Contacts of the helix formed by residues 206 - 225 (chain B) in PDB entry 6EBT
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 VAL 206 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B GLU* 3.0 36.9 + - + +
204B HIS 3.7 0.2 - - - -
205B GLU* 1.3 89.5 - - + +
207B LEU* 1.3 68.1 + - - +
208B LEU 3.6 0.7 - - - -
209B PRO* 3.8 2.0 - - - +
210B GLY* 3.1 17.7 + - - -
420B ALA 4.1 14.4 - - - +
421B ARG* 4.2 13.5 - - - -
424B GLY* 3.5 11.9 - - - -
425B ASP* 3.8 23.1 - - - +
428B VAL* 5.7 0.3 - - - +
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Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLU 3.0 6.7 + - - +
203B VAL* 3.7 19.7 - - + +
206B VAL* 1.3 78.6 - - - +
208B LEU* 1.3 63.8 + - - +
210B GLY* 3.7 0.7 - - - -
211B LEU* 3.0 42.0 + - + +
262B ILE* 3.7 36.3 - - + -
328B MET* 3.8 29.6 - - + -
420B ALA* 4.1 13.7 - - + +
423B LEU* 3.6 33.7 - - + -
424B GLY* 4.0 9.2 - - - +
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Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL* 2.9 40.2 + - + +
204B HIS* 4.4 18.8 - - + +
207B LEU* 1.3 73.5 - - - +
209B PRO* 1.3 64.0 - - + +
211B LEU* 3.1 2.8 + - + +
212B GLN* 2.7 31.5 + - - +
259B MET* 3.6 52.3 - - + +
262B ILE* 4.1 17.9 - - + -
263B LYS* 3.9 26.7 - - + -
266B MET* 6.0 0.2 - - + -
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Residues in contact with PRO 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL 3.8 0.2 - - - +
204B HIS 3.2 32.1 - - - +
205B GLU* 3.4 19.1 - - - +
206B VAL 3.8 4.7 - - - +
207B LEU 3.7 2.2 - - - -
208B LEU* 1.3 91.8 - - + +
210B GLY* 1.3 62.1 + - - +
212B GLN* 3.3 7.5 + - + +
213B LYS* 3.1 37.2 + - - +
428B VAL* 5.3 0.2 - - - -
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Residues in contact with GLY 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL 3.1 13.8 + - - -
207B LEU 3.7 2.9 - - - -
208B LEU 3.2 0.2 - - - -
209B PRO* 1.3 75.7 - - - +
211B LEU* 1.3 63.4 + - - +
213B LYS* 3.3 4.3 + - - +
214B LEU 3.2 16.3 + - - -
424B GLY 3.8 21.1 - - - -
427B SER* 3.3 17.6 - - - -
428B VAL* 3.8 14.5 - - - +
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LEU* 3.0 32.0 + - + +
208B LEU* 3.7 5.2 - - + +
210B GLY* 1.3 75.7 - - - +
212B GLN* 1.3 58.0 + - - +
214B LEU* 3.3 2.1 + - + +
215B HIS* 2.8 25.5 + - - +
255B VAL* 3.3 22.1 - - + +
258B ALA* 4.6 4.7 - - + -
259B MET* 3.7 24.9 - - + -
262B ILE* 3.3 34.5 - - + -
331B THR* 4.0 22.4 - - + -
335B LEU* 4.4 11.2 - - + -
423B LEU* 5.2 0.7 - - + +
427B SER* 3.5 20.2 - - - +
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Residues in contact with GLN 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B LEU 2.7 19.8 + - - +
209B PRO* 3.6 9.6 - - + +
211B LEU* 1.3 73.6 - - - +
213B LYS* 1.3 63.3 + - + +
215B HIS* 3.3 14.6 + - - -
216B ASP* 2.8 63.6 + - - +
259B MET* 3.2 27.5 - - + +
263B LYS* 5.6 1.0 + - - -
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Residues in contact with LYS 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B PRO* 3.1 23.8 + - - +
210B GLY* 3.7 8.7 - - - +
211B LEU 3.3 0.2 - - - -
212B GLN* 1.3 76.9 - - + +
214B LEU* 1.3 57.0 + - - +
216B ASP* 3.3 7.2 + - - +
217B ALA* 3.0 30.5 + - - +
428B VAL* 4.4 23.9 - - + +
431B THR* 3.7 17.7 - - + +
432B GLU* 4.6 18.6 - - + +
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Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B GLY 3.2 11.6 + - - +
211B LEU* 3.7 7.6 - - + +
213B LYS* 1.3 76.3 - - - +
215B HIS* 1.3 65.9 + - - +
217B ALA 3.4 0.2 + - - -
218B LEU* 2.9 52.3 + - + +
255B VAL* 4.2 11.7 - - + -
335B LEU* 3.6 31.0 - - + -
338B ILE* 5.4 2.0 - - + -
380B MET* 4.8 0.9 - - + -
427B SER* 4.0 17.7 - - - +
430B PHE* 3.9 30.5 - - + -
431B THR* 3.1 24.6 + - - +
435B VAL* 4.0 8.1 - - + -
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Residues in contact with HIS 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B LEU 2.8 21.0 + - - +
212B GLN* 3.6 16.0 + - - +
214B LEU* 1.3 73.8 - - - +
216B ASP* 1.3 78.4 + - - +
218B LEU* 3.4 4.3 + - - +
219B ASP* 2.9 37.1 + - + +
252B VAL* 3.5 42.2 - - + +
255B VAL* 3.6 16.3 - - + +
256B LYS* 3.8 29.1 - - + +
259B MET* 4.7 5.6 - - - -
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Residues in contact with ASP 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLN* 2.8 52.6 + - - +
213B LYS* 3.8 6.4 - - - +
215B HIS* 1.3 87.2 + - - +
217B ALA* 1.3 59.7 + - - +
219B ASP* 3.2 5.5 + - - +
220B ALA* 2.9 29.7 + - - +
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Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B LYS 3.0 18.1 + - - +
214B LEU 4.0 2.0 - - - +
216B ASP* 1.3 75.5 - - - +
218B LEU* 1.3 62.7 + - - +
220B ALA* 3.3 7.4 + - - +
221B LYS* 3.1 27.0 + - - +
431B THR* 3.5 23.1 - - + +
435B VAL* 3.6 17.3 - - + -
436B VAL* 3.8 15.4 - - + +
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 2.9 45.9 + - + +
215B HIS* 3.8 2.7 - - - +
217B ALA* 1.3 76.0 - - - +
219B ASP* 1.3 57.9 + - - +
221B LYS* 3.3 4.0 + - - +
222B SER* 2.8 28.2 + - - -
248B PHE* 4.0 28.6 - - + -
251B TYR* 4.1 23.3 - - + +
252B VAL* 3.5 16.3 - - + +
255B VAL* 3.8 20.4 - - + -
338B ILE* 4.4 14.6 - - + -
342B ILE* 4.5 2.2 - - + -
435B VAL* 4.0 19.1 - - + -
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Residues in contact with ASP 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B HIS* 2.9 25.9 + - + +
216B ASP* 3.2 8.0 + - - +
218B LEU* 1.3 76.8 - - - +
220B ALA* 1.3 62.4 + - - +
222B SER* 3.1 7.8 + - - -
223B LYS* 3.1 59.8 + - - +
252B VAL* 3.5 24.9 - - + +
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Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ASP 2.9 16.4 + - - +
217B ALA* 3.7 8.1 - - - +
218B LEU 3.3 0.2 - - - -
219B ASP* 1.3 76.1 + - - +
221B LYS* 1.3 59.9 + - + +
223B LYS* 3.3 10.0 + - - +
224B GLU* 3.0 28.3 + - - +
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Residues in contact with LYS 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B ALA 3.1 17.0 + - - +
218B LEU* 3.7 3.8 - - - +
220B ALA* 1.3 75.1 - - + +
222B SER* 1.3 66.1 + - - +
224B GLU* 3.1 29.6 + - - +
225B PHE* 2.9 44.7 + - + -
248B PHE* 4.0 19.3 - - + -
435B VAL* 3.3 24.5 - - + +
436B VAL* 3.1 30.1 + - - +
437B GLY* 4.2 1.0 - - - -
438B ILE* 2.6 28.7 + - + +
439B GLN* 5.4 1.6 - - - +
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Residues in contact with SER 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B LEU 2.8 15.5 + - - -
219B ASP* 3.1 17.4 + - - -
221B LYS* 1.3 76.6 - - - +
223B LYS* 1.3 60.6 + - - +
226B ALA* 3.3 10.4 + - - +
245B GLY* 2.8 44.5 + - - -
248B PHE* 3.8 18.3 - - - +
249B SER* 3.7 15.6 + - - -
252B VAL* 4.4 1.3 - - - -
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Residues in contact with LYS 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B ASP* 3.1 43.2 + - - +
220B ALA* 3.7 8.3 - - - +
221B LYS 3.1 0.2 - - - -
222B SER* 1.3 75.3 - - - +
224B GLU* 1.3 64.9 - - - +
225B PHE 3.1 1.6 - - - -
226B ALA* 3.1 21.7 + - - +
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Residues in contact with GLU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B ALA 3.0 16.1 + - - +
221B LYS* 3.1 39.9 + - - +
223B LYS* 1.3 76.0 - - - +
225B PHE* 1.3 76.8 + - + +
226B ALA 3.4 0.6 + - - -
227B GLN 5.1 0.9 + - - -
228B ILE* 4.5 5.4 - - - +
438B ILE 4.7 1.2 - - - +
439B GLN* 5.6 3.3 - - - +
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Residues in contact with PHE 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B LYS* 2.9 36.6 + - + +
222B SER 3.7 0.7 - - - -
223B LYS 3.1 0.2 - - - -
224B GLU* 1.3 101.8 - - + +
226B ALA* 1.3 63.3 + - - +
227B GLN 3.1 4.7 + - - -
228B ILE* 3.2 29.0 + - + -
244B LEU* 3.6 31.8 + - + -
245B GLY 3.0 17.5 + - - +
248B PHE* 4.4 14.1 - + - -
356B LEU* 4.4 8.5 - - + -
438B ILE* 3.8 34.5 - - + -
439B GLN* 4.2 1.3 - - - -
440B ALA* 3.8 25.6 - - + -
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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