Contacts of the helix formed by residues 217 - 238 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211L LEU* 3.5 19.0 - - - +
215L SER 3.6 0.4 + - - -
216L PRO* 1.3 76.1 - - - +
218L SER* 1.3 62.4 + - - +
219L ALA* 3.2 13.9 + - - +
220L SER* 3.0 24.4 + - - -
221L LEU* 3.1 25.9 + - - +
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Residues in contact with SER 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217L SER* 1.3 70.9 - - - +
219L ALA* 1.3 65.9 + - - +
220L SER 3.3 0.2 + - - -
221L LEU* 3.3 8.5 + - - +
222L ASN* 3.0 41.6 + - - +
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Residues in contact with ALA 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217L SER* 3.2 10.7 + - - +
218L SER* 1.3 80.1 + - - +
220L SER* 1.3 56.8 + - - +
222L ASN* 4.0 6.0 - - - +
223L PHE* 3.0 29.3 + - - +
266L TYR* 4.1 21.0 - - + -
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Residues in contact with SER 220 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194L HIS* 3.5 26.9 - - - -
197L ILE* 4.4 7.6 - - - +
211L LEU* 3.0 32.3 - - - +
217L SER* 3.0 21.0 + - - -
219L ALA* 1.3 73.0 - - - +
221L LEU* 1.3 61.8 + - - +
223L PHE* 3.3 6.1 + - - +
224L LEU* 2.9 35.1 + - - +
266L TYR* 5.2 4.6 + - - -
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Residues in contact with LEU 221 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194L HIS* 4.7 8.5 - - + +
216L PRO* 4.1 28.3 - - + +
217L SER 3.1 21.1 + - - +
218L SER* 3.3 7.2 + - - +
220L SER* 1.3 79.2 - - - +
222L ASN* 1.3 62.7 + - - +
224L LEU* 3.5 10.2 + - + +
225L HIS* 3.0 29.9 + - - +
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Residues in contact with ASN 222 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218L SER* 3.0 27.9 + - - +
219L ALA* 4.0 5.2 - - - +
221L LEU* 1.3 77.6 - - - +
223L PHE* 1.3 54.8 + - - +
225L HIS* 3.9 6.1 - - - +
226L ALA* 2.8 35.0 + - - +
262L CYS* 3.8 20.8 - - - -
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Residues in contact with PHE 223 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197L ILE* 4.4 18.2 - - + -
219L ALA 3.0 19.3 + - - +
220L SER* 3.5 5.2 - - - +
222L ASN* 1.3 77.0 - - - +
224L LEU* 1.3 62.1 + - - +
226L ALA* 3.3 5.9 + - - +
227L LEU* 3.0 46.5 + - + +
262L CYS* 4.6 3.7 - - - -
263L ILE* 4.2 29.6 - - + -
266L TYR* 3.8 56.5 - + + -
312L THR* 3.7 26.0 - - + -
313L ALA* 4.4 2.2 - - - -
316L VAL* 3.7 21.8 - - + -
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Residues in contact with LEU 224 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190L PRO* 5.6 1.6 - - + +
193L PHE* 3.7 27.1 - - + -
194L HIS* 3.9 28.3 - - + +
197L ILE* 3.9 14.4 - - + -
220L SER 2.9 21.0 + - - +
221L LEU* 3.9 10.3 - - + +
223L PHE* 1.3 69.7 - - + +
225L HIS* 1.3 65.9 + - - +
227L LEU* 3.2 11.4 + - + +
228L GLU* 3.0 23.9 + - - +
316L VAL* 3.7 30.7 - - + -
317L ASP* 5.3 3.2 - - - +
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Residues in contact with HIS 225 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221L LEU 3.0 17.4 + - - +
222L ASN* 3.9 6.5 - - - +
224L LEU* 1.3 72.4 - - - +
226L ALA* 1.3 66.2 + - - +
228L GLU* 3.2 18.1 + - + +
229L VAL* 3.1 43.3 + - + +
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Residues in contact with ALA 226 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222L ASN 2.8 23.1 + - - +
223L PHE* 3.4 7.4 - - - +
225L HIS* 1.3 74.0 + - - +
227L LEU* 1.3 57.3 + - - +
229L VAL* 5.0 1.3 - - - -
230L MET* 2.8 30.1 + - - +
259L ALA* 3.5 21.6 - - - +
262L CYS* 3.9 16.2 - - + -
263L ILE* 3.5 22.9 - - + +
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Residues in contact with LEU 227 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223L PHE* 3.0 47.4 + - + +
224L LEU* 3.2 11.0 + - + +
226L ALA* 1.3 74.8 - - - +
228L GLU* 1.3 57.8 + - - +
230L MET* 3.2 12.5 + - + +
231L PHE* 2.9 40.4 + - + -
263L ILE* 4.0 22.0 - - + -
313L ALA* 3.6 30.5 - - + +
316L VAL* 4.1 17.9 - - + -
317L ASP* 3.5 26.7 - - - +
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Residues in contact with GLU 228 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224L LEU 3.0 12.9 + - - +
225L HIS* 3.2 20.3 + - + +
227L LEU* 1.3 78.1 - - - +
229L VAL* 1.3 58.1 + - + +
231L PHE* 3.4 5.0 + - - +
232L LYS* 2.9 31.0 + - + +
317L ASP* 5.4 1.5 + - - +
490L ARG* 3.9 36.8 + - - +
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Residues in contact with VAL 229 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225L HIS* 3.1 39.1 + - + +
226L ALA* 4.0 3.6 - - - +
228L GLU* 1.3 73.9 - - + +
230L MET* 1.3 63.5 + - - +
232L LYS* 3.8 8.4 - - + +
233L SER* 2.9 29.8 + - - -
255L GLU* 3.7 48.9 - - + +
259L ALA* 3.9 6.7 - - + -
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Residues in contact with MET 230 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116L TRP* 3.6 26.7 - - + -
226L ALA 2.8 15.1 + - - +
227L LEU* 3.3 13.7 - - + +
229L VAL* 1.3 78.2 - - - +
231L PHE* 1.3 90.0 + - + +
233L SER* 4.1 2.9 - - - -
234L THR* 2.8 37.9 + - - -
256L HIS* 3.3 6.3 - - + -
259L ALA* 3.8 8.7 - - + +
260L TRP* 3.4 55.4 - - + +
263L ILE* 3.8 14.1 - - + -
313L ALA* 5.9 1.3 - - + -
602L 1CA 5.8 0.9 - - + -
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Residues in contact with PHE 231 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116L TRP* 4.3 0.4 - + - -
227L LEU* 2.9 34.3 + - + +
228L GLU* 3.8 6.7 - - - +
230L MET* 1.3 103.6 - - + +
232L LYS* 1.3 62.2 + - - +
234L THR* 3.1 13.6 + - - -
235L VAL* 3.2 19.2 + - - +
313L ALA 5.2 1.8 - - - -
317L ASP* 3.6 31.9 - - + -
318L THR* 5.9 0.7 - - + -
486L SER 3.3 19.1 - - - +
487L PHE* 3.5 31.9 - + + +
488L ILE* 4.0 22.9 - - + -
490L ARG* 4.6 8.3 - - - +
602L 1CA 4.0 26.5 - - + -
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Residues in contact with LYS 232 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59L GLN* 2.9 40.5 + - - +
60L GLY* 5.7 0.8 - - - -
228L GLU* 2.9 20.8 + - + +
229L VAL* 3.8 11.2 - - + +
230L MET 3.3 0.2 - - - -
231L PHE* 1.3 78.2 - - - +
233L SER* 1.3 63.5 + - - +
235L VAL* 3.3 12.5 + - - +
236L GLN* 3.1 44.4 + - - +
255L GLU* 4.1 15.3 - - - +
486L SER* 3.8 16.1 + - - +
490L ARG* 6.0 0.2 - - - +
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Residues in contact with SER 233 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229L VAL 2.9 20.1 + - - -
232L LYS* 1.3 75.9 - - - +
234L THR* 1.3 63.9 + - - +
236L GLN* 3.3 13.8 + - - +
237L LEU* 3.0 28.1 + - - +
252L VAL* 3.7 20.9 - - - -
255L GLU* 4.6 7.6 - - - -
256L HIS* 2.6 45.0 + - - +
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Residues in contact with THR 234 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113L LEU* 4.3 15.7 - - + -
115L PRO* 4.6 4.6 - - + +
116L TRP* 3.0 35.9 + - + +
230L MET* 2.8 25.4 + - - -
231L PHE* 3.1 11.1 + - - -
233L SER* 1.3 75.3 + - - +
235L VAL* 1.3 64.3 + - - +
237L LEU* 3.2 5.3 + - - +
238L MET* 3.0 30.8 + - + +
256L HIS* 3.0 10.6 - - - -
487L PHE* 4.1 24.2 - - + -
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Residues in contact with VAL 235 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55L ILE* 4.0 3.6 - - + +
60L GLY* 4.5 5.4 - - - -
61L TYR* 3.9 28.9 - - + +
231L PHE 3.2 15.4 + - - +
232L LYS 3.6 6.7 - - - +
233L SER 3.2 0.2 - - - -
234L THR* 1.3 77.9 - - - +
236L GLN* 1.3 61.3 + - - +
237L LEU 3.3 0.7 + - - -
238L MET* 3.5 17.3 + - + -
239L PHE* 3.6 32.6 - - + -
485L TYR* 4.3 9.9 - - + +
486L SER* 3.6 12.1 - - - +
487L PHE* 3.4 31.4 - - + +
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Residues in contact with GLN 236 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55L ILE* 3.4 34.7 - - + +
59L GLN* 3.1 43.6 - - - +
60L GLY* 4.4 1.6 - - - +
232L LYS* 3.1 45.4 + - - +
233L SER* 3.3 25.0 + - - +
235L VAL* 1.3 76.6 - - - +
237L LEU* 1.3 61.3 + - - +
238L MET 3.5 0.2 - - - -
240L MET* 4.1 10.9 - - - +
249L SER* 5.6 0.7 + - - -
252L VAL* 3.5 30.6 - - + +
255L GLU* 4.2 5.6 + - - +
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Residues in contact with LEU 237 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114L GLU* 6.0 0.3 - - - +
115L PRO* 3.8 23.7 - - + +
233L SER 3.0 20.0 + - - +
234L THR 3.7 0.4 - - - +
236L GLN* 1.3 77.6 - - - +
238L MET* 1.3 62.3 + - - +
239L PHE 3.5 2.0 - - - -
240L MET* 3.4 20.2 - - + +
245L SER* 4.1 12.1 + - - -
249L SER* 4.5 6.5 - - - +
252L VAL* 3.5 25.1 - - + +
253L TRP* 3.2 48.2 - - + +
256L HIS* 3.7 36.3 - - + -
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Residues in contact with MET 238 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113L LEU* 4.0 26.2 - - + -
115L PRO* 4.7 7.2 - - - -
234L THR* 3.0 13.4 + - + +
235L VAL* 3.5 33.1 + - + +
237L LEU* 1.3 78.1 - - - +
239L PHE* 1.3 90.4 + - + +
240L MET 3.5 5.6 + - - +
381L PHE* 5.8 4.9 - - - -
485L TYR* 4.2 16.8 - - + +
487L PHE* 4.3 19.7 - - + -
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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
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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