Contacts of the helix formed by residues 225 - 242 (chain B) in PDB entry 3ER8
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 THR 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A GLU* 3.9 20.0 - - - +
184B TRP* 3.1 15.8 - - - -
187B ASP* 3.2 21.5 - - - +
223B ARG* 4.0 11.2 - - - +
224B VAL* 1.3 77.6 - - - +
226B LYS* 1.3 60.4 + - - +
227B SER* 3.0 21.7 + - - -
228B ASP* 2.9 24.0 + - - +
229B ALA* 3.0 19.4 + - - +
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Residues in contact with LYS 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B PRO* 3.6 35.8 + - + -
182B ASP* 5.5 1.8 - - - +
184B TRP* 3.4 44.7 - - + +
187B ASP* 4.4 0.8 + - - -
225B THR* 1.3 73.3 - - - +
227B SER* 1.3 68.8 + - - +
228B ASP 3.1 1.3 - - - -
229B ALA* 3.5 3.9 - - - +
230B VAL* 3.2 23.3 + - + +
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Residues in contact with SER 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B THR* 3.0 13.6 + - - -
226B LYS* 1.3 79.6 - - - +
228B ASP* 1.3 81.2 + - - +
230B VAL* 3.1 19.3 + - - +
231B ASN* 3.4 6.2 + - - +
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Residues in contact with ASP 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLU* 4.6 5.0 - - - +
223B ARG 3.5 12.8 - - - +
224B VAL* 4.0 8.3 - - + -
225B THR* 2.9 36.0 + - - +
227B SER* 1.3 86.8 + - - +
229B ALA* 1.3 62.6 + - - +
231B ASN* 2.9 20.3 + - - +
232B TYR* 3.0 23.2 + - + -
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Residues in contact with ALA 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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178B CYS* 3.6 19.2 - - - +
179B PRO 3.7 9.8 - - - +
181B PRO* 3.4 19.2 - - + +
184B TRP* 3.4 34.1 - - + -
225B THR 3.0 7.0 + - - +
226B LYS* 3.2 11.2 + - - +
228B ASP* 1.3 75.3 - - - +
230B VAL* 1.3 59.2 + - - +
232B TYR* 3.3 4.7 - - - +
233B GLU* 3.2 17.2 + - - +
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Residues in contact with VAL 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B PRO* 3.6 24.2 - - + -
226B LYS* 3.2 17.9 + - + +
227B SER* 3.1 10.3 + - - +
228B ASP 2.9 0.8 + - - -
229B ALA* 1.3 74.0 - - - +
231B ASN* 1.3 57.5 + - - +
232B TYR 3.0 5.4 - - - -
233B GLU* 3.4 4.3 + - - +
234B LYS* 2.9 64.1 + - + +
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Residues in contact with ASN 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 3.5 14.4 - - - -
19B GLU* 4.6 10.9 + - - -
227B SER 3.4 6.9 + - - +
228B ASP* 2.9 11.4 + - - +
230B VAL* 1.3 80.4 - - - +
232B TYR* 1.3 60.2 + - - +
234B LYS* 4.0 5.8 - - - -
235B LYS* 3.2 60.2 + - - +
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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
----------------------------------------------------------
13B PHE* 3.3 42.1 - + - -
176B TRP* 3.0 38.7 + + - -
178B CYS* 3.3 33.0 - - + -
190B ILE* 5.4 0.2 - - - +
195B LYS* 4.0 14.9 - - - +
206B ALA* 5.8 3.4 - - + -
208B MET* 3.8 23.6 - - + -
224B VAL* 4.7 5.4 - - + -
228B ASP* 3.0 25.0 + - + -
229B ALA 3.3 9.0 - - - +
230B VAL 3.0 0.4 - - - -
231B ASN* 1.3 75.8 - - - +
233B GLU* 1.3 61.2 + - - +
236B MET* 2.9 38.7 + - + +
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Residues in contact with GLU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU 4.1 0.6 - - - +
22B TYR* 3.6 39.6 + - + +
180B PHE* 3.2 33.1 - - + -
181B PRO* 3.6 22.6 - - + +
182B ASP* 3.9 10.3 - - - +
206B ALA* 5.8 4.3 - - - -
229B ALA 3.2 11.7 + - - +
230B VAL* 3.9 5.2 - - - +
232B TYR* 1.3 78.1 - - - +
234B LYS* 1.3 70.9 + - + +
236B MET* 4.2 3.3 - - - +
237B TYR* 3.0 27.5 + - - +
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Residues in contact with LYS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLU* 3.5 29.0 + - + +
20B LEU 3.1 35.1 + - - +
21B ASP* 3.8 33.4 + - - +
22B TYR 4.6 2.7 - - - +
230B VAL* 2.9 45.8 + - + +
231B ASN* 4.1 5.4 - - - +
233B GLU* 1.3 87.2 - - + +
235B LYS* 1.3 65.2 + - + +
238B TYR 3.2 12.3 + - - -
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Residues in contact with LYS 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 3.8 21.4 + - + +
14B GLU 5.1 4.9 + - - -
16B ILE* 3.6 40.4 + - + +
17B ASP 5.4 1.6 - - - -
18B ASN 3.1 18.6 - - - +
19B GLU* 3.7 18.2 - - + +
231B ASN* 3.2 47.4 + - - +
234B LYS* 1.3 79.1 - - - +
236B MET* 1.3 63.5 + - - +
238B TYR* 3.2 4.5 + - - +
239B LEU* 3.0 21.1 + - - +
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Residues in contact with MET 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 4.0 12.8 - - + -
16B ILE* 4.3 0.9 - - - -
197B LEU* 4.3 7.9 - - + -
198B GLN 6.3 0.2 - - - +
205B SER 3.4 22.7 - - - +
206B ALA* 3.5 32.5 - - + +
207B GLU 4.6 5.6 - - - +
208B MET* 3.6 28.9 - - + -
232B TYR 2.9 23.2 + - - +
233B GLU* 4.2 2.2 - - - +
235B LYS* 1.3 76.1 - - - +
237B TYR* 1.3 56.2 + - - +
239B LEU* 2.9 34.2 + - + +
240B ASN* 2.9 35.4 + - - +
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Residues in contact with TYR 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 3.7 31.4 - - + +
21B ASP 3.8 11.2 - - - -
22B TYR* 3.4 32.5 - + + -
23B GLU* 3.5 42.1 + - + +
26B SER* 3.7 12.9 + - - -
204B TYR* 3.5 23.6 - + - -
233B GLU 3.0 21.5 + - - +
234B LYS 3.7 2.9 - - - +
236B MET* 1.3 75.9 - - - +
238B TYR* 1.3 55.5 + - - +
240B ASN* 3.9 7.6 - - - +
241B LYS* 2.9 57.4 + - + +
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Residues in contact with TYR 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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10B PHE* 4.4 3.8 - + - -
16B ILE* 3.7 14.4 - - + -
17B ASP* 3.2 21.4 + - - -
18B ASN* 3.1 45.2 + - + +
19B GLU* 3.6 21.1 - - - -
20B LEU* 3.9 17.9 - - + +
234B LYS 3.2 4.0 + - - -
235B LYS 3.2 8.0 + - - +
236B MET 3.0 0.4 - - - -
237B TYR* 1.3 74.9 - - - +
239B LEU* 1.3 67.5 + - - +
240B ASN 3.0 0.3 + - - -
242B ILE* 2.7 62.1 + - + +
243B VAL* 3.2 22.6 + - + +
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Residues in contact with LEU 239 (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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10B PHE* 3.3 43.3 - - + -
16B ILE* 4.0 9.2 - - + -
197B LEU* 3.9 21.3 - - + -
235B LYS 3.0 8.1 + - - +
236B MET* 2.9 41.0 + - + +
238B TYR* 1.3 80.8 - - - +
240B ASN* 1.3 57.8 + - - +
243B VAL* 3.1 18.6 - - + +
244B ARG* 2.7 45.5 + - + +
258B TYR* 4.3 7.4 - - + +
262B HIS* 6.6 0.2 - - + -
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Residues in contact with ASN 240 (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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203B SER 3.1 23.2 + - - +
204B TYR* 3.6 21.6 + - + +
205B SER 2.9 37.9 + - - +
236B MET* 2.9 24.2 + - - +
237B TYR* 4.2 2.3 - - - +
239B LEU* 1.3 81.7 - - - +
241B LYS* 1.3 59.1 + - - +
244B ARG* 3.0 37.2 + - - +
245B ASN* 3.1 18.0 + - - -
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Residues in contact with LYS 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 4.9 1.6 - - + -
23B GLU* 5.6 3.1 - - - +
26B SER* 4.8 1.6 - - - +
204B TYR* 2.9 26.7 + - + +
237B TYR* 2.9 52.5 + - + +
240B ASN* 1.3 72.9 - - - +
242B ILE* 1.3 79.7 + - + +
245B ASN* 2.5 28.8 + - - +
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Residues in contact with ILE 242 (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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20B LEU* 3.3 30.1 - - + -
238B TYR* 2.7 36.1 + - + +
241B LYS* 1.3 97.8 - - + +
243B VAL* 1.3 61.4 + - + +
245B ASN* 4.0 5.3 + - - +
246B LYS* 3.3 37.1 + - - +
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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