Contacts of the helix formed by residues 226 - 243 (chain D) in PDB entry 6IY6
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 226 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225D HIS* 1.3 72.6 - - - +
227D ALA* 1.3 58.4 + - - +
228D VAL* 3.3 20.6 + - - +
229D ASN* 3.0 40.4 + - - +
230D ALA* 3.0 28.5 + - - +
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Residues in contact with ALA 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D ASN* 1.3 74.2 - - - +
228D VAL* 1.3 60.7 + - + +
230D ALA* 4.1 0.5 - - - +
231D THR* 2.7 32.7 + - - -
57F TYR* 3.8 17.2 - - + -
60F ARG* 4.0 32.3 - - + +
61F VAL* 4.4 14.8 - - + +
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Residues in contact with VAL 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D ASN* 3.3 15.3 - - - +
227D ALA* 1.3 75.4 - - + +
229D ASN* 1.3 64.0 + - - +
231D THR* 3.8 2.6 - - - -
232D LEU* 3.0 33.3 + - + +
42F VAL* 4.8 3.1 - - + -
46F VAL* 3.8 37.9 - - + -
48F PHE* 4.0 5.0 - - + -
57F TYR* 3.7 29.6 - - + +
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Residues in contact with ASN 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D HIS* 4.1 22.1 + - + +
226D ASN* 3.0 30.6 + - - +
228D VAL* 1.3 78.3 - - - +
230D ALA* 1.3 53.9 + - - +
232D LEU* 2.8 15.8 + - - +
233D ILE* 2.6 43.9 + - + +
270D ALA* 4.4 18.0 + - + +
272D ASN* 4.8 14.3 - - - +
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Residues in contact with ALA 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D HIS* 4.0 13.1 - - + +
226D ASN 3.0 19.8 + - - +
227D ALA 4.1 0.2 - - - +
229D ASN* 1.3 75.0 - - - +
231D THR* 1.3 56.8 + - - +
233D ILE* 3.5 13.2 + - - +
234D ASP* 3.0 33.8 + - - +
60F ARG* 3.6 32.8 - - - +
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Residues in contact with THR 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D ALA 2.7 22.5 + - - -
228D VAL 3.8 3.6 - - - -
229D ASN 3.2 0.6 - - - -
230D ALA* 1.3 73.5 - - - +
232D LEU* 1.3 55.8 + - - +
234D ASP* 3.4 5.6 + - - +
235D SER* 2.8 32.3 + - - -
48F PHE* 3.6 26.5 - - + -
53F SER* 3.1 34.5 + - - +
56F ARG* 4.4 3.1 + - + -
57F TYR* 3.5 18.4 - - + +
60F ARG* 3.3 17.3 + - - +
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Residues in contact with LEU 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D VAL* 3.0 20.1 + - + +
229D ASN* 2.8 16.9 + - - +
231D THR* 1.3 71.7 - - - +
233D ILE* 1.3 61.3 + - + +
235D SER* 3.4 10.6 + - - -
236D TRP* 3.0 45.2 + - + +
269D LEU 4.8 11.2 - - - +
270D ALA* 5.6 5.8 - - - +
47F ILE 6.0 0.4 - - - +
48F PHE* 4.3 17.5 - - + -
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Residues in contact with ILE 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D HIS* 3.5 39.0 - - + +
229D ASN* 2.6 26.4 + - + +
230D ALA* 3.5 7.9 - - - +
232D LEU* 1.3 69.9 - - + +
234D ASP* 1.3 69.6 + - - +
236D TRP* 3.1 16.2 + - + +
237D VAL* 3.2 13.3 + - - +
270D ALA* 4.2 21.1 - - + -
275D THR* 3.7 17.9 - - + +
276D VAL* 3.4 32.3 - - + -
277D ALA* 3.7 14.9 - - + +
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Residues in contact with ASP 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D ARG* 3.2 54.2 + - - +
230D ALA 3.0 17.4 + - - +
231D THR 3.6 5.6 - - - +
233D ILE* 1.3 79.6 - - - +
235D SER* 1.3 61.6 + - - +
237D VAL* 3.3 2.3 + - - -
238D ASP* 3.2 13.1 + - - +
276D VAL* 5.3 0.3 - - - +
56F ARG* 3.1 32.8 + - - +
60F ARG* 3.1 25.5 + - - -
68F TYR* 3.8 2.9 + - - -
75F HIS* 5.2 0.7 - - - -
79F ASP* 4.6 0.3 - - - +
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Residues in contact with SER 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D THR 2.8 18.1 + - - -
232D LEU* 3.4 17.8 - - - +
233D ILE 3.2 0.2 - - - -
234D ASP* 1.3 75.5 - - - +
236D TRP* 1.3 60.1 + - - +
238D ASP* 3.4 9.6 + - - +
239D ILE* 3.1 36.0 + - - +
48F PHE* 4.9 6.4 - - - -
50F ASP* 5.1 4.0 + - - +
53F SER* 3.2 26.0 + - - -
56F ARG* 5.0 0.6 - - - +
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Residues in contact with TRP 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D LEU* 3.0 36.5 + - + +
233D ILE* 3.1 10.7 + - + +
235D SER* 1.3 71.0 - - - +
237D VAL* 1.3 65.1 + - - +
239D ILE* 3.5 32.4 - - + +
240D ALA* 3.2 22.5 + - - +
255D VAL* 4.7 3.4 - - + -
258D SER* 3.9 22.9 - - - -
259D MET* 3.6 41.1 - - + -
262D ALA* 4.2 7.5 - - + +
269D LEU* 3.7 49.3 + - + +
270D ALA* 5.8 0.4 - - - -
277D ALA* 3.6 20.0 - - + +
281D LEU* 3.7 18.2 - - + +
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Residues in contact with VAL 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D GLY* 3.7 31.0 - - - +
215D ARG* 3.5 26.7 - - + +
233D ILE 3.2 15.1 + - - +
234D ASP* 3.5 8.1 - - - +
235D SER 3.3 0.4 - - - -
236D TRP* 1.3 72.2 - - - +
238D ASP* 1.3 64.6 + - - +
240D ALA* 3.1 7.2 + - - +
241D ILE* 3.0 31.5 + - + +
276D VAL* 4.3 18.2 - - + -
277D ALA* 4.1 20.9 - - - +
280D VAL* 4.4 13.0 - - + -
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Residues in contact with ASP 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D ARG* 3.6 12.2 + - - -
234D ASP 3.2 10.1 + - - +
235D SER* 3.6 10.5 - - - +
237D VAL* 1.3 76.3 - - - +
239D ILE* 1.3 63.0 + - + +
241D ILE* 4.8 2.2 - - - -
242D PHE* 3.1 51.4 + - + +
243D GLN* 5.3 0.7 - - - +
50F ASP* 3.8 20.7 - - - +
52F ASN* 4.7 7.2 + - - +
56F ARG* 3.3 29.8 + - - -
83F GLU* 5.5 1.7 - - - +
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Residues in contact with ILE 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D SER* 3.1 22.3 + - - +
236D TRP* 3.5 38.8 - - + +
238D ASP* 1.3 76.0 - - + +
240D ALA* 1.3 60.7 + - - +
243D GLN* 3.0 47.0 + - - +
244D LEU 3.0 8.3 + - - -
255D VAL* 4.0 35.9 - - + -
258D SER* 6.2 1.8 - - - -
281D LEU* 5.4 0.9 - - + -
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Residues in contact with ALA 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D TRP 3.2 8.4 + - - +
237D VAL* 3.1 9.0 + - - +
239D ILE* 1.3 77.4 - - - +
241D ILE* 1.3 63.4 + - - +
244D LEU* 3.4 6.0 - - - +
245D LYS 3.1 22.3 + - - -
280D VAL* 4.2 5.2 - - + -
281D LEU* 3.4 48.9 - - + +
284D VAL* 3.5 17.4 - - + +
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Residues in contact with ILE 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D GLU* 3.8 24.9 - - + +
211D GLY* 3.9 33.7 - - - +
237D VAL* 3.0 20.9 + - + +
238D ASP* 4.0 3.4 - - - +
240D ALA* 1.3 76.7 - - - +
242D PHE* 1.3 86.1 - - + +
245D LYS* 3.2 32.3 - - + +
246D GLU* 4.5 3.1 + - - +
280D VAL* 3.7 23.1 - - + -
284D VAL* 4.6 5.2 - - + -
83F GLU* 5.3 3.8 - - - +
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Residues in contact with PHE 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D LYS* 5.9 2.7 - - - -
238D ASP* 3.1 39.4 + - + +
241D ILE* 1.3 93.6 - - + +
243D GLN* 1.3 70.4 + - + +
244D LEU 3.5 0.2 - - - -
246D GLU* 3.4 30.3 + - - +
83F GLU* 3.5 39.9 - - + -
86F ALA* 6.5 0.9 - - + -
87F THR* 4.4 18.6 - - + -
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Residues in contact with GLN 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D ASP 5.3 0.2 - - - +
239D ILE* 3.0 38.4 + - + +
242D PHE* 1.3 80.8 - - + +
244D LEU* 1.3 61.3 + - - +
247D GLY* 3.3 12.0 - - - -
251D GLU* 3.2 36.8 - - + +
252D LYS 5.3 0.2 + - - -
255D VAL* 4.9 9.5 - - + +
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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