441E TYR* 4.0 27.1 - - - +
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Residues in contact with ILE 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223E ASN* 2.9 28.8 + - + +
224E ALA* 3.9 7.6 - - - +
226E CYS* 1.3 77.3 - - - +
228E ALA* 1.3 58.5 + - - +
230E LEU* 3.3 5.9 + - - +
231E ARG* 2.9 56.5 + - + +
308E VAL* 4.3 19.3 - - + -
312E ILE* 4.5 26.9 - - + -
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Residues in contact with ALA 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210E LEU* 3.6 21.7 - - + +
213E GLN* 4.0 13.2 - - - +
214E TYR* 4.4 3.8 - - + +
219E VAL* 4.9 6.5 - - + -
224E ALA 2.9 18.1 + - - +
225E ARG* 4.1 2.7 - - - +
227E ILE* 1.3 74.7 - - - +
229E LEU* 1.3 59.9 + - - +
231E ARG* 3.8 7.7 - - - +
232E ALA* 2.9 30.0 + - - +
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Residues in contact with LEU 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E MET* 4.9 0.7 - - + -
210E LEU* 3.8 19.7 - - + -
214E TYR* 3.6 4.2 + - - +
225E ARG 2.9 20.0 + - - +
226E CYS* 3.5 4.7 - - - +
228E ALA* 1.3 77.3 - - - +
230E LEU* 1.3 58.2 + - + +
232E ALA* 3.3 2.3 + - - +
233E LEU* 2.9 48.4 + - + +
260E MET* 4.2 12.6 - - + -
263E LEU* 3.8 14.1 - - + -
273E MET* 3.7 53.2 - - + +
276E ALA* 4.1 13.9 - - + -
277E ILE* 4.6 7.2 - - + -
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Residues in contact with LEU 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E CYS* 2.9 34.2 + - - +
227E ILE* 3.9 4.9 - - - +
229E LEU* 1.3 82.8 - - + +
231E ARG* 1.3 64.1 + - - +
233E LEU* 3.4 13.2 + - + +
234E GLN* 2.9 33.8 + - - +
276E ALA* 3.8 29.4 - - + +
304E ILE* 3.7 26.7 - - + +
307E TYR* 3.7 29.4 - - + -
308E VAL* 3.8 21.8 - - + -
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Residues in contact with ARG 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E ILE* 2.9 41.1 + - + +
228E ALA* 3.8 7.4 - - - +
229E LEU 3.3 0.2 - - - -
230E LEU* 1.3 79.2 - - - +
232E ALA* 1.3 57.6 + - - +
234E GLN* 3.3 32.1 + - - +
235E GLN* 3.0 33.2 + - + +
305E ASP* 4.6 2.6 + - - -
308E VAL* 3.7 35.8 - - - +
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Residues in contact with ALA 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206E ALA* 4.1 19.3 - - + +
207E MET* 3.8 13.0 - - + -
210E LEU* 3.7 22.0 - - + -
228E ALA 2.9 17.8 + - - +
229E LEU 3.3 4.2 + - - +
231E ARG* 1.3 75.3 - - - +
233E LEU* 1.3 57.4 + - - +
235E GLN* 3.2 9.0 + - - +
236E VAL* 2.9 31.5 + - - +
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Residues in contact with LEU 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E MET* 3.7 18.6 - - + -
229E LEU* 2.9 43.6 + - + +
230E LEU* 3.7 16.2 - - + +
231E ARG 3.3 0.2 - - - -
232E ALA* 1.3 74.4 - - - +
234E GLN* 1.3 60.0 + - - +
236E VAL* 3.3 2.7 + - - +
237E ILE* 2.9 37.3 + - + +
256E LEU* 4.0 21.3 - - + -
260E MET* 4.1 11.4 - - + -
276E ALA* 5.5 3.8 - - + +
277E ILE* 5.8 2.2 - - + -
280E LEU* 3.7 37.2 - - + -
304E ILE* 4.5 7.2 - - + -
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Residues in contact with GLN 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E LEU 2.9 19.3 + - - +
231E ARG* 3.3 36.4 + - - +
233E LEU* 1.3 76.4 - - - +
235E GLN* 1.3 59.6 + - + +
237E ILE* 4.0 4.3 - - - +
238E GLN* 2.9 19.8 + - - +
301E ARG* 2.8 48.3 + - + +
304E ILE* 3.4 31.5 - - + +
305E ASP* 2.4 37.6 + - - +
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Residues in contact with GLN 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E HIS* 3.5 7.7 + - + -
206E ALA* 3.7 22.4 - - + -
231E ARG* 3.0 21.8 + - + +
232E ALA* 3.2 7.4 + - - +
234E GLN* 1.3 79.6 + - - +
236E VAL* 1.3 61.1 + - - +
238E GLN* 4.1 20.7 + - - +
239E ASP* 3.2 24.8 + - - +
301E ARG* 5.0 4.6 - - - +
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Residues in contact with VAL 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E HIS* 3.6 33.5 + - + +
206E ALA* 5.1 0.2 - - + -
207E MET* 3.7 25.4 - - + -
232E ALA 2.9 20.1 + - - +
233E LEU* 3.7 7.2 - - - +
234E GLN 3.2 0.2 - - - -
235E GLN* 1.3 75.5 - - - +
237E ILE* 1.3 67.1 + - + +
239E ASP 3.1 14.0 + - - +
240E TYR* 3.2 12.5 + - + +
252E LEU* 5.1 3.8 - - + -
255E LYS* 5.0 9.9 + - - +
256E LEU* 3.9 16.8 - - + -
259E TYR* 3.9 21.1 - - + -
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Residues in contact with ILE 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E LEU* 2.9 20.4 + - + +
234E GLN* 4.2 4.0 - - - +
236E VAL* 1.3 79.7 - - + +
238E GLN* 1.3 61.4 + - - +
240E TYR* 3.3 21.8 - - + +
252E LEU* 4.4 22.7 - - + -
256E LEU* 5.6 2.2 - - + -
280E LEU* 4.5 17.5 - - + -
297E LYS* 3.3 31.0 - - + +
300E LEU* 4.0 38.1 - - + -
301E ARG* 4.5 5.2 - - + -
304E ILE* 3.7 25.6 - - + -
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Residues in contact with GLN 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E GLN 2.9 17.2 + - - +
235E GLN* 4.1 22.4 + - - +
237E ILE* 1.3 77.9 - - - +
239E ASP* 1.3 55.5 + - + +
240E TYR 3.3 0.4 - - - -
297E LYS* 3.1 26.8 + - - +
301E ARG* 3.2 37.0 + - - +
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Residues in contact with ASP 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E HIS* 3.4 27.1 + - + +
205E PRO* 5.4 2.9 - - - +
235E GLN 3.2 18.0 + - - +
236E VAL 3.1 8.2 + - - +
238E GLN* 1.3 75.1 - - - +
240E TYR* 1.3 57.0 + - - +
241E THR* 4.2 1.0 + - - +
255E LYS* 4.8 5.5 + - - -
1I MET 5.4 5.7 + - - -
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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