Contacts of the helix formed by residues 216 - 236 (chain L) in PDB entry 6AH0
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 ALA 216 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212L MET* 2.9 12.3 + - - +
215L ILE* 1.3 78.7 - - - +
217L PRO* 1.3 65.4 - - - +
218L ASN 3.2 3.0 + - - -
219L LEU* 3.3 4.8 + - - +
220L SER* 2.9 22.7 + - - -
306L ASP* 5.4 10.8 - - - +
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Residues in contact with PRO 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213L SER* 3.1 29.2 - - - +
214L PHE 4.6 1.2 - - - -
215L ILE 4.0 0.4 - - - -
216L ALA* 1.3 73.8 - - - +
218L ASN* 1.3 61.6 + - - +
220L SER* 3.7 0.7 + - - -
221L ILE* 3.2 19.1 + - - -
306L ASP* 6.0 0.6 - - - -
311L SER 5.8 0.9 - - - +
312L THR* 5.5 7.4 - - - +
313L GLU 6.2 0.2 - - - -
314L GLY* 4.8 10.8 - - - +
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Residues in contact with ASN 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216L ALA 3.3 0.4 - - - -
217L PRO* 1.3 74.2 - - - +
219L LEU* 1.3 66.5 + - - +
221L ILE* 3.3 9.2 + - - +
222L ILE* 3.4 7.6 + - - -
302L ALA* 4.9 11.2 + - - +
306L ASP* 6.0 3.0 - - - +
311L SER 5.2 3.0 + - - -
314L GLY* 4.7 8.7 - - - -
317L GLY* 3.8 29.4 - - - +
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Residues in contact with LEU 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216L ALA* 3.3 7.7 + - - +
218L ASN* 1.3 72.7 - - - +
220L SER* 1.3 64.4 + - - +
222L ILE* 2.8 14.7 + - - -
223L ILE 3.2 9.5 + - - -
224L GLY 5.0 0.6 - - - +
228L ALA* 5.8 4.5 - - - -
299L CYS* 5.6 6.7 - - - +
302L ALA* 4.4 18.6 + - - +
303L ALA* 5.3 2.5 - - - +
306L ASP* 6.4 0.2 - - - +
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Residues in contact with SER 220 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212L MET 5.4 5.4 - - - -
213L SER* 5.9 1.6 - - - +
216L ALA 2.9 19.8 + - - -
217L PRO 4.0 1.3 - - - -
219L LEU* 1.3 69.6 - - - +
221L ILE* 1.3 57.6 + - - +
224L GLY* 2.6 48.7 + - - -
225L ALA* 4.3 6.3 - - - +
228L ALA* 5.6 3.0 - - - +
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Residues in contact with ILE 221 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217L PRO 3.2 15.3 + - - -
218L ASN* 3.3 5.1 + - - +
219L LEU 3.2 0.6 + - - -
220L SER* 1.3 73.7 - - - +
222L ILE* 1.3 60.5 + - - +
224L GLY 4.7 0.3 + - - -
317L GLY* 5.3 8.1 - - - -
321L LYS* 6.0 0.9 - - - -
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Residues in contact with ILE 222 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218L ASN 3.4 6.5 + - - -
219L LEU 2.8 15.0 + - - -
221L ILE* 1.3 74.6 - - - +
223L ILE* 1.3 57.4 + - - +
224L GLY 3.6 0.2 - - - -
279L ILE* 5.5 6.1 - - - -
317L GLY 5.2 6.4 + - - -
321L LYS* 5.6 7.6 - - - +
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Residues in contact with ILE 223 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219L LEU 3.2 8.6 + - - -
222L ILE* 1.3 77.0 - - - +
224L GLY* 1.3 65.0 + - - +
227L THR* 4.3 10.4 + - - +
228L ALA* 5.0 3.8 - - - +
277L SER* 5.5 2.8 - - - -
278L ASP 5.1 8.3 + - - -
279L ILE* 5.7 4.1 + - - +
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Residues in contact with GLY 224 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219L LEU 5.0 0.2 - - - +
220L SER* 2.6 26.0 + - - +
221L ILE 4.6 0.4 + - - -
222L ILE 3.6 0.8 - - - -
223L ILE* 1.3 73.5 - - - +
225L ALA* 1.3 68.4 - - - -
226L SER 3.2 2.5 - - - -
227L THR 3.5 0.6 + - - -
228L ALA* 3.1 20.1 + - - -
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Residues in contact with ALA 225 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208L VAL 4.9 13.2 - - - -
209L GLU* 5.1 9.0 - - - +
212L MET* 5.3 10.6 - - - +
220L SER* 4.0 11.3 + - - +
224L GLY* 1.3 71.6 - - - +
226L SER* 1.3 52.2 + - - +
228L ALA* 3.1 1.4 + - - +
229L ALA* 2.7 34.0 + - - -
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Residues in contact with SER 226 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97L ASN* 6.4 1.8 - - - +
208L VAL 6.1 0.2 - - - -
224L GLY 3.2 0.8 - - - -
225L ALA* 1.3 74.2 - - - +
227L THR* 1.3 63.2 + - - +
229L ALA* 3.0 4.5 + - - +
230L LYS* 2.9 18.2 + - - -
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Residues in contact with THR 227 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223L ILE* 4.3 9.7 + - - +
224L GLY 3.5 5.3 + - - -
225L ALA 3.5 0.4 - - - -
226L SER* 1.3 73.7 - - - +
228L ALA* 1.3 62.3 + - - +
230L LYS* 3.0 4.3 + - - +
231L ILE* 2.9 20.8 + - - -
273L TYR 5.9 3.6 - - - -
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Residues in contact with ALA 228 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219L LEU 5.8 2.2 - - - -
220L SER* 5.6 7.0 - - - +
223L ILE* 4.9 2.5 + - - +
224L GLY 3.1 14.8 + - - -
225L ALA* 3.4 4.7 - - - +
227L THR* 1.3 75.9 - - - +
229L ALA* 1.3 60.6 + - - +
231L ILE* 3.3 1.7 + - - +
232L MET* 2.9 21.0 + - - -
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Residues in contact with ALA 229 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93L ILE 5.9 1.3 - - - -
94L VAL* 4.7 17.6 - - - +
225L ALA 2.7 18.2 + - - -
226L SER* 3.0 4.0 + - - +
228L ALA* 1.3 72.3 - - - +
230L LYS* 1.3 62.7 + - - +
232L MET* 3.3 1.8 + - - +
233L GLY* 2.9 21.1 + - - -
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Residues in contact with LYS 230 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226L SER 2.9 13.8 + - - -
227L THR* 3.0 4.7 + - - +
229L ALA* 1.3 79.3 - - - +
231L ILE* 1.3 62.4 + - - +
233L GLY* 3.2 8.4 + - - -
234L VAL* 3.3 10.4 + - - -
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Residues in contact with ILE 231 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227L THR 2.9 15.8 + - - -
228L ALA* 3.9 2.0 - - - +
230L LYS* 1.3 72.1 - - - +
232L MET* 1.3 59.4 + - - +
234L VAL* 3.8 1.1 + - - +
235L ALA* 3.2 18.9 + - - -
241L LEU* 6.1 0.5 - - - -
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Residues in contact with MET 232 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228L ALA 2.9 15.1 + - - -
229L ALA* 3.7 3.6 - - - +
231L ILE* 1.3 75.2 - - - +
233L GLY* 1.3 58.3 + - - +
235L ALA* 3.3 0.6 + - - +
236L GLY* 2.8 25.6 + - - -
237L GLY* 3.0 20.9 + - - +
238L LEU* 6.3 0.2 - - - +
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Residues in contact with GLY 233 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94L VAL* 5.7 6.3 - - - -
229L ALA 2.9 16.0 + - - -
230L LYS* 3.2 3.3 + - - -
232L MET* 1.3 76.4 - - - +
234L VAL* 1.3 62.6 + - - +
236L GLY* 3.4 9.4 + - - -
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Residues in contact with VAL 234 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I U 4.4 18.5 + - - +
230L LYS 3.3 11.9 + - - -
231L ILE* 4.2 2.2 - - - +
233L GLY* 1.3 76.1 - - - +
235L ALA* 1.3 61.0 - - - +
236L GLY* 3.5 0.7 + - - -
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Residues in contact with ALA 235 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I U 5.0 2.9 + - - +
231L ILE 3.2 16.2 + - - -
232L MET* 3.8 2.9 - - - +
234L VAL* 1.3 75.9 - - - +
236L GLY* 1.3 63.2 + - - +
237L GLY 3.6 4.0 - - - -
240L ASN* 4.5 12.9 - - - +
241L LEU* 5.1 9.4 - - - +
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Residues in contact with GLY 236 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232L MET 2.8 6.1 + - - -
233L GLY* 3.4 7.6 + - - -
234L VAL 3.2 3.4 - - - -
235L ALA* 1.3 81.0 - - - +
237L GLY* 1.3 60.2 + - - +
240L ASN* 4.7 5.6 + - - -
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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
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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