Contacts of the helix formed by residues 229 - 243 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201D PHE* 3.3 6.5 - - - -
202D ALA* 5.3 1.3 - - - -
226D ARG* 4.4 5.8 - - - +
227D LEU 3.7 1.2 + - - +
228D GLY* 1.3 71.9 - - - -
230D PRO* 1.3 64.8 - - - +
231D ALA* 2.9 34.2 + - - +
232D GLU* 2.7 56.0 + - - +
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Residues in contact with PRO 230 (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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21D GLY* 4.3 7.2 - - - +
22D LEU* 4.1 20.5 - - + +
25D SER* 3.2 27.5 + - - -
201D PHE* 3.9 1.5 - - + -
202D ALA* 3.5 28.0 - - + +
203D THR* 4.2 13.7 - - + -
228D GLY 3.8 3.8 - - - +
229D ASP* 1.3 90.5 - - - +
231D ALA* 1.4 60.2 + - - +
233D TYR* 3.3 7.3 + - - +
234D ALA 3.2 16.3 + - - -
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Residues in contact with ALA 231 (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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25D SER* 3.4 12.0 + - - +
29D ARG* 4.9 6.2 + - - +
229D ASP* 2.9 19.6 + - - +
230D PRO* 1.4 77.3 - - - +
232D GLU* 1.3 58.8 + - + +
234D ALA* 3.5 5.2 + - + +
235D HIS* 3.1 25.3 + - - +
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Residues in contact with GLU 232 (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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243B ASN* 3.0 35.1 + - - +
244B PRO* 3.6 28.0 - - + +
245B PHE* 3.6 21.1 - - + +
201D PHE* 4.6 3.4 - - + -
226D ARG* 2.9 34.8 + - - -
228D GLY* 3.7 1.4 - - - -
229D ASP* 2.7 50.2 + - + +
231D ALA* 1.3 69.7 - - + +
233D TYR* 1.3 60.7 + - - +
235D HIS* 3.5 3.4 + - - +
236D LEU* 3.3 8.8 + - - +
253D LEU* 3.9 3.6 - - + +
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Residues in contact with TYR 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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22D LEU* 4.0 34.5 - - + -
26D THR* 3.4 24.7 - - - -
89D VAL* 4.0 9.5 - - + +
91D CYS* 3.5 20.0 - - - -
151D ILE* 4.7 3.6 - - - +
152D ASN 4.9 0.2 - - - -
153D THR* 2.7 28.0 + - - -
196D ILE* 3.7 37.4 - - + +
198D PRO* 4.2 10.3 - - + -
201D PHE* 4.0 15.6 - - + -
229D ASP 3.7 2.4 + - - -
230D PRO 3.3 8.6 + - - +
232D GLU* 1.3 77.3 - - - +
234D ALA* 1.4 60.3 + - - +
236D LEU* 3.2 5.2 + - - +
237D VAL* 3.1 34.0 + - + +
253D LEU* 3.7 13.4 - - + +
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Residues in contact with ALA 234 (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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25D SER* 3.6 28.7 - - - +
26D THR* 3.7 21.1 - - + +
29D ARG* 3.7 22.2 - - + -
30D LEU* 5.4 1.4 - - - +
230D PRO 3.2 10.5 + - - +
231D ALA* 3.7 9.9 - - - +
233D TYR* 1.4 77.4 - - - +
235D HIS* 1.3 62.2 + - - +
237D VAL* 3.3 5.2 + - - +
238D GLN* 3.1 18.2 + - - +
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Residues in contact with HIS 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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239B MET* 3.7 43.9 - - + +
242B GLU* 3.0 37.0 + - + +
243B ASN* 3.2 27.0 + - + +
244B PRO* 6.3 0.4 - - + -
29D ARG* 3.6 37.6 - - - +
231D ALA 3.1 16.5 + - - +
232D GLU* 3.8 6.3 - - - +
233D TYR 3.3 0.2 - - - -
234D ALA* 1.3 76.4 - - - +
236D LEU* 1.3 62.7 + - - +
238D GLN* 3.4 4.4 + - + +
239D MET* 3.1 20.7 + - + +
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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
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243B ASN* 4.0 8.7 - - - +
246B LEU* 4.5 17.0 - - + -
251B ILE* 6.1 0.9 - - + -
196D ILE* 3.8 39.0 - - + -
232D GLU 3.3 10.0 + - - +
233D TYR 3.2 8.3 + - - +
235D HIS* 1.3 77.2 + - - +
237D VAL* 1.3 62.7 + - - +
239D MET* 3.2 32.0 + - - +
240D VAL* 3.0 28.7 + - + +
251D ILE* 4.2 24.2 - - + -
253D LEU* 4.1 22.7 - - + -
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Residues in contact with VAL 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D THR* 3.8 24.9 - - + +
30D LEU* 4.7 2.0 - - + -
89D VAL* 4.3 9.4 - - + -
151D ILE* 3.9 20.9 - - + -
196D ILE* 3.9 15.9 - - + -
233D TYR* 3.1 45.5 + - + +
234D ALA 3.3 7.8 + - - +
236D LEU* 1.3 72.7 - - - +
238D GLN* 1.3 63.5 + - - +
240D VAL* 3.1 4.1 + - - +
241D ILE* 3.0 40.2 + - + +
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Residues in contact with GLN 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B MET* 4.8 6.7 - - + -
7D SER* 4.8 1.2 - - - +
8D VAL* 3.9 28.9 - - + +
29D ARG* 3.2 28.7 + - - +
30D LEU* 4.3 10.0 - - + +
33D GLN* 3.6 30.2 + - - +
234D ALA 3.1 12.6 + - - +
235D HIS* 3.7 8.5 - - + +
236D LEU 3.3 0.4 - - - -
237D VAL* 1.3 77.6 - - - +
239D MET* 1.3 62.1 + - - +
241D ILE* 3.3 12.3 + - - +
242D GLU* 2.9 49.7 + - - +
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Residues in contact with MET 239 (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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235B HIS* 3.7 7.5 - - + +
236B LEU* 2.9 52.3 - - + +
239B MET* 2.9 57.8 - - + +
240B VAL* 4.1 4.5 - - + +
246B LEU* 5.4 3.8 - - + -
251B ILE* 5.8 1.1 - - + -
235D HIS* 3.1 15.3 + - + +
236D LEU* 3.2 31.4 + - - +
238D GLN* 1.3 76.7 - - - +
240D VAL* 1.3 59.9 + - - +
242D GLU 3.3 0.7 + - - -
243D ASN* 3.0 28.7 + - + +
246D LEU* 4.9 7.6 - - + -
251D ILE* 6.0 1.3 - - - -
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Residues in contact with VAL 240 (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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149D VAL* 4.6 2.2 - - + +
151D ILE* 3.8 27.8 - - + -
192D ARG* 3.2 28.3 + - - +
194D VAL* 3.9 36.8 - - + -
196D ILE* 4.9 7.0 - - + -
236D LEU* 3.0 27.3 + - + +
237D VAL* 3.6 7.6 - - - +
239D MET* 1.3 74.9 - - + +
241D ILE* 1.3 64.9 + - - +
242D GLU 3.4 0.2 + - - -
243D ASN 3.6 4.0 + - - +
246D LEU* 4.2 20.0 - - + -
251D ILE* 4.4 11.2 - - + -
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Residues in contact with ILE 241 (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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7D SER 5.7 0.4 - - - +
8D VAL* 4.0 12.6 - - + -
11D LEU* 3.8 28.5 - - + -
30D LEU* 4.1 25.1 - - + -
87D VAL* 4.0 31.6 - - + -
146D GLN* 5.0 3.5 + - - -
149D VAL* 4.5 11.3 - - + +
151D ILE* 3.9 13.2 - - + -
192D ARG* 3.2 18.4 + - - +
237D VAL* 3.0 34.7 + - + +
238D GLN* 3.6 6.7 - - - +
240D VAL* 1.3 76.6 - - - +
242D GLU* 1.3 59.1 + - - +
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Residues in contact with GLU 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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29B ARG* 5.6 0.3 + - - -
235B HIS* 2.9 33.3 + - + +
239B MET* 3.7 12.2 - - - +
7D SER* 3.2 34.9 + - - +
8D VAL* 4.7 3.4 - - + -
192D ARG* 4.8 0.2 - - - -
238D GLN* 2.9 51.8 + - + +
239D MET 3.3 0.2 + - - -
241D ILE* 1.3 77.0 - - + +
243D ASN* 1.3 57.9 + - - +
244D PRO* 3.2 14.9 - - - +
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Residues in contact with ASN 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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232B GLU* 3.0 30.4 + - - +
235B HIS* 3.2 23.2 + - + +
236B LEU* 3.9 13.1 - - - +
253B LEU* 3.7 13.7 - - - +
192D ARG* 3.1 25.9 + - - -
239D MET* 3.0 17.6 + - + +
240D VAL 3.6 0.6 + - - +
241D ILE 3.5 1.2 - - - -
242D GLU* 1.3 73.6 - - - +
244D PRO* 1.3 66.6 - - - +
245D PHE* 3.0 30.0 + - - +
246D LEU* 3.5 21.0 + - + +
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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