Contacts of the helix formed by residues 229 - 248 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64D TYR* 4.6 0.9 - - - -
227D HIS* 2.9 21.5 + - + +
228D SER* 1.3 80.6 + - - +
230D PRO* 1.3 63.5 - - - +
231D GLU* 3.3 24.6 + - - +
232D GLU* 2.9 30.9 + - + +
233D LEU* 2.9 26.7 + - - +
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Residues in contact with PRO 230 (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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64D TYR* 3.3 35.9 - - + +
129D ILE* 3.5 13.7 - - + +
130D ALA* 4.4 6.1 - - - -
133D ALA* 3.5 25.6 - - + -
228D SER 3.7 7.2 - - - +
229D ASN* 1.3 88.9 - - - +
231D GLU* 1.3 72.8 + - - +
233D LEU* 3.2 9.1 + - + +
234D GLN* 2.9 25.8 + - - +
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Residues in contact with GLU 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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130D ALA* 3.9 24.1 - - + +
133D ALA* 5.7 0.3 - - - +
134D LYS* 4.4 14.4 + - - +
229D ASN* 3.4 24.3 + - - +
230D PRO* 1.3 88.9 - - - +
232D GLU* 1.3 63.2 + - - +
234D GLN* 3.1 9.3 + - - +
235D LYS* 3.0 21.3 + - - +
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Residues in contact with GLU 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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227D HIS* 3.1 37.7 - - + +
229D ASN* 2.9 22.5 + - + +
231D GLU* 1.3 75.0 - - - +
233D LEU* 1.3 64.7 + - - +
235D LYS* 3.2 28.0 + - - +
236D GLN* 3.1 46.5 + - - +
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Residues in contact with LEU 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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64D TYR* 3.5 38.8 - - + +
66D TRP* 4.0 12.6 - - + +
129D ILE* 4.2 7.6 - - + -
190D LEU* 3.8 18.2 - - + -
225D LEU* 3.6 39.9 - - + +
226D ILE 4.0 9.9 - - - +
227D HIS* 3.9 10.0 - - + +
229D ASN 2.9 13.8 + - - +
230D PRO* 3.5 9.6 - - + +
232D GLU* 1.3 77.1 - - - +
234D GLN* 1.3 56.5 + - - +
236D GLN* 3.4 6.3 + - - +
237D ALA* 2.8 31.1 + - - +
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Residues in contact with GLN 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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126D PRO 3.2 17.7 - - - +
127D ASP* 3.3 21.5 + - - +
128D GLN 3.8 0.4 - - - -
129D ILE* 3.1 22.3 - - + +
130D ALA* 2.8 42.3 - - - +
131D LYS 4.5 0.6 - - - +
230D PRO 2.9 13.2 + - - +
231D GLU* 3.4 10.1 - - - +
232D GLU 3.1 0.2 - - - -
233D LEU* 1.3 73.6 - - - +
235D LYS* 1.3 60.4 + - - +
237D ALA* 3.2 0.9 + - - +
238D ILE* 2.8 50.2 + - + +
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Residues in contact with LYS 235 (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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231D GLU 3.0 11.7 + - - +
232D GLU* 3.5 31.7 + - - +
234D GLN* 1.3 76.7 - - - +
236D GLN* 1.3 60.0 + - + +
238D ILE* 3.6 8.2 + - - +
239D ALA* 3.1 27.4 + - + +
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Residues in contact with GLN 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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225D LEU* 3.7 26.0 - - + +
226D ILE 4.9 6.9 + - - +
227D HIS* 3.8 14.7 + - - -
232D GLU* 3.1 43.7 + - - +
233D LEU* 3.8 6.1 - - - +
235D LYS* 1.3 75.3 - - + +
237D ALA* 1.3 58.9 + - - +
239D ALA* 3.3 5.4 + - - +
240D ALA* 2.9 31.9 + - - +
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Residues in contact with ALA 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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66D TRP* 3.9 22.3 + - + -
126D PRO* 3.9 9.4 - - + +
129D ILE* 3.8 22.4 - - + -
225D LEU* 3.5 13.8 - - + +
233D LEU 2.8 21.7 + - - +
234D GLN 3.7 3.8 - - - +
236D GLN* 1.3 72.9 - - - +
238D ILE* 1.3 61.9 + - - +
240D ALA* 3.5 3.0 + - - +
241D GLU* 3.3 25.8 + - - +
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Residues in contact with ILE 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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126D PRO* 3.8 19.7 - - + -
127D ASP* 3.8 21.3 - - + +
234D GLN* 2.8 42.9 + - + +
235D LYS* 3.8 7.0 - - - +
237D ALA* 1.3 73.6 - - - +
239D ALA* 1.3 69.2 + - - +
241D GLU* 3.1 5.5 + - - +
242D GLU* 2.9 36.4 + - - +
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Residues in contact with ALA 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 LYS* 3.1 16.6 + - + +
236D GLN* 3.8 5.6 - - - +
238D ILE* 1.3 80.2 - - - +
240D ALA* 1.3 57.3 + - - +
242D GLU* 3.2 8.7 + - - +
243D SER* 2.9 29.1 + - - -
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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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220D PRO* 3.6 10.7 - - + -
221D GLY* 3.5 30.0 + - - +
225D LEU* 4.3 14.8 - - + -
236D GLN 2.9 19.2 + - - +
237D ALA* 3.7 6.5 - - - +
238D ILE 3.2 0.2 - - - -
239D ALA* 1.3 76.8 - - - +
241D GLU* 1.3 56.8 + - - +
243D SER* 3.3 9.1 - - - -
244D LEU 3.1 19.2 + - - -
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Residues in contact with GLU 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D TRP* 5.5 4.5 - - - +
68D PRO* 5.3 0.2 - - - +
125D MSE 5.2 5.0 - - - +
126D PRO* 3.5 23.3 - - + +
188D ARG* 3.2 36.0 + - - -
221D GLY* 4.1 21.1 - - - +
237D ALA 3.3 10.9 + - - +
238D ILE* 3.1 7.4 + - - +
240D ALA* 1.3 76.3 - - - +
242D GLU* 1.3 56.2 + - - +
243D SER 3.2 0.4 - - - -
244D LEU* 3.1 14.8 + - + +
245D LYS* 2.7 42.0 + - + +
14E PHE* 5.1 5.9 - - - -
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Residues in contact with GLU 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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238D ILE* 2.9 27.0 + - + +
239D ALA* 3.4 14.1 - - - +
241D GLU* 1.3 77.1 - - - +
243D SER* 1.3 58.0 + - - +
245D LYS* 3.3 34.1 + - - +
246D LYS* 3.0 30.4 + - - +
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Residues in contact with SER 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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220D PRO* 3.6 20.8 - - - +
239D ALA 2.9 12.6 + - - -
240D ALA* 3.3 12.1 - - - -
242D GLU* 1.3 77.0 - - - +
244D LEU* 1.3 55.8 + - - +
246D LYS* 3.5 8.3 + - - +
247D ALA* 3.0 28.2 + - - +
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Residues in contact with LEU 244 (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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219D ILE* 6.1 1.1 - - + -
220D PRO* 3.7 16.4 - - - +
221D GLY* 4.0 23.1 - - - +
222D VAL* 4.4 13.7 - - + -
240D ALA 3.1 12.9 + - - +
241D GLU* 3.1 19.0 + - + +
243D SER* 1.3 75.4 + - - +
245D LYS* 1.3 65.8 + - - +
247D ALA* 3.4 8.6 + - + +
248D ALA* 3.1 24.1 + - + +
14E PHE* 6.1 1.3 - - + -
16E LEU* 4.1 23.6 - - + -
32E LEU* 4.7 19.3 - - + -
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Residues in contact with LYS 245 (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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241D GLU* 2.7 23.6 + - + +
242D GLU* 3.3 34.9 + - + +
244D LEU* 1.3 72.2 - - - +
246D LYS* 1.3 57.4 + - - +
248D ALA* 2.8 24.6 + - - +
249D SER* 3.3 13.8 + - - -
16E LEU* 4.3 31.7 + - + +
17E SER* 5.1 11.0 - - - +
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Residues in contact with LYS 246 (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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242D GLU 3.0 14.5 + - - +
243D SER* 3.7 8.5 - - - +
245D LYS* 1.3 78.6 - - - +
247D ALA* 1.3 63.0 + - - +
249D SER* 3.1 26.8 + - - +
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Residues in contact with ALA 247 (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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243D SER 3.0 17.9 + - - +
244D LEU* 3.7 10.1 - - + +
246D LYS* 1.3 77.1 - - - +
248D ALA* 1.3 56.6 + - - +
249D SER 3.2 8.2 + - - +
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Residues in contact with ALA 248 (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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244D LEU* 3.1 15.6 + - + +
245D LYS 2.8 7.7 + - - +
247D ALA* 1.3 76.9 - - - +
249D SER* 1.3 59.0 + - - +
16E LEU* 3.3 34.1 - - + -
30E THR* 4.0 16.0 - - + +
31E PHE 5.7 0.2 - - - +
32E LEU* 5.7 0.7 - - + -
33E PRO* 5.5 7.2 - - + -
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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