Contacts of the helix formed by residues 229 - 243 (chain C) in PDB entry 1E3S
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 ASP 229 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201C PHE* 3.4 5.9 - - - -
202C ALA* 5.5 0.9 - - - -
226C ARG* 3.8 7.9 - - - +
227C LEU 5.3 0.2 - - - +
228C GLY* 1.3 71.5 - - - -
230C PRO* 1.3 64.8 - - - +
231C ALA* 2.9 36.5 + - - +
232C GLU* 2.7 54.6 + - - +
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Residues in contact with PRO 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLY* 4.2 7.4 - - - +
22C LEU* 4.0 20.6 - - + +
25C SER* 3.3 27.6 + - - +
201C PHE* 4.0 2.0 - - + -
202C ALA* 3.5 26.9 - - + +
203C THR* 4.1 13.0 - - + -
228C GLY 3.9 4.7 - - - +
229C ASP* 1.3 91.1 - - - +
231C ALA* 1.3 60.3 + - - +
233C TYR* 3.1 7.5 + - - +
234C ALA 3.1 17.5 + - - -
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Residues in contact with ALA 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C SER* 3.3 13.1 + - - +
29C ARG* 4.9 6.6 + - - +
229C ASP* 2.9 19.2 + - - +
230C PRO* 1.3 76.6 - - - +
232C GLU* 1.3 58.3 + - + +
234C ALA* 3.5 5.1 + - - +
235C HIS* 3.1 25.1 + - - +
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Residues in contact with GLU 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ASN* 3.1 35.4 + - - +
244A PRO* 3.6 26.4 - - + +
245A PHE* 3.7 22.1 - - + +
201C PHE* 4.6 3.1 - - + -
226C ARG* 2.9 34.6 + - - -
228C GLY* 3.8 1.2 - - - -
229C ASP* 2.7 47.9 + - + +
231C ALA* 1.3 70.7 - - + +
233C TYR* 1.3 62.4 + - - +
235C HIS* 3.4 3.2 + - - +
236C LEU 3.2 8.0 + - - -
253C LEU* 3.9 5.2 - - + +
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Residues in contact with TYR 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU* 3.9 36.3 - - + -
26C THR* 3.4 24.5 - - - -
89C VAL* 3.9 9.4 - - - +
91C CYS* 3.5 19.7 - - - -
151C ILE* 4.6 3.5 - - - +
152C ASN 4.7 0.3 + - - -
153C THR* 2.8 32.2 + - + -
196C ILE* 3.8 36.3 - - + +
198C PRO* 4.3 6.5 - - + -
201C PHE* 4.1 15.4 - - + -
229C ASP 3.7 2.0 + - - -
230C PRO 3.1 8.8 + - - +
232C GLU* 1.3 77.7 - - - +
234C ALA* 1.3 61.5 + - - +
236C LEU* 3.1 4.7 + - - +
237C VAL* 3.0 36.0 + - + +
253C LEU* 3.7 14.2 - - + +
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Residues in contact with ALA 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C SER* 3.6 29.2 - - - +
26C THR* 3.7 22.2 - - + +
29C ARG* 3.6 22.3 - - + -
30C LEU* 5.3 1.7 - - - +
230C PRO 3.1 10.5 + - - +
231C ALA* 3.7 9.0 - - - +
232C GLU 3.3 0.4 - - - -
233C TYR* 1.3 76.2 - - - +
235C HIS* 1.3 62.2 + - - +
237C VAL* 3.4 5.0 + - - +
238C GLN* 3.1 17.7 + - - +
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Residues in contact with HIS 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A MET* 3.7 24.9 - - + +
242A GLU* 3.0 36.6 + - + +
243A ASN* 3.2 25.8 + - + +
244A PRO* 6.2 0.7 - - + -
29C ARG* 3.6 37.6 - - - +
231C ALA 3.1 17.7 + - - +
232C GLU* 3.7 6.7 - - - +
233C TYR 3.3 0.4 - - - -
234C ALA* 1.3 77.3 - - - +
236C LEU* 1.3 60.9 + - - +
238C GLN* 3.3 2.6 + - - +
239C MET* 3.1 52.0 + - + +
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Residues in contact with LEU 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A MET* 3.6 35.9 - - + -
243A ASN* 4.2 7.6 - - - +
246A LEU* 4.6 8.7 - - + -
196C ILE* 3.8 39.3 - - + -
232C GLU 3.2 9.1 + - - +
233C TYR 3.1 8.5 + - - +
235C HIS* 1.3 78.5 + - - +
237C VAL* 1.3 64.7 + - - +
239C MET* 3.2 3.5 + - - +
240C VAL* 3.0 29.8 + - + +
251C ILE* 4.2 21.5 - - + -
253C LEU* 4.0 23.3 - - + -
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Residues in contact with VAL 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C THR* 3.8 24.2 - - + +
30C LEU* 4.6 2.7 - - + -
89C VAL* 4.3 9.2 - - + -
151C ILE* 3.8 20.6 - - + +
196C ILE* 3.9 12.5 - - + +
233C TYR* 3.0 49.6 + - + +
234C ALA 3.6 7.9 - - - +
236C LEU* 1.3 75.5 - - - +
238C GLN* 1.3 64.2 + - - +
240C VAL* 3.1 4.7 + - - +
241C ILE* 3.0 38.9 + - + +
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Residues in contact with GLN 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C SER* 4.8 1.8 - - - +
8C VAL* 3.9 27.5 - - + +
29C ARG* 3.2 29.8 + - - +
30C LEU* 4.3 9.2 - - + +
33C GLN* 3.6 29.7 + - - +
234C ALA 3.1 10.2 + - - +
235C HIS 3.7 8.3 - - - +
236C LEU 3.3 0.2 - - - -
237C VAL* 1.3 79.4 - - - +
239C MET* 1.3 69.0 + - - +
241C ILE* 3.3 12.5 + - - +
242C GLU* 2.8 49.3 + - - +
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Residues in contact with MET 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A HIS* 3.6 17.2 - - + +
239A MET* 3.2 48.5 - - + -
242A GLU* 4.8 5.4 - - - +
29C ARG* 5.5 1.3 - - - -
235C HIS* 3.1 43.1 + - + +
236C LEU* 3.2 3.7 + - - +
238C GLN* 1.3 81.3 - - + +
240C VAL* 1.3 66.0 + - - +
242C GLU* 3.0 33.6 + - - +
243C ASN* 3.1 27.0 + - - +
246C LEU* 4.7 1.0 - - - +
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Residues in contact with VAL 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A MET* 5.6 0.4 - - - -
149C VAL* 4.6 2.5 - - + -
151C ILE* 3.8 27.1 - - + -
192C ARG* 3.2 27.4 + - - +
194C VAL* 3.9 38.4 - - + -
196C ILE* 4.9 6.5 - - + -
236C LEU* 3.0 27.5 + - + +
237C VAL* 3.1 8.0 + - - +
239C MET* 1.3 77.8 - - - +
241C ILE* 1.3 64.1 + - - +
242C GLU 3.4 0.2 + - - -
243C ASN 3.5 4.2 + - - +
246C LEU* 4.3 18.7 - - + +
251C ILE* 4.5 10.3 - - + -
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Residues in contact with ILE 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C SER 5.7 0.4 - - - +
8C VAL* 3.9 13.2 - - + -
11C LEU* 3.8 28.9 - - + -
30C LEU* 4.1 25.1 - - + -
87C VAL* 3.9 31.2 - - + -
146C GLN* 4.9 3.1 + - - -
149C VAL* 4.4 11.1 - - + +
151C ILE* 3.9 12.3 - - + -
192C ARG* 3.1 19.4 + - - +
237C VAL* 3.0 35.0 + - + +
238C GLN* 3.3 6.7 + - - +
240C VAL* 1.3 77.3 - - - +
242C GLU* 1.3 59.2 + - - +
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Residues in contact with GLU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ARG* 5.6 0.7 + - - -
235A HIS* 3.0 31.5 + - + +
7C SER* 3.3 30.7 + - - +
8C VAL* 4.5 7.9 - - + -
192C ARG* 4.7 0.2 - - - -
238C GLN* 2.8 46.1 + - + +
239C MET* 3.0 19.2 + - - +
240C VAL 3.3 0.2 - - - -
241C ILE* 1.3 78.8 - - - +
243C ASN* 1.3 58.0 + - - +
244C PRO* 3.2 14.4 - - - +
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Residues in contact with ASN 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A GLU* 3.1 29.9 + - - +
235A HIS* 3.2 24.3 + - - +
236A LEU* 3.9 12.9 - - + +
253A LEU* 3.7 12.9 - - - +
192C ARG* 3.0 25.0 + - - -
239C MET 3.1 16.6 + - - +
240C VAL 3.5 0.7 + - - +
241C ILE 3.5 1.4 - - - -
242C GLU* 1.3 74.6 - - - +
244C PRO* 1.3 66.6 - - - +
245C PHE* 2.9 20.8 + - - +
246C LEU* 3.6 21.3 + - + +
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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
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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