Contacts of the helix formed by residues 231 - 247 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234B HIS* 2.9 36.5 + - + +
230D LEU* 1.3 75.0 - - - +
232D PHE* 1.3 74.8 + - - +
233D MET* 2.9 41.6 + - - +
234D HIS* 3.0 20.4 + - - +
235D ILE* 3.1 9.7 + - - +
269D LEU* 5.5 0.2 - - - +
271D LYS 4.8 0.2 - - - +
272D GLU* 3.7 8.7 - - + -
273D LEU* 2.9 41.7 + - - +
274D TYR* 3.5 31.2 - - + +
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Residues in contact with PHE 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C PHE* 6.3 1.3 - + - -
157C LEU* 3.9 22.2 - - + -
159C ILE* 5.4 11.2 - - + -
194D LEU* 3.6 28.7 - - + -
196D ALA* 5.5 2.5 - - + -
219D LEU* 4.7 6.5 - - + -
223D LEU* 4.2 13.5 - - + -
230D LEU 3.9 0.6 + - - -
231D GLU* 1.3 73.3 - - - +
233D MET* 1.3 58.6 + - - +
235D ILE* 3.3 14.6 + - + +
236D LEU* 3.0 63.4 + - + +
269D LEU* 6.1 0.2 - - + -
273D LEU* 2.8 46.8 + - + +
275D PHE* 3.5 27.3 - + + -
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Residues in contact with MET 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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233B MET* 3.7 39.5 - - + -
234B HIS* 4.9 1.6 - - + +
237B THR* 4.2 19.3 - - + +
265B ILE* 5.7 0.7 - - + -
194D LEU* 4.0 15.3 - - + -
231D GLU* 2.9 28.4 + - - +
232D PHE* 1.3 78.3 - - + +
234D HIS* 1.3 55.7 + - + +
236D LEU* 3.5 5.1 + - - +
237D THR* 2.7 36.0 + - - -
265D ILE* 4.0 16.2 - - + +
267D SER* 3.3 35.9 - - - +
269D LEU* 4.2 17.5 - - + -
271D LYS 5.4 0.7 - - - +
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Residues in contact with HIS 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B GLU* 3.2 38.0 + - + +
233B MET* 5.2 1.3 - - + -
234B HIS* 3.3 37.5 + + - -
272B GLU* 3.5 39.1 + - + +
274B TYR* 4.2 3.4 - - - -
230D LEU* 4.3 20.3 - - + +
231D GLU* 3.0 15.4 + - - +
233D MET* 1.3 79.2 - - + +
235D ILE* 1.3 64.3 + - - +
237D THR* 3.4 9.5 + - - -
238D ARG* 3.1 27.2 + - - +
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Residues in contact with ILE 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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222D MET* 3.9 30.9 - - + +
223D LEU* 4.0 23.1 - - + +
226D TYR* 3.8 17.0 - - + +
227D ALA* 3.9 14.1 - - - -
230D LEU* 3.5 35.9 - - + +
231D GLU 3.1 10.2 + - - +
232D PHE* 3.5 20.0 - - + +
234D HIS* 1.3 77.2 - - - +
236D LEU* 1.3 58.4 + - + +
238D ARG* 3.1 9.7 + - - +
239D VAL* 2.9 28.9 + - + +
275D PHE* 4.6 5.2 - - + -
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Residues in contact with LEU 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D LEU* 3.9 13.5 - - + -
196D ALA* 4.3 15.5 - - + -
215D PHE* 5.1 3.6 - - + -
219D LEU* 3.7 29.6 - - + -
232D PHE* 3.0 54.0 + - + +
233D MET* 3.5 4.2 + - - +
235D ILE* 1.3 73.2 - - + +
237D THR* 1.3 59.6 + - - +
239D VAL* 3.2 11.5 + - + +
240D ASN* 2.9 32.6 + - - +
265D ILE* 3.6 39.0 - - + -
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Residues in contact with THR 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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233B MET* 5.1 9.5 - - - +
267B SER* 5.3 3.0 + - - +
269B LEU* 3.9 9.6 - - + +
270B THR 3.6 7.4 - - - +
271B LYS* 3.5 43.3 - - - +
272B GLU* 4.3 6.5 - - + +
233D MET* 2.7 23.5 + - - +
234D HIS* 3.5 12.4 - - - -
236D LEU* 1.3 77.6 - - - +
238D ARG* 1.3 57.7 + - + +
240D ASN* 3.1 10.2 + - - +
241D ARG* 3.1 22.3 + - - +
265D ILE* 4.0 9.4 - - - +
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Residues in contact with ARG 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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35A ASN 3.4 23.9 - - - +
272B GLU* 4.6 11.2 + - - +
222D MET* 3.8 16.7 - - - +
226D TYR* 3.2 47.9 + - - -
230D LEU* 3.3 29.0 - - - +
234D HIS 3.1 11.9 + - - +
235D ILE* 3.5 8.7 - - - +
237D THR* 1.3 75.0 - - + +
239D VAL* 1.3 64.8 + - - +
241D ARG* 3.2 36.3 + - - +
242D LYS* 3.0 24.4 + - - +
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Residues in contact with VAL 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D PHE* 3.8 35.0 - - + -
218D SER* 4.0 13.5 - - - -
219D LEU* 3.7 27.1 - - + +
222D MET* 3.6 25.4 - - + -
235D ILE* 2.9 20.5 + - + +
236D LEU* 3.2 16.1 + - + +
238D ARG* 1.3 75.6 - - - +
240D ASN* 1.3 63.5 + - - +
242D LYS* 3.4 3.9 + - - +
243D VAL* 3.1 24.9 + - + +
263D PRO* 4.6 1.8 - - + -
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Residues in contact with ASN 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B SER 3.5 15.4 + - - -
268B MET 4.1 1.4 - - - -
269B LEU 3.0 26.9 + - - +
270B THR* 4.4 0.4 - - - -
215D PHE* 5.3 0.5 - - - -
236D LEU 2.9 17.2 + - - +
237D THR 3.1 9.6 + - - +
239D VAL* 1.3 77.9 - - - +
241D ARG* 1.3 57.1 + - - +
243D VAL 3.6 0.3 + - - -
244D ALA* 3.0 30.8 + - - +
262D ILE* 3.7 10.1 - - + +
263D PRO* 3.2 39.0 + - - +
265D ILE* 3.4 26.4 - - - +
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Residues in contact with ARG 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASN* 3.7 30.6 + - - +
270B THR* 2.7 57.6 + - - +
271B LYS* 3.4 31.2 - - - +
237D THR* 3.1 7.9 + - - +
238D ARG* 3.2 42.5 + - - +
239D VAL 3.4 0.2 - - - -
240D ASN* 1.3 76.8 - - - +
242D LYS* 1.3 52.9 + - - +
244D ALA* 4.3 0.4 - - - -
245D THR* 2.4 56.4 + - + +
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Residues in contact with LYS 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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217D GLN* 5.3 2.0 - - - +
218D SER* 3.7 22.9 + - - +
221D ALA* 4.3 13.7 - - - -
222D MET* 3.7 29.8 - - + -
238D ARG 3.0 17.3 + - - +
239D VAL* 3.7 4.7 - - - +
240D ASN 3.2 0.2 - - - -
241D ARG* 1.3 75.7 - - - +
243D VAL* 1.3 60.2 + - - +
245D THR* 4.0 3.1 - - - -
246D GLU* 2.9 70.4 + - - +
247D PHE* 3.6 24.7 - - - -
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Residues in contact with VAL 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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214D TRP* 3.8 19.7 - - + +
215D PHE* 4.0 7.6 - - - -
218D SER* 3.3 22.7 - - - +
239D VAL* 3.1 18.8 + - + +
242D LYS* 1.3 74.3 - - - +
244D ALA* 1.3 62.1 + - - +
247D PHE* 3.6 27.1 + - - +
261D GLN* 3.3 46.7 + - + +
263D PRO* 3.8 22.0 - - + -
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Residues in contact with ALA 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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186B LYS 3.3 4.7 - - - +
187B ILE* 3.8 2.8 - - + -
188B PRO* 3.4 22.5 - - + +
191B ALA* 4.9 0.7 - - + -
270B THR* 4.2 11.4 - - + -
240D ASN 3.0 19.2 + - - +
241D ARG 3.9 3.6 - - - +
243D VAL* 1.3 79.1 - - - +
245D THR* 1.3 62.2 + - + +
260D LYS* 3.1 26.5 + - - -
261D GLN 3.6 8.5 + - - -
262D ILE* 3.9 14.8 - - + -
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Residues in contact with THR 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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185B HIS* 5.6 4.5 + - - -
186B LYS 4.3 6.8 + - - +
187B ILE* 4.3 17.5 - - + -
270B THR* 6.1 1.3 - - + -
241D ARG* 2.4 43.0 + - + +
242D LYS* 3.7 1.7 + - - -
244D ALA* 1.3 83.1 - - + +
246D GLU* 1.3 72.8 + - - +
247D PHE 3.5 1.1 + - - -
260D LYS* 4.1 6.5 + - - -
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Residues in contact with GLU 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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242D LYS* 2.9 56.0 + - - +
245D THR* 1.3 87.9 + - - +
247D PHE* 1.3 70.7 + - + +
248D GLU 4.3 0.2 + - - -
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Residues in contact with PHE 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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214D TRP* 3.4 60.0 - + + -
217D GLN* 3.9 25.8 - - + -
218D SER* 3.4 25.1 - - - -
242D LYS* 3.6 35.4 - - - -
243D VAL* 3.6 20.9 + - - +
245D THR 3.5 0.8 - - - -
246D GLU* 1.3 85.2 - - + +
248D GLU* 1.3 56.6 + - - +
260D LYS* 2.6 33.9 + - - +
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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