Contacts of the helix formed by residues 227 - 247 (chain D) in PDB entry 4K71
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 GLU 227 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D LYS 3.8 2.3 + - - +
226D ALA* 1.3 77.3 - - - +
228D PHE* 1.3 69.0 + - - +
229D ALA* 4.3 8.7 - - + +
230D GLU* 3.1 14.5 + - + +
231D VAL* 3.1 18.8 + - - +
270D SER 4.5 1.8 + - - -
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Residues in contact with PHE 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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216D VAL* 4.7 25.1 - - + -
220D SER* 6.1 0.9 - - - -
226D ALA 3.9 0.4 + - - -
227D GLU* 1.3 78.1 + - - +
229D ALA* 1.3 56.5 + - - +
231D VAL* 2.9 12.7 + - + +
232D SER* 2.8 54.6 + - - -
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Residues in contact with ALA 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D GLU* 3.4 6.0 - - + +
228D PHE* 1.3 81.7 - - - +
230D GLU* 1.3 57.7 + - - +
232D SER* 3.4 8.7 + - - -
233D LYS* 3.1 26.7 + - - +
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Residues in contact with GLU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D ALA* 4.5 4.0 - - + -
227D GLU* 3.1 20.3 + - + +
228D PHE 3.1 1.0 - - - -
229D ALA* 1.3 76.4 - - - +
231D VAL* 1.3 65.1 + - - +
233D LYS* 3.3 6.4 + - - +
234D LEU* 3.2 25.6 + - + +
263D TYR* 3.1 37.5 + - - -
267D ASN* 4.6 2.5 - - - +
270D SER* 3.6 39.7 - - - +
271D ILE* 4.0 18.0 - - + +
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Residues in contact with VAL 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D VAL* 4.1 11.9 - - + +
219D LEU* 4.0 18.8 - - + +
220D SER* 3.9 27.6 - - - +
223D PHE* 4.8 7.0 - - + +
226D ALA* 4.0 20.4 - - + +
227D GLU 3.1 15.1 + - - +
228D PHE* 2.9 13.7 + - + +
230D GLU* 1.3 74.4 - - - +
232D SER* 1.3 63.1 + - - +
234D LEU* 3.2 10.2 + - + +
235D VAL* 3.0 40.1 + - + +
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Residues in contact with SER 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D VAL* 5.5 5.5 - - - +
228D PHE* 2.8 40.4 + - - -
229D ALA* 3.5 13.5 - - - -
231D VAL* 1.3 72.3 - - - +
233D LYS* 1.3 61.1 + - - +
235D VAL* 3.3 8.3 + - - +
236D THR* 3.1 26.4 + - - -
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Residues in contact with LYS 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D ALA 3.1 14.1 + - - +
230D GLU* 3.3 13.0 + - - +
232D SER* 1.3 74.5 - - - +
234D LEU* 1.3 65.4 + - - +
236D THR* 3.3 7.9 + - + -
237D ASP* 2.7 48.6 + - - +
263D TYR* 3.5 54.1 - - + +
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Residues in contact with LEU 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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219D LEU* 3.6 17.9 - - + -
223D PHE* 4.1 30.1 - - + -
230D GLU* 3.2 16.8 + - + +
231D VAL* 3.2 7.4 + - + +
233D LYS* 1.3 74.9 - - + +
235D VAL* 1.3 60.8 + - - +
237D ASP* 3.2 2.3 + - - +
238D LEU* 2.8 34.9 + - + +
260D LEU* 3.7 29.0 - - + +
263D TYR* 4.1 20.2 - - + -
264D ILE* 3.8 19.1 - - + -
271D ILE* 4.0 22.2 - - + -
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Residues in contact with VAL 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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211D PHE* 4.9 0.2 - - - -
212D LYS* 3.8 35.0 - - + +
215D ALA* 3.7 23.3 - - + -
216D VAL* 3.6 38.8 - - + +
219D LEU* 4.1 6.3 - - + -
231D VAL* 3.0 21.8 + - + +
232D SER* 3.6 6.7 - - - +
233D LYS 3.3 0.2 - - - -
234D LEU* 1.3 76.7 - - - +
236D THR* 1.3 50.7 + - - +
238D LEU* 3.9 5.0 - - - +
239D THR* 2.7 41.6 + - - -
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Residues in contact with THR 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D LYS* 3.6 22.7 + - - +
232D SER 3.1 13.6 + - - -
233D LYS* 3.6 11.8 - - + -
234D LEU 3.2 0.2 - - - -
235D VAL* 1.3 77.4 - - - +
237D ASP* 1.3 70.6 + - - +
239D THR* 3.3 7.1 + - - -
240D LYS* 3.0 22.3 + - + +
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Residues in contact with ASP 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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233D LYS* 2.7 50.4 + - - +
234D LEU 3.8 3.6 - - - +
236D THR* 1.3 84.3 - - - +
238D LEU* 1.3 58.0 + - - +
240D LYS* 3.3 10.0 + - - +
241D VAL* 3.1 31.7 + - - +
260D LEU* 3.9 27.9 - - + +
263D TYR* 5.2 2.3 - - - +
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Residues in contact with LEU 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D TYR* 5.1 3.8 - - - +
211D PHE* 3.9 6.9 - - + -
214D TRP* 5.1 8.3 - - + -
215D ALA* 4.6 14.4 - - + -
219D LEU* 4.1 31.4 - - + -
222D ARG* 6.0 0.9 - - - +
234D LEU 2.8 16.5 + - - +
235D VAL 3.9 2.5 - - - +
237D ASP* 1.3 75.6 - - - +
239D THR* 1.3 63.6 + - - +
241D VAL* 3.4 6.3 + - + +
242D HIS* 3.1 56.9 + - + +
257D ARG* 6.1 1.8 - - + +
260D LEU* 4.0 21.8 - - + -
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Residues in contact with THR 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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203D LEU* 4.3 7.1 - - + +
208D GLU* 3.6 31.4 - - + +
211D PHE* 3.3 31.7 - - + -
212D LYS* 3.5 19.7 - - + +
235D VAL* 2.7 29.4 + - - +
236D THR* 3.6 7.2 - - - -
238D LEU* 1.3 74.2 - - - +
240D LYS* 1.3 56.8 + - - +
242D HIS* 3.9 0.7 - - - +
243D THR* 2.6 40.4 + - - +
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Residues in contact with LYS 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 THR* 3.0 14.2 + - + +
237D ASP* 3.3 12.7 + - - +
239D THR* 1.3 76.0 - - - +
241D VAL* 1.3 63.3 + - - +
243D THR* 3.3 6.4 + - - -
244D GLU* 3.1 49.2 + - + +
256D ASP* 4.0 14.6 + - + +
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Residues in contact with VAL 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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150D TYR* 3.4 25.6 - - + +
237D ASP* 3.1 16.9 + - + +
238D LEU* 3.7 12.1 - - + +
240D LYS* 1.3 74.8 - - - +
242D HIS* 1.3 60.7 + - + +
244D GLU* 3.3 10.9 + - - +
245D CYS 3.0 22.9 + - - -
253D CYS* 3.5 26.2 - - - +
256D ASP* 3.7 16.8 - - + +
257D ARG* 3.7 29.4 - - + +
260D LEU* 4.9 6.5 - - + -
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Residues in contact with HIS 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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150D TYR* 3.5 32.3 + + - -
196D GLN* 3.0 41.1 + - - +
199D LYS* 3.6 21.6 - - + +
203D LEU* 3.8 9.4 - - + -
211D PHE* 3.8 28.2 - + + -
238D LEU* 3.1 41.8 + - + +
239D THR 4.3 0.7 - - - +
241D VAL* 1.3 77.0 - - + +
243D THR* 1.3 58.9 + - - +
245D CYS* 4.4 4.3 - - - -
246D CYS* 2.9 35.7 + - - +
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Residues in contact with THR 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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203D LEU* 3.8 27.6 - - + +
208D GLU* 4.8 3.8 + - - +
239D THR* 2.6 29.9 + - - +
240D LYS* 3.7 6.2 - - - -
242D HIS* 1.3 76.9 - - - +
244D GLU* 1.3 60.2 + - + +
246D CYS* 4.0 2.1 - - - +
247D HIS* 3.2 29.4 + - + +
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Residues in contact with GLU 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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240D LYS* 3.1 34.2 + - + +
241D VAL* 3.5 5.8 - - - +
243D THR* 1.3 75.0 - - + +
245D CYS* 1.3 58.5 + - - +
247D HIS* 3.3 8.6 + - - -
249D ASP* 2.8 51.5 + - + +
252D GLU* 3.3 27.8 - - + +
253D CYS* 3.6 5.9 + - + -
256D ASP* 2.6 33.0 - - - +
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Residues in contact with CYS 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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106D LYS* 5.0 4.2 + - - -
150D TYR* 3.8 26.0 - - + -
151D ALA* 4.3 5.2 - - - -
152D PRO* 3.9 13.0 - - - -
196D GLN* 4.7 3.6 - - - +
241D VAL 3.0 10.6 + - - +
242D HIS* 4.0 3.6 - - - +
244D GLU* 1.3 74.5 - - - +
246D CYS* 1.3 58.6 + - - +
248D GLY* 3.0 16.1 + - - -
250D LEU* 3.4 29.1 - - + +
253D CYS* 2.0 44.5 - - - +
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Residues in contact with CYS 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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103D LEU* 4.9 3.3 - - - +
106D LYS* 5.0 2.0 + - - -
148D TYR* 4.2 13.3 - - - -
196D GLN* 3.8 12.8 - - - -
199D LYS 4.5 0.7 - - - -
200D CYS* 2.0 63.3 - - + -
203D LEU* 4.1 12.6 - - + -
204D GLN* 2.9 26.9 + - + +
242D HIS* 2.9 25.6 + - - +
243D THR 4.2 2.9 - - - +
245D CYS* 1.3 76.2 - - - +
247D HIS* 1.3 56.9 + - - +
248D GLY 3.3 1.2 + - - -
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Residues in contact with HIS 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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30D TYR* 5.0 0.2 + - - -
67D HIS* 4.4 8.7 - + - -
99D ASN* 4.3 10.2 + - - -
100D GLU* 2.9 31.4 + - - -
103D LEU* 3.1 41.6 - - + +
204D GLN* 4.8 4.3 - - - +
243D THR* 3.2 21.4 + - + +
244D GLU* 3.8 1.6 - - - +
245D CYS 3.2 0.8 - - - -
246D CYS* 1.3 73.7 - - - +
248D GLY* 1.3 60.3 + - - +
249D ASP* 2.7 28.2 + - - +
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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
------------------------------------------------------------
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