Contacts of the helix formed by residues 223 - 242 (chain D) in PDB entry 6F0X
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 SER 223 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C HIS 5.3 3.5 + - - +
218C PHE* 3.2 15.0 - - - +
219C SER* 2.9 44.2 + - - -
220C LYS* 5.0 2.6 + - - -
221D TRP 3.5 0.4 + - - -
222D PHE* 1.3 97.5 - - - +
224D GLU* 1.3 63.7 + - - +
225D SER* 3.5 4.3 + - - +
226D GLY* 4.3 4.0 + - - +
227D LYS* 4.3 10.4 + - - +
275D ARG* 4.9 8.1 - - - +
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Residues in contact with GLU 224 (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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220C LYS* 2.8 46.1 + - + +
114D GLU* 3.3 35.5 - - - +
219D SER* 3.1 24.0 - - - +
221D TRP* 3.3 27.1 + - + +
222D PHE 3.2 3.8 - - - +
223D SER* 1.3 77.8 - - - +
225D SER* 1.3 67.2 + - - +
226D GLY 3.1 0.2 - - - -
227D LYS* 2.9 23.4 + - - +
228D LEU* 2.9 12.7 + - + +
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Residues in contact with SER 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D LEU* 3.8 22.7 - - - -
218D PHE* 4.9 7.0 - - - -
219D SER* 3.6 9.8 + - - -
221D TRP 4.4 0.6 + - - -
223D SER* 3.5 3.9 + - - +
224D GLU* 1.3 78.3 - - - +
226D GLY* 1.3 66.3 + - - +
228D LEU* 3.1 4.7 + - - +
229D VAL* 2.9 29.4 + - - +
272D ASP* 4.2 9.9 + - - +
275D ARG* 4.6 5.2 + - - +
276D VAL* 3.1 32.3 + - - +
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Residues in contact with GLY 226 (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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215C HIS* 4.3 25.1 - - - -
223D SER* 4.3 4.5 + - - +
224D GLU 2.9 1.2 + - - -
225D SER* 1.3 82.7 + - - +
227D LYS* 1.3 63.2 + - - +
229D VAL* 3.1 7.8 + - - +
230D THR* 2.9 30.5 + - - +
275D ARG* 4.3 11.7 + - - +
276D VAL* 5.5 0.4 - - - -
279D ALA* 5.1 2.2 - - - -
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Residues in contact with LYS 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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116C THR* 3.1 36.7 - - - +
117C GLU 6.0 0.2 - - - -
119C ILE* 4.9 13.7 - - + -
215C HIS 4.7 4.4 + - - -
216C SER* 6.3 1.8 - - - +
114D GLU* 3.6 32.2 + - - +
223D SER 4.3 7.1 + - - +
224D GLU* 2.9 15.4 + - - +
226D GLY* 1.3 74.6 - - - +
228D LEU* 1.3 62.1 + - - +
230D THR* 2.5 24.7 + - - +
231D LYS* 2.9 31.2 + - + +
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Residues in contact with LEU 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D LEU* 6.0 3.3 - - + +
114D GLU* 2.9 29.4 + - + +
120D ILE* 5.3 8.1 - - + -
216D SER* 3.4 19.7 - - - +
217D LEU* 3.2 46.4 - - + +
218D PHE 4.2 3.8 - - - +
219D SER* 5.6 3.1 - - - -
224D GLU* 2.9 12.9 + - + +
225D SER* 3.2 11.2 - - - +
227D LYS* 1.3 77.9 - - - +
229D VAL* 1.3 58.9 + - - +
231D LYS* 3.2 2.3 + - - +
232D MET* 2.9 49.8 + - + +
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Residues in contact with VAL 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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217D LEU* 3.4 36.3 - - + -
225D SER 2.9 17.8 + - - +
226D GLY* 3.1 6.7 + - - +
228D LEU* 1.3 75.9 - - - +
230D THR* 1.3 64.6 + - - +
232D MET* 3.1 12.4 + - + +
233D PHE* 3.0 32.2 + - + +
276D VAL* 4.4 10.1 - - + +
279D ALA* 4.9 6.3 - - + -
280D VAL* 3.6 34.3 - - + +
283D GLN* 5.1 5.2 - - + -
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Residues in contact with THR 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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119C ILE* 6.0 2.1 - - - +
120C ILE* 5.9 7.4 + - - -
213C ASN* 4.5 17.3 - - - +
215C HIS* 5.2 3.6 - - + -
216C SER* 5.6 4.5 - - - +
226D GLY 2.9 13.5 + - - +
227D LYS* 2.5 32.0 + - - +
229D VAL* 1.3 76.5 - - - +
231D LYS* 1.3 56.8 + - - +
233D PHE* 3.4 2.3 + - - +
234D GLN* 2.8 27.3 + - - +
279D ALA* 4.8 13.0 - - + -
283D GLN* 4.2 27.3 - - + +
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Residues in contact with LYS 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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117C GLU 4.4 14.3 + - - -
118C ASN* 4.8 10.7 + - - +
119C ILE* 5.8 1.6 - - - +
112D LEU* 5.1 9.2 - - + -
113D GLU* 4.4 31.7 + - + +
114D GLU* 4.6 14.1 - - - +
227D LYS* 2.9 38.4 + - - +
228D LEU 3.7 3.8 - - - +
230D THR* 1.3 73.8 + - - +
232D MET* 1.3 68.3 + - - +
234D GLN* 2.9 22.8 + - + +
235D LYS* 3.0 25.9 + - + +
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Residues in contact with MET 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D LEU* 3.4 42.6 - - + +
121D ALA 5.3 0.9 - - - +
122D ALA* 4.5 10.5 - - + -
210D ILE* 5.2 3.1 - - + -
212D ILE* 3.5 40.2 - - + -
216D SER* 5.5 3.6 - - - +
217D LEU* 5.5 3.4 - - + -
228D LEU* 2.9 39.3 + - + +
229D VAL* 3.2 12.1 - - + +
231D LYS* 1.3 77.1 - - - +
233D PHE* 1.3 74.9 + - + +
235D LYS* 3.1 4.5 + - - +
236D ILE* 3.0 25.6 + - + +
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Residues in contact with PHE 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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212D ILE* 3.4 29.8 - - + -
229D VAL* 3.0 18.3 + - + +
230D THR 3.6 1.6 - - - +
232D MET* 1.3 84.8 - - + +
234D GLN* 1.3 57.0 + - - +
236D ILE* 3.4 27.1 - - + +
237D GLN* 2.7 29.6 + - - +
249D VAL* 5.0 9.6 - - + -
251D ILE* 5.5 3.1 - - + -
280D VAL* 4.4 11.4 - - + -
283D GLN* 3.3 47.6 - - + +
284D ILE* 4.0 25.1 - - + -
287D ILE* 4.7 19.2 - - + +
295D ILE* 5.8 1.6 - - + -
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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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118C ASN* 4.9 17.5 - - + +
120C ILE* 5.6 5.5 - - - +
230D THR 2.8 15.2 + - - +
231D LYS* 2.9 25.1 + - + +
233D PHE* 1.3 76.9 - - - +
235D LYS* 1.3 58.1 + - + +
237D GLN* 3.2 15.5 + - - +
238D ASP* 2.9 25.1 + - - +
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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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110D GLU* 3.6 19.5 + - - +
111D ASN* 3.7 8.7 - - - +
112D LEU* 2.9 49.1 - - + +
113D GLU* 4.5 4.9 - - - +
231D LYS* 3.0 22.1 + - + +
232D MET* 3.8 6.3 - - - +
234D GLN* 1.3 78.8 - - + +
236D ILE* 1.3 64.4 + - + +
238D ASP* 3.0 26.0 - - + +
239D LEU* 3.0 11.9 + - - +
162P LYS* 3.6 26.8 - - + +
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Residues in contact with ILE 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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210D ILE* 3.8 37.2 - - + -
212D ILE* 4.0 8.1 - - + -
232D MET* 3.0 17.4 + - + +
233D PHE* 3.4 40.8 - - + +
235D LYS* 1.3 77.1 - - + +
237D GLN* 1.3 58.5 + - - +
239D LEU* 3.1 9.1 + - + +
240D ILE* 2.9 46.0 + - + +
247D VAL* 4.6 7.1 - - + +
249D VAL* 3.9 25.4 - - + -
287D ILE* 5.6 6.3 - - + -
293D VAL* 5.9 0.4 - - + -
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Residues in contact with GLN 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 PHE 2.7 23.4 + - - +
234D GLN* 3.2 17.7 - - - +
236D ILE* 1.3 70.4 - - - +
238D ASP* 1.3 61.7 + - - +
240D ILE* 2.9 22.0 + - - +
241D ASP* 2.7 50.5 + - - +
286D GLN* 5.6 2.9 - - - +
287D ILE* 4.3 12.6 - - - +
290D HIS* 3.8 28.8 + - - -
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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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234D GLN* 2.9 11.3 + - - +
235D LYS* 3.0 23.0 - - + +
237D GLN* 1.3 74.3 - - - +
239D LEU* 1.3 62.4 + - - +
241D ASP* 2.7 34.7 + - - +
242D ASP* 4.0 1.9 + - - +
160P SER* 4.9 6.6 + - - -
237P ARG* 3.4 31.6 + - - +
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Residues in contact with LEU 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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124D HIS* 3.5 35.9 - - + +
208D GLN* 4.0 29.6 - - + +
210D ILE* 3.6 23.6 - - + -
235D LYS 3.0 11.8 + - - +
236D ILE* 3.1 8.3 + - - +
238D ASP* 1.3 84.5 - - + +
240D ILE* 1.3 62.3 + - - +
241D ASP 3.4 0.2 + - - -
242D ASP* 3.9 13.6 + - - +
245D ALA* 4.6 8.1 - - - +
247D VAL* 4.1 15.2 - - + +
160P SER* 4.5 21.1 - - - +
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Residues in contact with ILE 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 ILE* 2.9 33.3 + - + +
237D GLN* 2.9 31.8 + - - +
239D LEU* 1.3 76.5 - - - +
241D ASP* 1.3 65.1 + - - +
242D ASP 2.8 13.5 - - - +
243D LYS* 4.7 0.9 - - - +
247D VAL* 3.9 12.8 - - + -
287D ILE* 4.4 18.8 - - + -
290D HIS* 3.6 46.0 - - + +
292D ASN* 3.9 11.4 + - - +
293D VAL* 3.8 23.1 - - + -
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Residues in contact with ASP 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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237D GLN* 2.7 39.6 + - - +
238D ASP* 2.7 37.7 + - - +
240D ILE* 1.3 72.0 - - - +
242D ASP* 1.3 59.5 + - - +
243D LYS* 3.1 16.6 + - - +
290D HIS* 6.1 2.0 - - - -
237P ARG* 3.6 33.6 + - - +
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Residues in contact with ASP 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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206D TYR* 3.8 8.9 + - - +
238D ASP 4.0 1.8 + - - +
239D LEU 3.9 10.4 + - - +
240D ILE* 2.8 15.3 - - - +
241D ASP* 1.3 77.1 - - - +
243D LYS* 1.3 63.7 + - - +
244D ASP* 2.7 38.3 + - - +
245D ALA* 3.8 14.5 + - + +
292D ASN* 3.8 5.2 + - - -
233P ARG* 2.6 30.6 + - - -
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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