Contacts of the helix formed by residues 207 - 225 (chain B) in PDB entry 6ATH
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 THR 207 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B MET* 3.6 17.4 - - - +
205B ASP 4.0 9.0 - - - +
206B ILE* 1.3 82.5 - - - +
208B ASN* 1.3 65.3 + - - +
209B SER* 2.6 26.8 + - - +
210B MET* 3.1 23.1 + - + +
211B ARG* 3.0 18.7 + - - +
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Residues in contact with ASN 208 (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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200B MET* 3.3 39.5 - - - +
207B THR* 1.3 74.7 - - - +
209B SER* 1.3 57.5 + - - +
211B ARG* 3.3 4.1 + - - +
212B ALA* 2.9 28.9 + - - +
342B ILE 4.8 1.9 - - - +
343B ASP* 6.1 0.2 - - - -
344B ALA* 3.4 30.0 + - + +
345B ASP* 3.9 22.7 + - + +
348B LEU* 5.8 0.4 - - - +
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Residues in contact with SER 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B THR* 2.6 23.4 + - - +
208B ASN* 1.3 76.1 - - - +
210B MET* 1.3 64.4 + - - +
212B ALA* 3.5 8.1 + - - +
213B ILE* 3.1 30.4 + - - +
406B GLN* 5.1 0.5 + - - -
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Residues in contact with MET 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ASP 3.5 20.0 - - - +
206B ILE* 3.8 17.0 - - - -
207B THR* 3.1 27.6 + - + +
209B SER* 1.3 77.0 + - - +
211B ARG* 1.3 65.8 + - - +
213B ILE* 3.2 6.5 + - + +
214B LEU* 2.9 22.5 + - - +
250B ARG* 3.6 49.4 - - - +
253B LEU* 3.8 14.7 - - + +
33C PHE* 3.8 30.1 - - + -
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Residues in contact with ARG 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B TYR* 3.5 17.7 + - - +
200B MET* 3.9 11.7 - - + -
206B ILE* 6.2 0.9 - - + +
207B THR 3.0 13.2 + - - +
208B ASN 3.5 7.8 + - - +
210B MET* 1.3 78.3 - - - +
212B ALA* 1.3 57.5 + - - +
214B LEU* 3.2 9.4 + - + +
215B VAL* 2.9 44.1 + - + +
236B VAL* 3.4 14.5 - - - +
239B ILE* 5.5 5.3 - - + +
240B ASP* 2.7 37.0 + - - -
243B LEU* 5.4 7.4 - - + -
253B LEU* 4.3 6.4 - - + +
340B SER 5.4 0.6 + - - -
341B LEU* 2.9 31.1 + - - +
342B ILE 3.2 20.4 + - - -
344B ALA* 3.6 32.0 - - - +
348B LEU* 4.9 3.0 - - - +
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Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ASN 2.9 17.1 + - - +
209B SER* 3.6 8.5 - - - +
210B MET 3.2 0.2 - - - -
211B ARG* 1.3 77.0 - - - +
213B ILE* 1.3 61.6 + - - +
215B VAL* 3.4 1.9 + - - +
216B ASP* 3.0 26.9 + - - +
342B ILE* 3.5 31.3 + - + +
343B ASP* 4.8 4.0 - - - +
404B HIS* 5.0 0.4 - - + -
406B GLN* 3.6 23.8 - - - +
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Residues in contact with ILE 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 SER* 3.1 19.2 + - - +
210B MET* 3.2 9.6 + - + +
212B ALA* 1.3 75.0 - - - +
214B LEU* 1.3 63.9 + - - +
216B ASP* 3.5 2.7 + - - +
217B TRP* 3.1 21.8 + - - +
406B GLN* 3.8 22.7 - - - +
30C ARG* 5.0 5.6 + - - +
32C LEU* 4.1 23.1 - - + +
33C PHE* 3.9 31.6 - - + -
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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
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210B MET 2.9 13.4 + - - +
211B ARG* 3.4 11.9 - - + +
213B ILE* 1.3 77.9 - - - +
215B VAL* 1.3 64.7 + - + +
217B TRP* 3.2 17.1 + - + +
218B LEU* 3.0 26.5 + - + +
239B ILE* 4.0 31.0 - - + -
253B LEU* 3.8 35.9 - - + +
254B GLN* 3.9 27.6 - - - -
257B GLY* 4.2 8.7 - - - -
32C LEU* 3.9 18.8 - - + +
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Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ARG* 2.9 41.4 + - + +
212B ALA 4.1 1.1 - - - +
214B LEU* 1.3 77.5 - - + +
216B ASP* 1.3 64.4 + - - +
218B LEU* 3.0 11.8 + - + +
219B VAL* 3.0 26.5 + - + +
232B LEU* 4.9 2.9 - - + -
236B VAL* 4.0 27.8 - - + -
239B ILE* 5.6 4.7 - - + -
341B LEU* 3.8 29.2 - - + +
342B ILE* 3.7 21.5 - - + -
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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
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212B ALA 3.0 8.2 + - - +
213B ILE* 3.8 3.8 - - - +
215B VAL* 1.3 76.4 - - - +
217B TRP* 1.3 62.4 + - - +
219B VAL* 3.3 15.1 + - - +
220B GLU* 3.3 9.5 + - - +
342B ILE* 3.7 11.6 - - + +
406B GLN* 3.3 44.2 - - + +
407B GLN 4.2 1.6 + - - -
408B SER* 2.6 49.7 + - - -
409B ILE* 4.3 2.3 + - - +
30C ARG* 3.7 12.4 + - - +
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Residues in contact with TRP 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 ILE 3.1 14.3 + - - +
214B LEU* 3.2 22.6 + - + +
216B ASP* 1.3 75.1 + - - +
218B LEU* 1.3 88.9 + - + +
220B GLU* 3.0 6.2 + - - +
221B VAL* 2.9 44.7 + - + +
254B GLN* 3.3 36.8 - - + -
258B THR* 3.4 26.5 - - + -
278B PHE* 6.2 0.7 - + - -
281B ILE* 3.5 23.6 + - + -
282B THR* 3.9 3.6 - - + -
28C ALA* 2.8 28.2 + - - -
30C ARG* 3.6 38.8 + - + +
32C LEU* 4.1 13.9 - - + -
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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* 3.0 24.7 + - + +
215B VAL* 3.0 11.6 + - - +
217B TRP* 1.3 103.7 - - + +
219B VAL* 1.3 57.2 + - - +
221B VAL* 3.3 7.0 + - + +
222B GLY* 2.9 26.2 + - - -
232B LEU* 3.9 14.0 - - + +
235B ALA* 4.7 11.0 - - + -
236B VAL* 5.0 6.1 - - + -
239B ILE* 3.5 31.9 - - + -
257B GLY 3.8 16.6 - - - +
261B MET* 3.9 27.7 - - + +
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Residues in contact with VAL 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 VAL* 3.0 22.0 + - + +
216B ASP* 3.3 12.3 - - - +
217B TRP 3.2 0.2 - - - -
218B LEU* 1.3 75.7 - - - +
220B GLU* 1.3 57.3 + - - +
222B GLY* 3.3 2.8 + - - -
223B GLU* 3.0 28.2 + - + +
232B LEU* 3.8 25.1 - - + -
338B GLU* 4.1 1.8 - - - +
341B LEU* 6.0 0.2 - - + -
342B ILE* 4.8 1.3 - - + -
408B SER* 4.1 16.4 - - - +
409B ILE* 3.6 37.0 - - + -
412B LYS* 4.0 26.6 + - + +
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Residues in contact with GLU 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 3.7 4.9 - - - +
217B TRP* 3.0 8.8 + - - +
219B VAL* 1.3 76.6 - - - +
221B VAL* 1.3 60.7 + - - +
223B GLU* 3.2 8.3 + - - +
224B GLU* 2.9 29.1 + - - +
408B SER* 3.3 26.2 - - - +
27C SER* 3.5 28.2 + - - +
28C ALA* 3.7 14.2 - - + +
30C ARG* 2.4 44.1 + - - -
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Residues in contact with VAL 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 TRP* 2.9 58.7 + - + +
218B LEU* 3.6 11.4 - - + +
220B GLU* 1.3 74.3 - - - +
222B GLY* 1.3 65.2 + - - +
224B GLU* 3.2 2.8 + - - -
225B TYR* 3.0 42.1 + - + +
227B LEU* 5.0 1.6 - - + -
261B MET* 4.6 9.9 - - + -
278B PHE* 4.4 18.2 - - + -
281B ILE* 4.0 19.5 - - + -
28C ALA* 4.3 5.8 - - - +
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Residues in contact with GLY 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 2.9 14.6 + - - -
219B VAL* 3.3 4.5 + - - -
221B VAL* 1.3 78.2 - - - +
223B GLU* 1.3 58.4 + - - +
226B LYS* 2.9 8.1 + - - -
227B LEU* 2.8 52.6 + - - +
232B LEU* 6.2 1.6 - - - -
261B MET* 4.1 5.6 - - - +
412B LYS* 6.3 0.7 - - - -
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Residues in contact with GLU 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 VAL* 3.0 18.3 + - + +
220B GLU* 3.2 10.7 + - - +
222B GLY* 1.3 76.0 - - - +
224B GLU* 1.3 65.0 + - - +
226B LYS* 3.3 17.5 + - - +
227B LEU 5.5 1.7 - - - +
412B LYS* 3.5 54.4 + - + +
415B ASN* 5.0 9.2 + - - -
417B LYS* 4.8 10.4 + - - -
418B TYR* 4.8 5.3 + - - -
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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 GLU 2.9 17.4 + - - +
221B VAL* 3.6 4.7 - - - +
223B GLU* 1.3 77.9 - - - +
225B TYR* 1.3 82.5 + - + +
226B LYS* 3.3 6.8 + - - +
280B TYR* 5.9 0.6 - - + -
281B ILE* 4.1 10.1 - - + -
26C PRO* 3.5 32.9 - - - +
27C SER 5.4 0.2 + - - -
28C ALA* 4.0 11.7 - - + +
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Residues in contact with TYR 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 VAL* 3.0 30.1 + - + +
224B GLU* 1.3 88.4 - - + +
226B LYS* 1.3 76.1 + - - +
227B LEU* 3.3 24.3 + - + +
273B PRO* 4.1 20.2 - - + -
277B GLU* 2.7 58.5 + - + -
278B PHE* 5.6 2.5 - + - -
280B TYR* 3.6 14.2 - - - -
281B ILE* 3.9 31.9 - - + +
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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