Contacts of the helix formed by residues 226 - 243 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225I HIS* 1.3 77.2 + - - +
227I ALA* 1.3 59.3 - - - +
228I VAL* 3.4 8.9 + - + +
229I ASN* 3.5 17.3 + - - +
230I ALA* 3.0 27.8 + - - +
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Residues in contact with ALA 227 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226I ASN* 1.3 73.6 - - - +
228I VAL* 1.3 59.7 + - + +
230I ALA* 4.1 0.7 - - - +
231I THR* 2.7 33.3 + - - -
57K TYR* 3.8 22.7 - - + +
60K ARG* 4.2 28.4 - - + +
61K VAL* 4.6 13.2 - - + +
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Residues in contact with VAL 228 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226I ASN* 3.2 5.7 - - + +
227I ALA* 1.3 75.7 - - + +
229I ASN* 1.3 68.9 + - - +
231I THR* 3.7 2.9 + - - -
232I LEU* 3.0 34.4 + - + +
42K VAL* 4.6 4.0 - - + -
43K SER* 5.3 1.8 - - - +
46K VAL* 3.4 42.8 - - + -
48K PHE* 4.0 4.2 - - + -
57K TYR* 3.9 26.5 - - + +
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Residues in contact with ASN 229 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225I HIS* 4.1 21.3 + - + +
226I ASN* 3.5 19.7 + - - +
228I VAL* 1.3 81.3 - - - +
230I ALA* 1.3 53.9 + - - +
232I LEU* 2.8 15.5 + - - +
233I ILE* 2.6 43.7 + - + +
270I ALA* 4.2 18.5 + - + +
272I ASN* 4.1 27.3 + - - +
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Residues in contact with ALA 230 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225I HIS* 4.0 12.3 - - + +
226I ASN 3.0 19.8 + - - +
227I ALA 4.1 0.2 - - - +
229I ASN* 1.3 74.9 - - - +
231I THR* 1.3 57.2 + - - +
233I ILE* 3.5 12.2 + - - +
234I ASP* 3.0 36.2 + - - +
60K ARG* 3.5 37.9 - - - +
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Residues in contact with THR 231 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227I ALA 2.7 22.2 + - - -
228I VAL 3.8 3.4 - - - -
229I ASN 3.2 0.6 - - - -
230I ALA* 1.3 72.7 - - - +
232I LEU* 1.3 55.6 + - - +
234I ASP* 3.4 8.3 + - - +
235I SER* 2.8 31.8 + - - -
48K PHE* 3.6 26.2 - - + -
53K SER* 3.0 36.5 + - - +
56K ARG* 4.0 8.3 - - + +
57K TYR* 3.5 20.8 + - + +
60K ARG* 4.1 6.0 - - - +
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Residues in contact with LEU 232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228I VAL* 3.0 20.3 + - + +
229I ASN* 2.8 15.4 + - - +
231I THR* 1.3 73.1 - - - +
233I ILE* 1.3 61.9 + - + +
235I SER* 3.4 10.4 + - - -
236I TRP* 3.0 48.7 + - + +
269I LEU 4.5 13.7 - - - +
270I ALA* 5.7 5.8 - - - +
47K ILE 5.9 0.9 - - - +
48K PHE* 4.3 16.6 - - + -
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Residues in contact with ILE 233 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225I HIS* 3.5 38.8 - - + +
229I ASN* 2.6 27.7 + - + +
230I ALA* 3.5 7.6 - - - +
232I LEU* 1.3 70.6 - - + +
234I ASP* 1.3 68.6 + - - +
236I TRP* 3.1 15.9 + - + +
237I VAL* 3.2 14.0 + - - +
269I LEU 6.0 0.2 - - - -
270I ALA* 4.1 20.0 - - + -
275I THR* 3.7 18.6 - - + +
276I VAL* 3.4 32.1 - - + -
277I ALA* 3.7 14.4 - - + +
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Residues in contact with ASP 234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215I ARG* 3.2 52.4 + - - +
230I ALA 3.0 18.6 + - - +
231I THR 3.4 4.9 + - - +
233I ILE* 1.3 80.9 - - - +
235I SER* 1.3 60.9 + - - +
237I VAL* 3.3 2.7 + - - -
238I ASP* 3.2 13.7 + - - +
276I VAL* 5.3 0.5 - - - +
56K ARG* 3.0 38.7 + - - +
60K ARG* 3.8 12.6 + - - -
68K TYR* 3.8 8.1 + - - -
75K HIS* 5.3 1.0 - - - -
79K ASP* 4.6 0.3 - - - +
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Residues in contact with SER 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231I THR 2.8 17.3 + - - -
232I LEU* 3.4 15.5 - - - -
233I ILE 3.2 0.2 - - - -
234I ASP* 1.3 76.3 - - - +
236I TRP* 1.3 61.2 + - - +
238I ASP* 3.4 9.8 + - - +
239I ILE* 3.2 33.1 + - - +
48K PHE* 5.0 5.1 - - - -
50K ASP* 3.4 13.9 + - - +
53K SER* 3.0 26.0 + - - -
56K ARG* 4.8 0.6 - - - +
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Residues in contact with TRP 236 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232I LEU* 3.0 37.7 + - + +
233I ILE* 3.1 9.8 + - + +
235I SER* 1.3 71.5 - - - +
237I VAL* 1.3 63.4 + - - +
239I ILE* 3.5 33.1 - - + +
240I ALA* 3.2 23.0 + - - +
255I VAL* 4.8 0.9 - - + -
258I SER* 3.9 24.0 - - - -
259I MET* 3.6 40.8 - - + -
262I ALA* 4.0 9.4 - - + +
269I LEU* 3.7 49.1 + - + +
277I ALA* 3.6 19.7 - - + +
281I LEU* 3.7 19.0 - - + +
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Residues in contact with VAL 237 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211I GLY* 3.6 31.6 - - - +
215I ARG* 3.5 27.1 - - + +
233I ILE 3.2 14.9 + - - +
234I ASP* 3.5 8.1 - - - +
235I SER 3.3 0.2 - - - -
236I TRP* 1.3 72.5 - - - +
238I ASP* 1.3 63.5 - - - +
240I ALA* 3.1 8.3 + - - +
241I ILE* 3.0 30.6 + - + +
276I VAL* 4.4 17.0 - - + -
277I ALA* 4.1 21.1 - - - +
280I VAL* 4.4 12.3 - - + -
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Residues in contact with ASP 238 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215I ARG* 3.6 13.4 + - - +
234I ASP 3.2 8.7 + - - +
235I SER* 3.6 11.1 - - - +
237I VAL* 1.3 77.7 - - - +
239I ILE* 1.3 62.7 + - - +
241I ILE* 3.5 2.4 + - - -
242I PHE* 3.1 53.2 + - + +
243I GLN* 5.2 0.4 - - - +
50K ASP* 5.0 9.6 - - - +
52K ASN* 4.5 14.2 + - - +
53K SER* 5.2 1.4 + - - -
56K ARG* 3.3 29.9 + - - -
83K GLU* 5.2 4.7 - - - +
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Residues in contact with ILE 239 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235I SER* 3.2 23.2 + - - +
236I TRP* 3.5 39.7 - - + +
238I ASP* 1.3 75.3 - - - +
240I ALA* 1.3 61.3 + - - +
243I GLN* 3.0 53.1 + - - +
244I LEU 3.1 8.1 + - - -
255I VAL* 4.0 31.6 - - + -
258I SER* 5.7 3.6 - - - +
281I LEU* 5.6 0.7 - - + -
50K ASP* 4.7 9.2 - - - +
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Residues in contact with ALA 240 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236I TRP 3.2 9.2 + - - +
237I VAL* 3.1 8.9 + - - +
239I ILE* 1.3 78.0 - - - +
241I ILE* 1.3 63.4 + - - +
244I LEU* 3.4 14.0 - - - +
245I LYS 3.1 21.1 + - - -
280I VAL* 4.2 5.4 - - + -
281I LEU* 3.7 37.5 - - + +
284I VAL* 3.5 18.8 - - + +
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Residues in contact with ILE 241 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210I GLU* 3.4 41.7 - - + +
211I GLY* 3.8 23.6 - - - +
237I VAL* 3.0 21.8 + - + +
238I ASP* 4.0 3.8 - - - +
240I ALA* 1.3 74.3 - - - +
242I PHE* 1.3 86.2 + - + +
245I LYS* 3.1 29.3 - - + +
246I GLU* 4.4 2.8 + - - +
280I VAL* 3.7 22.0 - - + -
284I VAL* 4.5 6.1 - - + -
83K GLU* 4.9 5.8 - - - +
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Residues in contact with PHE 242 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194I LYS* 5.6 3.4 - - - -
238I ASP* 3.1 39.5 + - + +
241I ILE* 1.3 93.5 - - + +
243I GLN* 1.3 71.0 + - + +
244I LEU 3.5 0.2 - - - -
246I GLU* 3.4 29.7 + - - +
83K GLU* 3.4 43.3 - - + -
86K ALA* 6.0 3.1 - - + -
87K THR* 3.8 24.0 - - + -
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Residues in contact with GLN 243 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238I ASP 5.2 0.2 - - - +
239I ILE* 3.0 40.7 + - - +
242I PHE* 1.3 79.8 - - + +
244I LEU* 1.3 61.2 + - - +
247I GLY* 3.4 11.8 - - - -
251I GLU* 3.2 33.3 - - + +
252I LYS 5.3 0.2 + - - -
255I VAL* 4.8 10.4 - - + +
50K ASP* 5.3 8.1 + - - -
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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