Contacts of the helix formed by residues 229 - 243 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A PHE* 3.4 5.4 - - - -
202A ALA* 5.4 0.9 - - - -
226A ARG* 3.7 6.0 - - - +
227A LEU 3.7 1.0 + - - +
228A GLY* 1.3 71.7 - - - -
230A PRO* 1.3 67.7 - - - +
231A ALA* 3.0 23.7 + - - +
232A GLU* 2.7 55.6 + - - +
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Residues in contact with PRO 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLY* 4.3 6.7 - - - +
22A LEU* 4.0 20.3 - - + +
25A SER* 3.4 27.9 + - - +
201A PHE* 3.9 2.7 - - + -
202A ALA* 3.6 25.1 - - + +
203A THR* 4.2 13.2 - - + -
228A GLY 3.8 6.3 - - - +
229A ASP* 1.3 90.9 - - - +
231A ALA* 1.3 60.1 + - - +
233A TYR* 3.1 14.0 + - - +
234A ALA 3.2 9.2 + - - -
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Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER* 3.4 13.5 + - - +
29A ARG* 4.9 6.1 + - - +
229A ASP* 2.9 19.4 + - - +
230A PRO* 1.3 77.0 - - - +
232A GLU* 1.3 58.3 + - + +
233A TYR 3.4 0.2 - - - -
234A ALA* 3.5 5.6 + - - +
235A HIS* 3.1 25.3 + - - +
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Residues in contact with GLU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PHE* 4.6 3.6 - - + -
226A ARG* 2.9 34.9 + - - -
228A GLY* 3.8 1.0 - - - -
229A ASP* 2.7 49.4 + - + +
231A ALA* 1.3 70.8 - - + +
233A TYR* 1.3 61.2 + - - +
235A HIS* 3.5 3.7 + - - -
236A LEU* 3.2 9.2 + - - +
253A LEU* 3.9 3.2 - - + +
243C ASN* 3.1 34.3 + - - +
244C PRO* 3.6 28.6 - - + +
245C PHE* 3.7 19.7 + - + +
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Residues in contact with TYR 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 3.9 41.5 - - + -
26A THR* 3.4 24.2 - - - -
89A VAL* 4.0 9.3 - - + +
91A CYS* 3.5 19.6 - - - -
151A ILE* 4.7 3.3 - - - +
152A ASN 4.7 0.3 + - - -
153A THR* 2.7 32.8 + - + -
196A ILE* 3.8 36.3 - - + +
198A PRO* 4.3 6.1 - - + -
201A PHE* 4.1 8.7 - - + -
229A ASP 3.8 2.0 + - - -
230A PRO 3.1 9.0 + - - +
232A GLU* 1.3 76.8 - - - +
234A ALA* 1.3 63.3 + - - +
236A LEU* 3.2 4.5 + - - +
237A VAL* 3.0 35.4 + - + +
253A LEU* 3.7 14.4 - - + +
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Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A SER* 3.6 29.6 - - - +
26A THR* 3.7 21.7 - - + +
29A ARG* 3.6 21.0 - - + -
30A LEU* 5.4 1.6 - - - +
230A PRO 3.2 7.7 + - - +
231A ALA* 3.7 8.7 - - - +
232A GLU 3.3 0.2 - - - -
233A TYR* 1.3 80.4 - - - +
235A HIS* 1.3 62.0 + - - +
237A VAL* 3.3 5.3 + - - +
238A GLN* 3.2 17.8 + - - +
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Residues in contact with HIS 235 (chain A).
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* 3.6 38.5 - - - +
231A ALA 3.1 14.8 + - - +
232A GLU* 3.7 9.2 - - - +
233A TYR 3.3 0.2 - - - -
234A ALA* 1.3 74.8 - - - +
236A LEU* 1.3 62.7 + - - +
238A GLN* 3.3 5.7 + - + +
239A MET* 3.1 21.4 + - + +
239C MET* 3.6 40.3 - - + +
242C GLU* 3.0 35.4 + - + +
243C ASN* 3.2 28.6 + - + +
244C PRO* 6.2 0.7 - - + -
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Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ILE* 3.8 39.0 - - + -
232A GLU 3.2 8.9 + - - +
233A TYR 3.2 9.1 + - - +
235A HIS* 1.3 78.9 + - - +
237A VAL* 1.3 62.2 + - - +
239A MET* 3.2 42.3 + - + +
240A VAL* 3.1 24.8 + - + +
251A ILE* 4.2 21.8 - - + -
253A LEU* 4.0 20.2 - - + -
243C ASN* 4.1 9.0 - - + +
246C LEU* 4.5 16.6 - - + -
251C ILE* 6.1 0.2 - - + -
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Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A THR* 3.8 24.2 - - + +
30A LEU* 4.6 2.7 - - + -
89A VAL* 4.3 10.1 - - + -
151A ILE* 3.9 23.2 - - + +
196A ILE* 3.8 15.7 - - + -
233A TYR* 3.0 45.6 + - + +
234A ALA 3.6 7.6 - - - +
235A HIS 3.3 0.2 - - - -
236A LEU* 1.3 75.3 - - - +
238A GLN* 1.3 63.3 + - - +
240A VAL* 3.2 4.7 + - - +
241A ILE* 3.1 34.3 + - + +
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Residues in contact with GLN 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A SER* 4.8 1.2 - - - +
8A VAL* 3.8 29.2 - - + +
29A ARG* 3.3 29.9 + - - +
30A LEU* 4.3 9.2 - - + +
33A GLN* 3.6 28.0 + - - +
234A ALA 3.2 10.1 + - - +
235A HIS* 3.3 8.3 + - + +
237A VAL* 1.3 80.0 - - - +
239A MET* 1.3 60.9 + - - +
241A ILE* 3.3 12.4 + - - +
242A GLU* 2.8 49.8 + - - +
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Residues in contact with MET 239 (chain A).
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* 3.1 13.6 + - + +
236A LEU* 3.2 37.0 + - + +
238A GLN* 1.3 76.5 - - - +
240A VAL* 1.3 65.4 + - + +
242A GLU* 3.5 2.1 + - - -
243A ASN* 3.0 28.9 + - + +
246A LEU* 3.5 29.6 - - + -
251A ILE* 4.2 8.5 - - + -
235C HIS* 3.7 10.7 - - + -
236C LEU* 3.6 22.9 - - + -
239C MET* 3.2 49.4 - - + +
240C VAL* 5.3 0.9 - - - -
246C LEU* 5.3 5.2 - - - -
251C ILE* 5.5 2.5 - - + -
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A VAL* 4.6 2.5 - - + -
151A ILE* 3.8 20.0 - - + -
192A ARG* 3.1 29.3 + - - +
194A VAL* 3.8 42.2 - - + -
196A ILE* 4.9 6.5 - - + -
236A LEU* 3.1 19.1 + - + +
237A VAL* 3.2 9.4 + - - +
239A MET* 1.3 91.6 - - + +
241A ILE* 1.3 65.4 + - - +
242A GLU 3.5 0.2 + - - -
243A ASN* 3.6 4.9 + - - +
246A LEU* 4.3 12.6 - - + -
251A ILE* 4.5 6.3 - - + -
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Residues in contact with ILE 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A SER 5.7 0.7 - - - +
8A VAL* 4.0 12.3 - - + -
11A LEU* 3.7 29.2 - - + -
30A LEU* 4.1 24.0 - - + -
87A VAL* 4.0 31.0 - - + -
146A GLN* 4.9 3.3 + - - -
149A VAL* 4.5 10.0 - - + +
151A ILE* 3.9 13.0 - - + -
192A ARG* 3.2 18.2 + - - +
237A VAL* 3.1 32.0 + - + +
238A GLN* 3.3 6.7 + - - +
240A VAL* 1.3 77.5 - - - +
242A GLU* 1.3 58.3 + - + +
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Residues in contact with GLU 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A SER* 3.3 30.5 + - - +
8A VAL* 4.6 7.2 - - + -
238A GLN* 2.8 52.1 + - + +
239A MET* 5.1 0.3 - - - -
241A ILE* 1.3 78.5 - - + +
243A ASN* 1.3 57.1 + - - +
244A PRO* 3.1 15.6 - - - +
29C ARG* 5.6 0.5 + - - -
235C HIS* 3.0 31.8 + - + +
239C MET* 4.8 5.9 - - - +
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Residues in contact with ASN 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ARG* 3.0 25.4 + - - -
239A MET* 3.0 18.7 + - + +
240A VAL 3.6 0.5 + - - +
241A ILE 3.5 1.2 - - - -
242A GLU* 1.3 73.5 - - - +
244A PRO* 1.3 67.6 - - - +
245A PHE* 3.0 18.9 + - - +
246A LEU* 3.6 20.8 + - + +
232C GLU* 3.1 30.2 + - - +
235C HIS* 3.2 23.1 + - + +
236C LEU* 3.9 13.1 - - - +
253C LEU* 3.7 13.8 - - - +
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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