Contacts of the helix formed by residues 229 - 246 (chain W) 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 ASN 229 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228W ASN* 1.3 72.3 - - - +
230W ILE* 1.3 65.2 + - - +
231W LYS* 3.1 4.9 - - - +
232W ALA* 3.0 13.9 + - - +
233W ASN* 3.0 11.3 + - - -
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Residues in contact with ILE 230 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227W LEU 4.2 6.9 + - - -
228W ASN 3.2 5.5 + - - -
229W ASN* 1.3 73.1 - - - +
231W LYS* 1.3 49.9 + - - +
232W ALA* 2.7 13.9 + - - -
233W ASN 3.1 1.3 + - - -
234W ASP* 2.9 36.0 + - - +
531W ASP* 5.2 10.9 - - - +
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Residues in contact with LYS 231 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229W ASN* 3.1 4.1 - - - +
230W ILE* 1.3 70.0 - - - +
232W ALA* 1.3 53.3 + - - +
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Residues in contact with ALA 232 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229W ASN* 3.0 7.0 + - - +
230W ILE 2.7 6.4 + - - -
231W LYS* 1.3 72.8 - - - +
233W ASN* 1.3 54.3 + - - +
234W ASP 3.9 0.7 - - - -
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Residues in contact with ASN 233 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229W ASN 3.0 11.8 + - - -
230W ILE* 3.8 1.6 - - - -
232W ALA* 1.3 78.7 - - - +
234W ASP* 1.3 56.8 + - - +
235W TYR 3.5 2.0 - - - -
236W ALA* 3.4 7.8 + - - +
237W ASN* 3.1 24.3 + - - -
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Residues in contact with ASP 234 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230W ILE* 2.9 25.5 + - - +
232W ALA 3.9 0.4 - - - -
233W ASN* 1.3 73.0 - - - +
235W TYR* 1.3 58.7 + - - +
237W ASN* 3.3 3.6 + - - +
238W ALA* 3.0 23.7 + - - -
514W TYR* 3.7 22.8 - - - +
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Residues in contact with TYR 235 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233W ASN 3.5 0.2 - - - -
234W ASP* 1.3 72.3 - - - +
236W ALA* 1.3 61.4 + - - +
238W ALA* 3.0 12.6 + - - +
239W VAL* 3.1 11.1 + - - -
317W GLY 5.1 5.8 - - - -
318W ASP* 5.0 4.3 - - - +
319W GLY* 4.5 25.5 - - - +
514W TYR* 5.2 6.4 - - - +
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Residues in contact with ALA 236 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233W ASN* 3.4 9.6 + - - +
234W ASP 3.3 0.6 - - - -
235W TYR* 1.3 73.5 - - - +
237W ASN* 1.3 57.3 + - - +
239W VAL* 3.3 2.8 + - - +
240W LEU* 3.0 26.9 + - - -
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Residues in contact with ASN 237 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233W ASN 3.1 13.7 + - - -
234W ASP* 3.3 4.4 + - - +
236W ALA* 1.3 72.4 - - - +
238W ALA* 1.3 59.3 + - - +
240W LEU* 4.1 1.7 - - - +
241W GLN* 3.1 24.9 + - - -
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Residues in contact with ALA 238 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234W ASP 3.0 13.6 + - - -
235W TYR* 3.0 5.1 + - - +
237W ASN* 1.3 73.7 - - - +
239W VAL* 1.3 62.5 + - - +
241W GLN* 3.5 0.9 + - - -
242W ALA* 3.0 19.4 + - - -
319W GLY* 6.2 0.4 - - - -
514W TYR 5.2 4.7 - - - -
515W ARG 6.1 0.2 - - - -
516W ILE* 5.6 9.9 - - - +
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Residues in contact with VAL 239 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235W TYR 3.1 11.6 + - - -
236W ALA* 3.3 2.8 + - - +
238W ALA* 1.3 71.1 - - - +
240W LEU* 1.3 66.2 + - - +
242W ALA* 2.9 13.6 + - - +
243W LEU* 3.0 13.5 + - - -
319W GLY* 5.6 8.7 - - - -
322W PHE 6.3 0.2 - - - -
323W LEU* 5.6 9.2 - - - +
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Residues in contact with LEU 240 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236W ALA 3.0 15.8 + - - -
237W ASN* 4.1 2.0 - - - +
239W VAL* 1.3 73.0 - - - +
241W GLN* 1.3 56.6 + - - +
243W LEU* 5.5 0.4 - - - +
244W SER* 3.0 26.7 + - - -
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Residues in contact with GLN 241 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223W GLY 6.1 0.9 - - - -
237W ASN 3.1 17.3 + - - -
238W ALA 3.9 1.3 - - - -
240W LEU* 1.3 74.5 - - - +
242W ALA* 1.3 62.1 + - - +
244W SER* 3.9 1.2 - - - +
245W ASN* 3.1 18.9 + - - -
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Residues in contact with ALA 242 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238W ALA 3.0 11.5 + - - -
239W VAL* 2.9 9.2 + - - +
241W GLN* 1.3 73.4 - - - +
243W LEU* 1.3 61.6 + - - +
245W ASN* 3.0 11.8 + - - -
246W VAL* 3.1 10.9 + - - -
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Residues in contact with LEU 243 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239W VAL 3.0 12.2 + - - -
240W LEU* 4.2 0.7 - - - +
242W ALA* 1.3 73.3 - - - +
244W SER* 1.3 56.5 + - - +
246W VAL* 3.1 24.9 + - - +
249W LEU* 4.9 3.1 - - - -
250W ARG 4.3 5.0 + - - -
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Residues in contact with SER 244 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240W LEU 3.0 19.1 + - - -
241W GLN* 3.9 1.8 - - - +
243W LEU* 1.3 74.6 - - - +
245W ASN* 1.3 58.6 + - - +
250W ARG* 4.5 16.3 - - - +
281W MET* 5.8 8.3 - - - +
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Residues in contact with ASN 245 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241W GLN 3.1 11.8 + - - -
242W ALA 3.0 9.6 + - - -
244W SER* 1.3 77.5 - - - +
246W VAL* 1.3 63.6 + - - +
247W PRO* 3.0 7.1 - - - +
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Residues in contact with VAL 246 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242W ALA 3.1 8.6 + - - -
243W LEU* 3.1 11.3 + - - +
245W ASN* 1.3 71.6 - - - +
247W PRO* 1.4 63.3 - - - +
248W PRO 3.5 2.2 - - - -
249W LEU* 3.2 7.3 + - - -
250W ARG* 2.9 20.3 + - - -
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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