Contacts of the helix formed by residues 215 - 230 (chain E) in PDB entry 2R6C
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 215 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213E SER* 3.4 3.7 - - - +
214E VAL* 1.3 80.1 - - - +
216E LYS* 1.3 62.2 + - - +
217E THR 3.3 3.1 - - - -
218E ALA* 3.4 13.3 + - - -
219E PHE* 2.9 24.6 + - - +
396E LEU* 3.8 5.2 - - - -
431E PHE* 5.2 6.3 - - - -
438E PHE* 3.3 15.1 - - - -
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Residues in contact with LYS 216 (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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208E VAL* 4.7 2.5 - - + +
210E ALA* 3.6 37.0 + - + +
211E ARG 4.4 7.2 + - - +
212E PRO* 4.5 5.7 - - - +
213E SER 5.1 2.1 - - - +
214E VAL 5.7 0.2 - - - +
215E GLY* 1.3 74.8 - - - +
217E THR* 1.3 74.0 + - - +
219E PHE* 3.5 1.7 + - - +
220E ALA 3.1 20.8 + - - -
320E ASP* 5.1 1.6 - - - -
321E TYR* 4.8 17.7 - - - -
360E LEU* 3.3 39.2 - - + +
361E SER 4.1 13.0 - - - +
362E GLN* 3.2 29.4 + - - +
396E LEU* 3.4 20.1 - - + +
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Residues in contact with THR 217 (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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215E GLY 3.3 0.2 - - - -
216E LYS* 1.3 86.6 - - - +
218E ALA* 1.3 53.7 + - - +
219E PHE 3.0 5.1 + - - -
220E ALA* 3.0 2.8 + - + +
221E LEU* 2.7 54.3 + - + +
241E GLU* 5.2 4.7 + - - -
242E MET* 4.4 26.8 - - + +
247E LEU* 5.9 1.6 - - + -
250E ARG* 6.0 0.9 - - - -
320E ASP* 4.1 29.2 + - - +
360E LEU* 4.3 8.5 - - + -
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Residues in contact with ALA 218 (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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215E GLY* 3.4 13.7 + - - +
217E THR* 1.3 78.2 - - - +
219E PHE* 1.3 54.5 + - - +
221E LEU* 4.4 6.5 - - - -
222E ASN* 2.3 39.2 + - - +
250E ARG* 6.3 0.9 - - - +
431E PHE* 4.4 12.3 - - + -
436E ASN* 3.5 35.7 - - - +
438E PHE* 3.6 5.7 - - - -
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Residues in contact with PHE 219 (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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190E PHE* 4.2 13.0 - + - -
193E LEU* 4.0 18.4 - - + -
200E PHE* 5.6 2.2 - + - -
208E VAL* 3.7 41.5 - - + -
215E GLY 2.9 17.0 + - - +
216E LYS 3.7 2.2 - - - +
217E THR 3.0 0.2 - - - -
218E ALA* 1.3 76.1 - - - +
220E ALA* 1.3 67.9 + - + +
221E LEU 3.2 1.3 - - - -
222E ASN* 3.3 3.0 + - - +
223E ILE* 3.2 51.9 + - + +
394E ALA* 5.4 2.7 - - + -
396E LEU* 3.6 16.6 - - + -
414E ILE* 3.5 34.8 - - + -
429E LEU* 4.5 0.2 - - + -
438E PHE* 3.3 27.1 - + + -
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Residues in contact with ALA 220 (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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216E LYS 3.1 7.9 + - - +
217E THR* 3.0 3.6 + - + +
219E PHE* 1.3 77.6 - - + +
221E LEU* 1.3 62.5 + - + +
223E ILE* 3.5 12.6 + - - +
224E ALA* 3.1 22.9 + - - +
318E VAL* 3.7 24.0 - - + +
358E ILE* 4.8 5.6 - - + -
360E LEU* 3.5 38.6 - - + -
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Residues in contact with LEU 221 (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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217E THR* 2.7 39.0 + - + +
218E ALA* 4.4 3.4 - - - -
220E ALA* 1.3 76.5 - - + +
222E ASN* 1.3 61.9 + - - +
224E ALA* 3.3 4.4 - - - +
225E GLN* 2.8 35.3 + - - +
237E ILE* 4.2 20.9 - - + -
242E MET* 5.2 0.4 - - - -
247E LEU* 3.8 56.1 - - + +
250E ARG* 4.1 24.0 - - + +
251E MET* 4.7 11.7 - - + +
318E VAL* 6.1 1.1 - - + -
436E ASN* 5.8 0.4 - - - +
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Residues in contact with ASN 222 (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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190E PHE* 4.1 18.8 - - + -
218E ALA* 2.3 33.8 + - - +
219E PHE* 3.3 5.5 + - - +
220E ALA 3.3 0.2 - - - -
221E LEU* 1.3 79.2 - - - +
223E ILE* 1.3 59.0 + - - +
225E GLN* 3.6 9.6 - - - +
226E ASN* 2.4 42.7 + - - +
250E ARG 5.3 1.8 + - - -
251E MET* 5.9 0.2 - - - +
254E ALA* 4.2 14.8 - - - +
436E ASN* 3.7 7.6 + - - +
437E LYS* 3.5 11.3 - - - +
438E PHE* 3.2 26.4 + - + +
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Residues in contact with ILE 223 (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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188E THR* 4.1 22.7 - - - +
190E PHE* 4.4 4.0 - - + -
193E LEU* 5.2 1.1 - - + -
200E PHE* 3.8 32.5 - - + -
208E VAL* 5.8 0.2 - - + -
219E PHE* 3.2 57.7 + - + +
220E ALA* 3.8 9.0 - - - +
222E ASN* 1.3 73.7 - - - +
224E ALA* 1.3 66.6 + - - +
226E ASN* 3.1 7.2 + - - +
227E VAL* 2.9 30.5 + - + +
316E MET* 3.9 18.2 - - + -
358E ILE* 4.4 11.9 - - + -
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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
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220E ALA 3.1 11.7 + - - +
221E LEU* 3.3 11.2 - - - +
223E ILE* 1.3 78.4 - - - +
225E GLN* 1.3 56.9 + - - +
227E VAL 3.4 1.0 + - - -
228E ALA* 2.9 29.5 + - - +
235E VAL* 3.8 12.1 - - + +
237E ILE* 3.6 34.5 - - + -
251E MET* 5.7 0.4 - - - -
288E ILE* 5.2 1.1 - - + -
316E MET* 3.5 18.5 - - + +
318E VAL* 4.5 4.5 - - + -
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Residues in contact with GLN 225 (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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221E LEU 2.8 19.1 + - - +
222E ASN* 3.6 12.3 - - - +
224E ALA* 1.3 73.3 - - - +
226E ASN* 1.3 57.8 + - - +
228E ALA* 2.7 25.3 + - - +
229E THR* 2.8 24.7 + - + +
251E MET* 3.3 39.3 - - - +
254E ALA* 3.5 22.8 + - - +
255E GLU* 3.0 33.4 + - - +
283E LEU* 3.7 20.2 - - + -
288E ILE* 4.9 4.5 - - - -
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Residues in contact with ASN 226 (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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187E PRO 4.8 3.4 - - - +
188E THR 3.4 15.6 - - - +
189E GLY* 4.0 23.1 - - - +
190E PHE* 3.8 15.2 - - - -
222E ASN* 2.4 28.6 + - - +
223E ILE 3.8 2.5 - - - +
225E GLN* 1.3 80.9 - - - +
227E VAL* 1.3 61.0 + - - +
229E THR* 4.0 7.3 + - - -
230E LYS* 3.1 50.7 + - + +
231E THR* 3.9 1.2 + - - -
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Residues in contact with VAL 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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186E ILE* 3.6 34.8 - - + -
187E PRO* 4.3 3.8 - - + +
188E THR* 4.3 12.1 - - - +
200E PHE* 5.9 0.2 - - + -
223E ILE* 2.9 28.9 + - + +
224E ALA 3.8 4.3 - - - +
226E ASN* 1.3 76.2 - - - +
228E ALA* 1.3 59.3 - - - +
231E THR* 2.4 41.1 - - + +
233E GLU* 3.6 11.6 - - + +
235E VAL* 3.7 16.8 - - + -
315E GLY 5.7 0.7 - - - -
316E MET* 3.6 21.8 - - + -
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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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224E ALA 2.9 15.3 + - - +
225E GLN 2.7 6.1 + - - +
227E VAL* 1.3 80.6 - - - +
229E THR* 1.3 60.7 + - - +
230E LYS 3.6 0.3 + - - -
231E THR 4.3 2.9 + - - -
232E ASN* 4.4 9.0 + - - -
233E GLU 4.3 7.0 + - - -
235E VAL* 4.4 3.1 - - + -
285E ASN 5.3 0.2 - - - +
286E ALA* 3.8 10.0 - - + -
287E GLY* 3.7 25.0 + - - +
288E ILE* 3.6 29.2 - - + -
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Residues in contact with THR 229 (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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225E GLN* 2.8 27.3 + - + +
226E ASN* 4.0 6.2 + - - -
228E ALA* 1.3 74.6 - - - +
230E LYS* 1.3 67.2 + - - +
231E THR 5.4 0.2 - - - -
255E GLU* 4.2 18.4 + - - +
282E SER* 4.0 21.3 - - - +
283E LEU* 3.9 28.3 - - + -
286E ALA* 4.0 10.3 - - + +
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Residues in contact with LYS 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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189E GLY* 4.9 14.0 + - - -
226E ASN* 3.1 43.8 + - + +
229E THR* 1.3 87.2 - - - +
231E THR* 1.3 63.8 + - - +
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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