Contacts of the helix formed by residues 229 - 243 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B PHE* 3.3 6.1 - - - -
202B ALA* 5.4 0.9 - - - -
226B ARG* 4.4 5.8 - - - +
227B LEU 3.7 0.8 + - - -
228B GLY* 1.3 73.0 - - - -
230B PRO* 1.3 65.6 - - - +
231B ALA* 3.0 24.1 + - - +
232B GLU* 2.7 56.6 + - - +
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Residues in contact with PRO 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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21B GLY* 4.2 7.2 - - - +
22B LEU* 4.0 20.7 - - + +
25B SER* 3.4 26.1 + - - +
201B PHE* 3.9 2.0 - - + -
202B ALA* 3.6 24.9 - - + +
203B THR* 4.1 14.4 - - + -
228B GLY 3.9 7.0 - - - +
229B ASP* 1.3 90.9 - - - +
231B ALA* 1.3 58.3 + - - +
233B TYR* 3.1 7.3 + - - +
234B ALA 3.1 18.0 + - - -
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Residues in contact with ALA 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER* 3.3 13.5 + - - +
29B ARG* 5.0 5.7 + - - +
229B ASP* 3.0 19.0 + - - +
230B PRO* 1.3 76.2 - - - +
232B GLU* 1.3 58.9 + - + +
234B ALA* 3.4 5.0 + - - +
235B HIS* 3.1 26.9 + - - +
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Residues in contact with GLU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B PHE* 4.5 3.6 - - + -
226B ARG* 2.8 35.5 + - - -
228B GLY* 3.7 0.9 - - - -
229B ASP* 2.7 49.5 + - + +
231B ALA* 1.3 70.4 - - + +
233B TYR* 1.3 61.5 + - - +
235B HIS* 3.5 2.5 + - - -
236B LEU* 3.2 9.9 + - - +
253B LEU* 3.9 2.8 - - + +
243D ASN* 3.0 35.0 + - - +
244D PRO* 3.6 27.5 - - + +
245D PHE* 3.6 21.6 - - + +
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Residues in contact with TYR 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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22B LEU* 4.0 42.4 - - + -
26B THR* 3.4 24.0 - - - -
89B VAL* 3.9 8.9 - - + +
91B CYS* 3.5 19.8 - - - -
151B ILE* 4.8 1.2 - - - +
152B ASN 4.8 1.7 + - - -
153B THR* 2.7 32.7 + - + -
196B ILE* 3.8 36.8 - - + +
198B PRO* 4.3 6.3 - - + -
201B PHE* 4.0 9.3 - - + -
229B ASP 3.7 2.0 + - - -
230B PRO 3.1 7.5 + - - +
232B GLU* 1.3 73.5 - - - +
234B ALA* 1.4 67.0 + - - +
236B LEU* 3.1 4.9 + - - +
237B VAL* 3.0 34.8 + - + +
253B LEU* 3.7 13.9 - - + +
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER* 3.6 27.6 - - - +
26B THR* 3.7 23.7 - - - +
29B ARG* 3.6 22.4 - - + -
30B LEU* 5.4 1.0 - - - +
230B PRO 3.1 11.5 + - - +
231B ALA* 3.7 9.0 - - - +
232B GLU 3.4 0.4 - - - -
233B TYR* 1.4 78.1 - - - +
235B HIS* 1.3 60.9 + - - +
237B VAL* 3.4 4.9 + - - +
238B GLN* 3.1 18.0 + - - +
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Residues in contact with HIS 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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29B ARG* 3.7 37.4 - - - +
231B ALA 3.1 17.7 + - - +
232B GLU* 3.8 6.5 - - - +
233B TYR 3.3 0.4 - - - -
234B ALA* 1.3 75.0 - - - +
236B LEU* 1.3 63.2 + - - +
238B GLN* 3.4 3.3 + - + +
239B MET* 3.1 43.3 + - + +
239D MET* 3.7 26.0 - - + +
242D GLU* 2.9 36.8 + - + +
243D ASN* 3.2 25.8 + - + +
244D PRO* 6.3 0.2 - - + -
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Residues in contact with LEU 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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196B ILE* 3.7 40.4 - - + -
232B GLU 3.2 9.8 + - - +
233B TYR 3.1 8.9 + - - +
235B HIS* 1.3 76.7 + - - +
237B VAL* 1.3 64.2 + - - +
239B MET 3.2 1.7 + - - -
240B VAL* 3.1 23.2 + - + +
251B ILE* 4.4 30.7 - - + -
253B LEU* 3.9 22.2 - - + -
239D MET* 2.9 41.6 - - + +
243D ASN* 4.1 8.5 - - - +
246D LEU* 4.6 14.1 - - + -
251D ILE* 6.1 0.9 - - + -
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Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B THR* 3.8 23.8 - - + +
30B LEU* 4.6 2.5 - - + -
89B VAL* 4.1 12.3 - - + -
151B ILE* 3.9 13.5 - - + -
196B ILE* 3.8 16.8 - - + -
233B TYR* 3.0 41.4 + - + +
234B ALA 3.6 7.6 - - - +
235B HIS 3.4 0.2 - - - -
236B LEU* 1.3 74.8 - - - +
238B GLN* 1.4 65.6 + - - +
240B VAL* 3.0 7.5 + - - +
241B ILE* 3.0 39.1 + - + +
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Residues in contact with GLN 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B SER* 4.8 1.4 - - - +
8B VAL* 3.9 27.7 - - + +
29B ARG* 3.2 30.5 + - - +
30B LEU* 4.3 9.0 - - + +
33B GLN* 3.6 30.3 + - - +
234B ALA 3.1 10.2 + - - +
235B HIS* 3.7 8.3 - - + +
236B LEU 3.4 0.2 - - - -
237B VAL* 1.4 79.5 - - - +
239B MET* 1.3 70.3 + - + +
241B ILE* 3.3 11.6 + - - +
242B GLU* 2.8 49.7 + - - +
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Residues in contact with MET 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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235B HIS* 3.1 24.2 + - + +
236B LEU 3.2 0.2 + - - -
237B VAL 3.2 0.2 - - - -
238B GLN* 1.3 82.9 - - - +
240B VAL* 1.3 59.3 + - - +
242B GLU* 3.3 25.6 + - - +
243B ASN* 3.1 27.4 + - - +
246B LEU* 5.3 0.4 - - - -
29D ARG* 6.2 0.4 - - - +
235D HIS* 3.7 20.7 - - + +
238D GLN* 4.8 5.8 - - + -
239D MET* 2.9 63.3 - - + +
242D GLU* 3.7 26.0 - - - +
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Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B VAL* 4.6 2.5 - - + -
151B ILE* 3.8 26.2 - - + -
192B ARG* 3.1 28.6 + - - +
194B VAL* 3.9 39.3 - - + -
196B ILE* 4.9 7.2 - - + -
236B LEU* 3.1 21.5 + - + +
237B VAL* 3.0 9.5 + - - +
239B MET* 1.3 76.1 - - - +
241B ILE* 1.3 63.2 + - - +
242B GLU 3.4 0.2 + - - -
243B ASN 3.6 4.2 + - - +
246B LEU* 4.3 18.8 - - + -
251B ILE* 4.5 10.3 - - + -
239D MET* 4.6 4.3 - - + -
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Residues in contact with ILE 241 (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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7B SER 5.8 0.7 - - - +
8B VAL* 4.0 11.7 - - + -
11B LEU* 3.8 28.9 - - + -
30B LEU* 4.1 22.7 - - + -
87B VAL* 3.9 33.7 - - + -
146B GLN* 4.9 3.3 + - - -
149B VAL* 4.4 11.4 - - + +
151B ILE* 3.8 13.7 - - + -
192B ARG* 3.2 17.9 + - - +
237B VAL* 3.0 33.8 + - + +
238B GLN* 3.6 7.0 - - - +
240B VAL* 1.3 77.1 - - - +
242B GLU* 1.3 57.6 + - - +
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Residues in contact with GLU 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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7B SER* 3.3 35.1 + - - +
8B VAL* 4.6 3.1 - - + -
238B GLN* 2.8 50.7 + - + +
239B MET* 3.3 11.3 + - - +
241B ILE* 1.3 78.7 - - + +
243B ASN* 1.3 59.1 + - - +
244B PRO* 3.1 15.6 - - - +
29D ARG* 5.5 0.9 + - - -
235D HIS* 3.0 33.0 + - + +
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Residues in contact with ASN 243 (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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192B ARG* 3.1 24.7 + - - -
239B MET 3.1 16.5 + - - +
240B VAL 3.6 0.6 + - - +
241B ILE 3.6 1.0 - - - -
242B GLU* 1.3 73.7 - - - +
244B PRO* 1.3 66.1 - - - +
245B PHE* 3.1 18.2 + - - +
246B LEU* 3.5 20.5 + - + +
232D GLU* 3.0 30.6 + - - +
235D HIS* 3.2 25.6 + - - +
236D LEU* 3.8 14.7 - - + +
253D LEU* 3.7 13.9 - - - +
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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
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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