Contacts of the helix formed by residues 224 - 238 (chain B) in PDB entry 4IYM
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 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221B PHE* 4.3 2.0 - - - -
223B GLY* 1.3 74.3 - - - -
225B THR* 1.3 58.9 + - - +
226B PRO* 3.8 10.7 - - - +
227B ILE* 3.3 25.7 + - - +
228B ALA* 2.9 26.7 + - - +
246B GLY* 4.1 0.7 - - - -
247B GLY* 4.6 4.9 - - - +
381B GLU* 5.5 4.7 - - - -
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Residues in contact with THR 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B SER* 1.3 67.9 - - - +
226B PRO* 1.3 75.5 - - + +
228B ALA* 3.2 4.0 + - - +
229B ARG* 2.9 44.6 + - + +
246B GLY* 3.8 4.9 - - - -
247B GLY* 2.9 28.4 + - - +
381B GLU* 5.8 0.2 + - - -
406B GLU* 6.2 1.8 - - - -
407B TYR* 3.3 20.3 + - + -
453B SER* 3.0 35.8 + - - +
456B PHE* 4.5 1.6 - - + -
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Residues in contact with PRO 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B SER* 3.5 14.1 - - - +
225B THR* 1.3 97.3 - - + +
227B ILE* 1.3 70.1 - - + +
229B ARG* 3.3 11.7 - - + +
230B TYR* 3.1 20.6 + - - +
407B TYR* 5.4 3.4 - - - +
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Residues in contact with ILE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B VAL* 6.1 2.0 - - + -
221B PHE* 3.5 28.9 - - + -
224B SER* 3.3 19.3 + - - +
225B THR 3.3 0.2 - - - -
226B PRO* 1.3 80.4 - - + +
228B ALA* 1.3 60.5 + - - +
230B TYR* 3.2 13.4 + - + +
231B VAL* 2.8 35.0 + - + +
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Residues in contact with ALA 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B PHE* 3.5 27.0 - - + -
224B SER 2.9 18.0 + - - +
225B THR* 3.5 7.6 - - - +
227B ILE* 1.3 76.5 - - - +
229B ARG* 1.3 53.1 + - - +
232B TYR* 2.8 38.5 + - - +
244B CYS* 3.8 13.9 - - + +
245B PHE 4.2 11.0 - - - +
456B PHE* 4.1 14.4 - - + -
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Residues in contact with ARG 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ALA 5.0 1.7 - - - +
237A MSE 5.3 4.1 + - - +
238A ASN 5.2 2.8 + - - -
239A GLY* 4.6 10.7 - - - +
225B THR* 2.9 26.0 + - - +
226B PRO* 3.3 13.5 - - - +
227B ILE 3.3 0.2 - - - -
228B ALA* 1.3 74.1 - - - +
230B TYR* 1.3 57.7 + - - +
232B TYR* 3.9 4.8 - - - +
233B GLY* 3.0 25.6 + - - -
406B GLU* 5.8 2.2 + - - +
453B SER* 3.8 26.5 - - - +
456B PHE* 3.5 34.6 - - + -
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Residues in contact with TYR 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A MSE 5.2 3.4 - - + +
204B LYS* 3.1 23.6 + - + -
207B VAL* 5.1 3.4 - - + -
208B ASP* 2.6 31.2 + - - -
211B LEU* 4.1 9.9 - - + -
226B PRO 3.1 9.0 + - - +
227B ILE* 3.2 19.3 + - + +
229B ARG* 1.3 77.5 - - - +
231B VAL* 1.3 70.3 + - + +
233B GLY* 3.3 1.6 + - - -
234B THR* 2.8 60.4 + - + +
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Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ILE* 4.4 1.3 - - + -
207B VAL* 4.2 21.8 - - + -
211B LEU* 4.0 12.3 - - + +
219B VAL* 3.9 22.4 - - + -
221B PHE* 3.6 45.5 - - + -
227B ILE* 2.8 29.5 + - + +
228B ALA 3.9 2.2 - - - +
230B TYR* 1.3 77.0 - - + +
232B TYR* 1.3 57.2 + - - +
234B THR 3.2 0.2 + - - -
235B ALA* 2.8 38.7 + - + +
244B CYS* 3.9 4.7 - - - -
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Residues in contact with TYR 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ALA* 3.4 36.8 - - + +
239A GLY 4.3 4.7 - - - -
240A LYS 2.8 29.1 + - - -
241A ARG* 3.6 6.1 - - - -
242A ALA* 4.3 3.5 + - - +
228B ALA 2.8 23.1 + - - +
229B ARG* 3.9 3.4 - - - +
231B VAL* 1.3 74.0 - - - +
233B GLY* 1.3 62.8 + - - +
235B ALA* 4.0 1.9 - - - +
236B ALA* 3.2 25.4 + - + +
242B ALA* 3.9 26.9 - - + +
244B CYS* 3.6 14.1 - - - -
456B PHE* 3.4 32.1 - + + -
457B GLY* 3.3 37.1 + - - -
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Residues in contact with GLY 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ALA* 4.2 16.6 - - - -
237A MSE 3.4 34.2 - - - +
229B ARG 3.0 13.8 + - - -
230B TYR 3.8 1.6 - - - -
232B TYR* 1.3 77.9 - - - +
234B THR* 1.3 57.6 + - - +
236B ALA* 3.3 2.4 + - - +
237B MSE 2.9 25.8 + - - +
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Residues in contact with THR 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A MSE 3.8 12.7 - - + +
208B ASP* 5.3 0.4 - - - +
211B LEU* 3.8 26.5 - - + -
212B THR* 5.1 6.1 - - + -
230B TYR* 2.8 48.4 + - - +
233B GLY* 1.3 71.4 - - - +
235B ALA* 1.3 64.1 - - - +
237B MSE 3.3 3.3 + - + +
238B ASN* 2.6 45.6 + - - +
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B LEU* 3.9 20.7 - - + +
219B VAL* 4.4 6.7 - - + -
231B VAL 2.8 23.0 + - - +
234B THR* 1.3 72.0 - - - +
236B ALA* 1.3 62.2 + - - +
238B ASN* 3.2 10.0 + - - +
239B GLY 3.2 0.2 + - - -
240B LYS* 3.0 43.3 + - + +
242B ALA* 3.9 22.7 - - + -
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Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ARG 5.1 1.4 - - - +
232A TYR* 3.3 42.2 - - + +
233A GLY* 4.0 4.8 - - - -
236A ALA* 3.2 36.3 - - + -
232B TYR* 3.2 10.0 + - + +
233B GLY 3.7 0.7 - - - +
234B THR 3.1 0.6 - - - -
235B ALA* 1.3 75.7 - - - +
237B MSE 1.3 56.5 + - - +
238B ASN 3.0 1.8 - - - -
239B GLY* 2.8 19.1 + - - -
240B LYS 4.0 2.9 - - - +
242B ALA* 5.7 2.0 - - + -
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Residues in contact with MSE 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ARG* 5.3 6.8 - - - +
230A TYR* 5.4 7.0 - - + +
233A GLY* 3.6 26.6 - - - +
234A THR* 4.2 4.7 - - - -
237A MSE 3.3 37.0 - - + -
233B GLY 2.9 10.8 + - - +
234B THR* 3.3 8.5 + - + +
236B ALA* 1.3 74.7 - - - +
238B ASN* 1.3 61.9 + - - +
239B GLY 3.3 1.1 + - - -
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Residues in contact with ASN 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ARG* 5.0 6.8 + - - -
211B LEU 3.3 26.9 + - - +
212B THR* 3.6 25.0 - - - +
234B THR* 2.6 37.2 + - - +
235B ALA 3.5 7.4 - - - +
236B ALA 3.0 1.0 - - - -
237B MSE 1.3 80.6 - - - +
239B GLY* 1.3 60.1 + - - +
240B LYS* 3.4 13.4 + - - +
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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
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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