Contacts of the helix formed by residues 231 - 247 (chain H) in PDB entry 5IC4
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 231 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234F HIS* 3.1 31.3 + - + +
237F THR* 6.1 0.4 - - - +
230H LEU* 1.3 77.1 - - - +
232H PHE* 1.3 77.8 + - - +
233H MET* 2.9 42.5 + - - +
234H HIS* 3.0 19.4 + - - +
235H ILE* 3.1 10.1 + - - +
269H LEU* 5.5 1.4 - - - +
271H LYS 4.6 1.4 - - - +
272H GLU* 3.6 20.4 - - + -
273H LEU* 2.9 40.5 + - - +
274H TYR* 3.5 22.7 - - + +
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Residues in contact with PHE 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G PHE* 6.2 2.0 - + - -
157G LEU* 3.9 18.6 - - + -
159G ILE* 5.1 13.2 - - + -
194H LEU* 3.6 32.8 - - + -
196H ALA* 5.6 0.2 - - + -
219H LEU* 4.8 6.3 - - + -
223H LEU* 4.3 14.1 - - + -
230H LEU 3.9 0.2 + - - -
231H GLU* 1.3 74.5 - - - +
233H MET* 1.3 60.3 + - + +
235H ILE* 3.3 14.6 + - + +
236H LEU* 2.9 58.0 + - + +
269H LEU* 5.3 2.0 - - + -
273H LEU* 2.9 47.6 + - + +
275H PHE* 3.5 25.3 - + + -
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Residues in contact with MET 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F MET* 3.5 44.4 - - + +
234F HIS* 5.1 0.9 - - + +
237F THR* 5.0 11.7 - - - +
265F ILE* 5.4 1.3 - - + -
194H LEU* 4.3 10.3 - - - -
231H GLU* 2.9 26.6 + - - +
232H PHE* 1.3 80.1 - - - +
234H HIS* 1.3 53.1 + - + +
236H LEU* 3.4 8.4 + - - +
237H THR* 2.6 36.8 + - - +
265H ILE* 3.6 25.7 - - + +
267H SER* 3.6 35.2 - - - +
269H LEU* 4.9 7.6 - - + -
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Residues in contact with HIS 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231F GLU* 2.9 42.5 + - + +
233F MET* 5.0 1.3 - - + -
234F HIS* 3.3 36.5 + + - -
272F GLU* 3.7 35.4 + - + +
274F TYR* 4.2 4.7 - - - -
230H LEU* 4.2 20.4 - - + +
231H GLU* 3.0 13.4 + - - +
233H MET* 1.3 79.4 - - + +
235H ILE* 1.3 67.0 + - - +
237H THR* 3.3 9.3 + - - -
238H ARG* 3.0 28.2 + - - +
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Residues in contact with ILE 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219H LEU* 5.4 0.4 - - + -
222H MET* 3.9 30.4 - - + +
223H LEU* 4.1 17.9 - - + +
226H TYR* 3.8 18.4 - - + +
227H ALA* 3.9 13.7 - - - -
230H LEU* 3.6 36.3 - - + +
231H GLU 3.1 10.8 + - - +
232H PHE* 3.5 25.1 - - + +
234H HIS* 1.3 76.7 - - - +
236H LEU* 1.3 57.8 + - + +
238H ARG* 3.2 7.7 + - - +
239H VAL* 2.9 32.5 + - + +
275H PHE* 4.6 4.7 - - + -
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Residues in contact with LEU 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194H LEU* 3.9 12.6 - - + -
196H ALA* 4.4 15.9 - - + -
215H PHE* 5.2 4.7 - - + -
219H LEU* 3.7 30.3 - - + -
232H PHE* 2.9 53.6 + - + +
233H MET* 3.7 6.7 - - - +
235H ILE* 1.3 73.8 - - - +
237H THR* 1.3 60.8 + - - +
239H VAL* 3.2 8.6 + - + +
240H ASN* 3.0 32.2 + - - +
265H ILE* 3.7 37.7 - - + -
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Residues in contact with THR 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F MET* 5.1 9.7 - - - +
267F SER* 5.3 2.4 + - - -
269F LEU* 3.9 9.9 - - + +
270F THR 3.7 6.6 - - - +
271F LYS* 3.5 42.8 - - - +
272F GLU* 4.3 5.8 - - + +
233H MET 2.6 26.9 + - - -
234H HIS* 3.5 13.8 - - - -
235H ILE 3.2 0.2 - - - -
236H LEU* 1.3 77.0 - - - +
238H ARG* 1.3 61.3 + - + +
240H ASN* 3.1 20.4 + - - +
241H ARG 3.2 6.1 + - - -
265H ILE* 3.9 11.3 - - - +
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Residues in contact with ARG 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E ASN 3.5 28.3 - - - +
270F THR 5.1 0.4 - - - -
272F GLU* 3.9 18.3 + - - +
222H MET* 3.9 18.1 - - + +
226H TYR* 3.7 35.4 + - - -
230H LEU* 3.2 37.0 - - - +
234H HIS 3.0 9.6 + - - +
235H ILE* 3.2 8.9 + - - +
237H THR* 1.3 74.9 - - + +
239H VAL* 1.3 64.7 + - - +
241H ARG* 3.5 24.6 + - - +
242H LYS* 3.2 23.0 + - - +
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Residues in contact with VAL 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215H PHE* 3.7 35.0 - - + -
218H SER* 4.1 13.9 - - - -
219H LEU* 3.8 26.5 - - + +
222H MET* 3.6 25.6 - - + -
235H ILE* 2.9 20.3 + - + +
236H LEU* 3.3 16.4 - - + +
237H THR 3.2 0.2 - - - -
238H ARG* 1.3 77.2 - - - +
240H ASN* 1.3 62.4 + - - +
242H LYS* 3.3 4.4 + - - +
243H VAL* 3.1 24.7 + - + +
263H PRO* 4.7 1.3 - - + -
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Residues in contact with ASN 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267F SER 3.5 14.6 + - - -
268F MET* 4.0 4.6 - - - +
269F LEU 3.0 27.1 + - - +
270F THR* 4.4 0.4 - - - -
215H PHE* 5.3 0.5 - - - -
236H LEU 3.0 17.5 + - - +
237H THR 3.1 9.8 + - - +
239H VAL* 1.3 78.4 - - - +
241H ARG* 1.3 56.7 + - - +
243H VAL* 3.5 1.7 + - - +
244H ALA* 3.0 30.2 + - - +
262H ILE* 3.7 10.7 - - + +
263H PRO* 3.2 33.7 + - - +
265H ILE* 3.4 26.3 - - - +
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Residues in contact with ARG 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E ASN* 3.0 59.0 + - - +
270F THR* 3.2 40.3 + - - +
271F LYS* 4.6 15.0 - - - +
237H THR 3.2 5.4 + - - +
238H ARG* 3.5 30.0 + - - +
239H VAL 3.4 0.2 - - - -
240H ASN* 1.3 77.3 - - - +
242H LYS* 1.3 55.6 + - - +
244H ALA* 4.2 1.3 - - - -
245H THR* 2.4 57.5 + - + +
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Residues in contact with LYS 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217H GLN* 5.5 1.1 - - - -
218H SER* 3.6 32.5 - - - +
221H ALA* 4.4 11.9 - - - +
222H MET* 3.7 25.0 - - + +
238H ARG 3.2 17.4 + - - +
239H VAL* 3.7 5.2 - - - +
240H ASN 3.3 0.2 - - - -
241H ARG* 1.3 77.2 - - - +
243H VAL* 1.3 57.5 + - - +
245H THR* 3.9 4.0 - - - -
246H GLU* 2.6 77.5 + - + +
247H PHE* 3.5 10.2 - - + -
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Residues in contact with VAL 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H TRP* 3.9 19.9 - - + +
215H PHE* 4.0 8.1 - - - -
218H SER* 3.5 21.3 - - - +
239H VAL* 3.1 18.0 + - + +
242H LYS* 1.3 76.9 - - - +
244H ALA* 1.3 61.6 + - - +
247H PHE* 3.6 27.4 + - - +
261H GLN* 3.3 44.0 + - + +
263H PRO* 3.7 25.8 - - + -
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Residues in contact with ALA 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F LYS 3.6 2.9 - - - +
187F ILE* 4.0 2.4 - - + -
188F PRO* 3.4 26.3 - - + +
191F ALA* 4.9 0.2 - - + -
270F THR* 4.3 8.5 - - + -
240H ASN 3.0 19.6 + - - +
241H ARG* 3.9 7.2 - - - +
243H VAL* 1.3 79.6 - - - +
245H THR* 1.3 62.7 + - + +
260H LYS* 3.0 27.6 + - - -
261H GLN 3.7 8.1 - - - -
262H ILE* 3.9 11.7 - - + -
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Residues in contact with THR 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186F LYS 4.5 5.9 + - - +
187F ILE* 4.5 16.6 - - + -
270F THR* 6.1 0.9 - - + -
241H ARG* 2.4 50.4 + - + +
242H LYS* 3.8 1.9 + - - -
244H ALA* 1.3 84.0 - - + +
246H GLU* 1.3 70.8 + - - +
247H PHE 3.5 1.3 + - - -
260H LYS* 4.2 8.0 + - - +
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Residues in contact with GLU 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242H LYS* 2.6 60.6 + - - +
245H THR* 1.3 87.3 + - - +
247H PHE* 1.3 72.4 + - + +
248H GLU 4.3 0.5 + - - -
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Residues in contact with PHE 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H TRP* 3.3 67.5 - + + -
217H GLN* 4.2 21.3 - - + -
218H SER* 3.5 25.1 - - - -
242H LYS* 3.5 27.4 - - + -
243H VAL* 3.6 18.0 + - - +
245H THR 3.5 0.4 - - - -
246H GLU* 1.3 91.6 - - + +
248H GLU* 1.3 58.2 + - - +
260H LYS* 2.7 33.3 + - - +
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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