Contacts of the helix formed by residues 229 - 248 (chain E) in PDB entry 2WFK
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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E TYR* 4.5 1.1 - - - -
227E HIS* 3.0 19.4 + - + +
228E SER* 1.3 79.6 + - - +
230E PRO* 1.3 64.5 - - - +
231E GLU* 3.2 26.6 + - - +
232E GLU* 2.8 31.4 + - + +
233E LEU* 3.0 27.3 + - - +
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Residues in contact with PRO 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E TYR* 3.3 39.2 - - + +
129E ILE* 3.4 17.5 - - + +
130E ALA* 4.3 10.3 + - - -
133E ALA* 3.5 25.8 - - + -
228E SER 3.8 1.6 - - - +
229E ASN* 1.3 90.1 - - - +
231E GLU* 1.3 74.5 + - - +
233E LEU* 3.4 6.6 + - + -
234E GLN* 3.0 18.9 + - - +
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Residues in contact with GLU 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E ALA* 3.8 32.6 - - + +
133E ALA* 5.8 0.2 - - - +
134E LYS* 4.3 12.1 - - - +
229E ASN* 3.2 26.1 + - - +
230E PRO* 1.3 85.5 - - - +
232E GLU* 1.3 65.6 + - - +
234E GLN* 3.1 6.2 + - - +
235E LYS* 3.0 21.7 + - - +
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Residues in contact with GLU 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E HIS* 3.1 37.7 - - + +
229E ASN* 2.8 24.6 + - + +
231E GLU* 1.3 72.5 - - - +
233E LEU* 1.3 62.6 + - - +
235E LYS* 3.3 25.8 + - - +
236E GLN* 3.1 51.3 + - - +
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Residues in contact with LEU 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E TYR* 3.5 36.6 - - + +
66E TRP* 4.0 13.9 - - + +
129E ILE* 4.2 7.9 - - + -
190E LEU* 3.8 20.0 - - + -
225E LEU* 3.6 40.2 - - + +
226E ILE 4.1 3.8 - - - +
227E HIS* 3.9 16.4 - - + +
229E ASN 3.0 13.2 + - - +
230E PRO* 3.6 9.2 - - + +
232E GLU* 1.3 77.1 - - - +
234E GLN* 1.3 56.1 + - - +
236E GLN* 3.5 5.5 + - - +
237E ALA* 2.8 32.1 + - - +
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Residues in contact with GLN 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B ASN* 3.4 23.5 + - - +
126E PRO 3.2 18.6 - - - +
127E ASP* 3.1 25.7 + - - -
128E GLN 3.8 0.2 - - - -
129E ILE* 3.1 13.7 - - + +
130E ALA* 2.8 40.9 - - - +
131E LYS 4.5 0.2 - - - +
230E PRO 3.0 13.7 + - - +
231E GLU* 3.1 9.8 + - - +
233E LEU* 1.3 74.7 - - - +
235E LYS* 1.3 58.5 + - - +
237E ALA* 3.7 0.2 - - - +
238E ILE* 2.8 52.3 + - + +
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Residues in contact with LYS 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E GLU 3.0 11.0 + - - +
232E GLU* 3.5 30.9 + - - +
234E GLN* 1.3 77.4 - - - +
236E GLN* 1.3 59.3 + - + +
238E ILE* 3.7 7.3 - - - +
239E ALA* 3.1 29.0 + - + +
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Residues in contact with GLN 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225E LEU* 3.8 26.4 - - + +
226E ILE 5.0 5.5 + - - -
227E HIS* 3.8 14.7 + - - -
232E GLU* 3.1 44.0 + - - +
233E LEU* 3.8 6.1 - - - +
235E LYS* 1.3 77.0 - - + +
237E ALA* 1.3 59.2 + - - +
239E ALA* 3.3 5.2 + - - +
240E ALA* 2.9 32.4 + - - +
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Residues in contact with ALA 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E TRP* 3.9 22.7 + - + -
126E PRO* 3.8 15.5 - - + +
129E ILE* 3.8 22.9 - - + -
225E LEU* 3.5 12.9 - - + +
233E LEU 2.8 22.0 + - - +
234E GLN 3.7 2.7 - - - +
236E GLN* 1.3 74.1 - - - +
238E ILE* 1.3 60.5 + - - +
240E ALA* 3.7 2.4 + - - +
241E GLU* 3.3 21.5 + - - +
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Residues in contact with ILE 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ASN* 5.0 3.8 - - - +
126E PRO* 3.9 21.8 - - + -
127E ASP* 3.8 17.9 - - + +
234E GLN* 2.8 41.6 + - + +
235E LYS* 3.7 7.2 - - - +
237E ALA* 1.3 74.7 - - - +
239E ALA* 1.3 67.7 + - - +
241E GLU* 3.1 6.2 + - - +
242E GLU* 2.9 36.7 + - - +
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Residues in contact with ALA 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E LYS* 3.1 16.0 + - + +
236E GLN* 3.8 5.8 - - - +
238E ILE* 1.3 81.1 - - - +
240E ALA* 1.3 57.3 + - - +
242E GLU* 3.1 9.5 + - - +
243E SER* 2.8 30.4 + - - -
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Residues in contact with ALA 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E PRO* 3.6 9.0 - - + -
221E GLY* 3.5 29.8 + - - +
225E LEU* 4.4 14.4 - - + -
236E GLN 2.9 18.1 + - - +
237E ALA 3.9 5.4 - - - +
238E ILE 3.2 0.2 - - - -
239E ALA* 1.3 77.4 - - - +
241E GLU* 1.3 57.0 + - - +
243E SER* 3.4 8.9 - - - -
244E LEU 3.1 20.1 + - - -
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Residues in contact with GLU 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL 5.5 1.0 - - - +
16D LEU* 4.0 31.5 - - + +
66E TRP* 5.3 4.4 - - - +
68E PRO* 5.3 1.0 - - + +
125E MSE 5.2 4.7 - - - +
126E PRO* 3.5 20.7 - - + +
188E ARG* 3.1 35.0 + - - -
221E GLY* 4.1 21.0 - - - +
237E ALA 3.3 12.4 + - - +
238E ILE* 3.1 7.8 + - - +
240E ALA* 1.3 76.7 - - - +
242E GLU* 1.3 57.0 + - - +
244E LEU* 3.2 6.3 + - + +
245E LYS* 2.8 41.3 + - + +
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Residues in contact with GLU 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E ILE* 2.9 27.2 + - - +
239E ALA* 3.3 13.5 - - - +
241E GLU* 1.3 77.7 - - - +
243E SER* 1.3 56.1 + - - +
245E LYS* 3.2 34.6 + - - +
246E LYS* 2.9 30.4 + - - +
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Residues in contact with SER 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E PRO* 3.7 21.2 - - - +
239E ALA 2.8 12.1 + - - -
240E ALA* 3.4 11.9 - - - -
242E GLU* 1.3 76.7 - - - +
244E LEU* 1.3 56.4 + - - +
246E LYS* 3.5 9.0 + - - +
247E ALA* 3.0 29.5 + - - +
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Residues in contact with LEU 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 3.5 21.5 - - + -
32D LEU* 3.5 35.4 - - + -
33D PRO* 5.8 0.2 - - + -
219E ILE* 6.0 0.7 - - + -
220E PRO* 3.7 15.7 - - - +
221E GLY* 3.8 25.6 - - - +
222E VAL* 4.4 10.1 - - + -
240E ALA 3.1 13.6 + - - +
241E GLU* 3.2 10.3 + - + +
243E SER* 1.3 73.4 + - - +
245E LYS* 1.3 65.8 + - - +
247E ALA* 3.3 9.7 + - + +
248E ALA* 3.0 26.5 + - + +
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Residues in contact with LYS 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LYS* 5.9 4.2 - - - +
16D LEU* 3.7 36.1 - - + +
17D SER* 3.0 43.4 + - - +
30D THR* 4.9 7.0 + - + +
241E GLU* 2.8 22.6 + - + +
242E GLU* 3.2 35.4 + - + +
244E LEU* 1.3 72.9 - - - +
246E LYS* 1.3 55.7 + - - +
248E ALA* 2.8 24.8 + - - +
249E SER* 3.2 14.0 + - - -
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Residues in contact with LYS 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242E GLU 2.9 13.4 + - - +
243E SER* 3.6 8.5 - - - +
245E LYS* 1.3 78.4 - - - +
247E ALA* 1.3 63.6 + - - +
249E SER* 3.1 27.0 + - - +
250E ASP 3.8 1.2 + - - -
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Residues in contact with ALA 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243E SER* 3.0 17.4 + - - +
244E LEU* 3.7 10.3 - - + +
245E LYS 3.2 0.4 - - - -
246E LYS* 1.3 75.7 - - - +
248E ALA* 1.3 58.4 + - - +
249E SER 3.2 7.7 + - - +
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Residues in contact with ALA 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ASN* 2.7 44.6 + - - +
16D LEU* 4.7 7.4 - - + -
30D THR* 5.1 4.9 - - + +
31D PHE 5.0 1.3 - - - +
33D PRO* 4.2 22.0 - - + -
244E LEU* 3.0 13.8 + - + +
245E LYS* 2.8 12.1 + - - +
247E ALA* 1.3 76.1 - - - +
249E SER* 1.3 58.1 + - - +
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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
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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