Contacts of the helix formed by residues 217 - 239 (chain I) in PDB entry 4DVQ
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 217 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211I LEU* 3.8 14.7 - - - +
215I SER 3.7 1.2 + - - -
216I PRO* 1.3 73.3 - - - +
218I SER* 1.3 63.6 + - - +
219I ALA* 3.4 9.7 + - - +
220I SER* 2.7 41.6 + - - -
221I LEU* 2.9 15.1 + - - +
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Residues in contact with SER 218 (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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217I SER* 1.3 73.7 - - - +
219I ALA* 1.3 54.9 + - - +
221I LEU* 3.2 10.0 + - - -
222I ASN* 2.7 50.2 + - - +
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Residues in contact with ALA 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217I SER* 3.2 8.6 + - - +
218I SER* 1.3 82.3 + - - +
220I SER* 1.3 57.6 + - - +
222I ASN* 3.8 6.6 - - - +
223I PHE* 2.9 31.6 + - - +
266I TYR* 4.3 20.1 - - + -
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Residues in contact with SER 220 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194I HIS* 3.1 25.8 - - - -
197I ILE* 4.3 7.9 - - - +
211I LEU* 3.6 22.0 - - - +
217I SER* 2.7 45.5 + - - -
219I ALA* 1.3 77.3 - - - +
221I LEU* 1.3 55.7 + - - +
223I PHE* 3.6 6.4 + - - +
224I LEU* 3.2 32.4 + - - +
266I TYR* 4.9 4.2 - - - -
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Residues in contact with LEU 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194I HIS* 4.2 10.5 - - - +
216I PRO* 3.7 28.9 - - + +
217I SER 2.9 19.0 + - - +
218I SER* 3.6 10.1 - - - +
220I SER* 1.3 74.7 - - - +
222I ASN* 1.3 69.1 + - - +
224I LEU* 3.3 8.8 + - + +
225I HIS* 3.0 23.9 + - - +
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Residues in contact with ASN 222 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218I SER* 2.7 33.5 + - - +
219I ALA* 3.9 6.2 - - - +
221I LEU* 1.3 73.5 - - - +
223I PHE* 1.3 57.1 + - - +
225I HIS* 3.8 5.3 - - - +
226I ALA* 2.9 31.2 + - - +
262I CYS* 3.6 17.1 - - - -
265I GLN* 6.3 0.7 - - - +
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Residues in contact with PHE 223 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197I ILE* 4.0 19.7 - - + -
219I ALA 2.9 18.2 + - - +
220I SER* 3.7 4.9 - - - +
222I ASN* 1.3 77.7 - - - +
224I LEU* 1.3 56.4 + - - +
226I ALA* 3.5 2.3 + - - +
227I LEU* 3.0 46.9 + - + +
262I CYS* 4.6 3.1 - - - -
263I ILE* 4.0 32.5 - - + -
266I TYR* 3.7 57.9 - + + -
312I THR* 4.0 22.4 - - + -
313I ALA* 4.4 4.0 - - - -
316I VAL* 3.7 21.3 - - + -
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Residues in contact with LEU 224 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190I PRO* 6.3 0.4 - - + -
193I PHE* 3.6 27.6 - - + -
194I HIS* 3.7 31.9 - - + +
197I ILE* 3.8 13.5 - - + -
220I SER 3.2 16.5 + - - +
221I LEU* 3.9 9.0 - - + +
223I PHE* 1.3 73.0 - - - +
225I HIS* 1.3 67.1 + - - +
227I LEU* 3.6 10.1 + - + +
228I GLU* 3.1 23.4 + - - +
316I VAL* 3.5 31.9 - - + -
317I ASP* 5.1 3.2 - - - +
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Residues in contact with HIS 225 (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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221I LEU 3.0 15.9 + - - +
222I ASN* 3.8 7.0 - - - +
224I LEU* 1.3 76.7 - - - +
226I ALA* 1.3 63.9 + - - +
228I GLU* 3.1 18.3 + - - +
229I VAL* 3.0 48.8 + - + +
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Residues in contact with ALA 226 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222I ASN 2.9 19.6 + - - +
223I PHE* 3.7 3.6 - - - +
225I HIS* 1.3 74.0 + - - +
227I LEU* 1.3 69.3 + - - +
229I VAL* 2.9 9.2 + - - +
230I MET* 2.6 23.9 + - - +
259I ALA* 3.7 22.2 - - - +
262I CYS* 3.6 23.1 - - + -
263I ILE* 3.8 10.3 - - + -
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Residues in contact with LEU 227 (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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223I PHE* 3.0 54.7 + - + +
224I LEU* 3.7 9.2 - - + +
226I ALA* 1.3 76.8 - - - +
228I GLU* 1.3 62.4 + - - +
230I MET* 3.2 5.8 + - + +
231I PHE* 3.0 38.3 + - + -
263I ILE* 4.0 19.7 - - + +
313I ALA* 3.6 26.0 - - + +
316I VAL* 4.0 19.5 - - + -
317I ASP* 3.4 27.4 - - - +
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Residues in contact with GLU 228 (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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224I LEU 3.1 9.2 + - - +
225I HIS* 3.1 21.5 + - - +
227I LEU* 1.3 79.5 - - - +
229I VAL* 1.3 59.3 + - + +
231I PHE* 3.9 8.8 - - - +
232I LYS* 3.1 27.5 + - + +
317I ASP* 5.1 4.2 + - - +
486I SER* 5.0 1.2 + - - -
490I ARG* 4.4 26.2 + - - +
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Residues in contact with VAL 229 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225I HIS* 3.0 42.3 + - + +
226I ALA* 2.9 7.2 + - - +
228I GLU* 1.3 73.6 - - + +
230I MET* 1.3 68.4 + - - +
231I PHE 3.1 0.2 - - - -
232I LYS* 4.2 9.6 - - + -
233I SER* 2.9 28.4 + - - +
255I GLU* 3.9 34.1 - - + +
259I ALA* 4.0 15.7 - - + -
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Residues in contact with MET 230 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I TRP* 3.5 16.2 - - + -
226I ALA 2.6 20.9 + - - +
227I LEU* 3.4 7.6 - - + +
229I VAL* 1.3 71.1 - - - +
231I PHE* 1.3 93.0 + - + +
233I SER* 3.3 7.2 + - - -
234I THR* 2.5 47.7 + - - -
256I HIS* 3.6 1.6 + - + -
259I ALA* 3.9 9.1 - - + +
260I TRP* 3.2 54.1 - - + +
263I ILE* 3.7 20.0 - - + -
313I ALA* 6.2 0.9 - - + -
602I 1CA 5.6 1.1 - - + -
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Residues in contact with PHE 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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116I TRP* 4.2 0.4 - + - -
227I LEU* 3.0 32.1 + - + +
228I GLU* 3.9 7.2 - - - +
230I MET* 1.3 98.1 - - + +
232I LYS* 1.3 69.6 + - - +
234I THR* 2.8 20.5 + - - -
235I VAL* 3.3 8.3 + - - +
313I ALA 5.3 1.6 - - - -
317I ASP* 3.5 28.3 - - + -
486I SER* 3.3 21.2 - - - +
487I PHE* 3.7 31.0 - + + +
488I ILE* 3.6 34.5 - - + -
602I 1CA 3.9 22.4 - - + -
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Residues in contact with LYS 232 (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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59I GLN* 3.2 40.5 + - - +
60I GLY* 5.6 0.3 - - - -
228I GLU 3.1 16.8 + - - +
229I VAL* 3.3 12.3 + - + +
231I PHE* 1.3 81.9 - - - +
233I SER* 1.3 63.4 - - - +
235I VAL* 3.0 15.4 + - - +
236I GLN* 3.3 22.6 + - - +
255I GLU* 4.4 13.0 + - - +
486I SER* 3.6 16.4 + - - +
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Residues in contact with SER 233 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229I VAL 2.9 21.9 + - - -
230I MET 3.3 1.4 + - - -
232I LYS* 1.3 73.6 - - - +
234I THR* 1.3 62.4 + - - +
236I GLN* 3.3 15.1 + - - +
237I LEU* 3.2 26.5 + - - +
252I VAL* 4.1 9.0 - - - -
255I GLU* 3.8 20.0 - - - -
256I HIS* 2.8 48.0 + - - +
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Residues in contact with THR 234 (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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113I LEU* 4.5 6.7 - - + -
115I PRO* 4.5 4.5 - - + +
116I TRP* 3.0 35.9 + - + +
230I MET* 2.5 23.6 + - - -
231I PHE* 2.8 22.5 + - - -
233I SER* 1.3 71.8 - - - +
235I VAL* 1.3 59.4 + - - -
237I LEU* 3.3 2.3 + - - +
238I MET* 3.0 26.0 + - + +
256I HIS* 3.3 10.1 - - - -
487I PHE* 3.6 32.5 - - + -
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Residues in contact with VAL 235 (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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55I ILE* 3.8 6.8 - - + +
60I GLY* 4.5 7.2 - - - -
61I TYR* 3.8 35.2 - - + +
231I PHE 3.7 5.6 - - - +
232I LYS* 3.0 11.8 + - - +
234I THR* 1.3 76.4 - - - +
236I GLN* 1.3 67.2 + - - +
237I LEU 3.2 0.5 + - - -
238I MET* 3.4 19.2 + - - +
239I PHE* 3.9 14.9 + - + -
485I TYR* 4.1 15.5 - - + +
486I SER* 3.9 11.7 - - - +
487I PHE* 3.6 29.6 - - + +
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Residues in contact with GLN 236 (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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55I ILE* 3.6 22.5 + - + +
56I TRP* 5.7 0.8 + - - +
59I GLN* 3.2 51.3 - - - +
232I LYS* 3.3 21.4 + - - +
233I SER* 3.3 25.3 + - - +
235I VAL* 1.3 81.5 - - - +
237I LEU* 1.3 61.4 + - + +
239I PHE* 4.4 3.3 + - - -
240I MET* 4.2 14.4 - - - +
249I SER* 5.5 0.4 + - - -
252I VAL* 3.1 38.7 - - + +
255I GLU* 3.9 7.8 + - - +
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Residues in contact with LEU 237 (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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114I GLU* 5.6 1.4 - - - +
115I PRO* 3.9 23.6 - - + +
233I SER 3.2 7.6 + - - +
234I THR 4.2 0.2 - - - +
235I VAL 3.2 0.6 - - - -
236I GLN* 1.3 79.7 - - - +
238I MET* 1.3 62.1 + - - +
239I PHE 3.4 1.5 + - - -
240I MET* 3.4 23.2 + - - +
245I SER* 3.9 14.0 + - - -
249I SER* 4.7 5.8 - - - +
252I VAL* 3.5 34.5 - - + +
253I TRP* 3.3 67.5 - - + +
256I HIS* 4.4 11.4 - - + -
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Residues in contact with MET 238 (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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113I LEU* 4.3 20.4 - - + -
114I GLU* 5.5 2.0 - - - +
115I PRO* 4.4 8.7 - - + -
234I THR* 3.0 18.6 + - + +
235I VAL* 3.4 22.9 + - - +
237I LEU* 1.3 78.2 - - - +
239I PHE* 1.3 98.9 + - + +
240I MET 3.3 6.0 + - - +
381I PHE* 4.5 13.5 - - + -
383I GLU* 5.9 1.1 - - - +
485I TYR* 3.9 22.2 - - - +
487I PHE* 4.2 20.4 - - + -
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Residues in contact with PHE 239 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I ARG* 3.3 40.2 - - - +
52I LEU* 3.3 23.8 - - - +
55I ILE* 3.3 35.2 - - + -
61I TYR* 3.9 17.3 - + - -
64I LEU* 4.4 18.4 - - + -
83I LEU* 6.2 0.7 - - + -
88I MET* 6.1 2.9 - - + -
235I VAL* 3.9 10.6 + - + +
236I GLN 4.4 1.5 + - - +
237I LEU 3.4 1.0 - - - -
238I MET* 1.3 121.7 - - + +
240I MET* 1.3 61.3 + - - +
381I PHE* 5.6 2.7 - + - -
485I TYR* 5.2 0.7 - + - -
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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