Contacts of the helix formed by residues 186 - 199 (chain A) in PDB entry 5ETE
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 SER 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A TRP* 1.3 77.5 - - - +
187A ASP* 1.3 62.7 + - - +
188A THR* 3.3 12.0 + - - -
189A LEU* 3.0 43.4 + - - +
190A ALA* 3.0 23.4 + - - +
261A GLN* 3.7 23.8 - - - +
262A VAL 3.0 7.3 + - - -
263A GLY* 4.1 1.4 - - - -
302A DIO 4.1 4.9 - - - -
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Residues in contact with ASP 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU* 5.2 4.5 - - - +
185A TRP* 4.0 16.1 + - - -
186A SER* 1.3 72.2 + - - +
188A THR* 1.3 57.1 + - - +
190A ALA* 3.8 5.9 - - - +
191A SER* 3.0 35.5 + - - +
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Residues in contact with THR 188 (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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186A SER* 3.2 9.0 + - - -
187A ASP* 1.3 78.9 - - - +
189A LEU* 1.3 61.7 + - - +
191A SER* 3.4 4.5 + - - -
192A TYR* 3.2 21.7 + - - +
213A TYR* 4.2 17.4 + - - +
302A DIO 4.3 15.9 - - - +
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Residues in contact with LEU 189 (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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186A SER* 3.0 16.9 + - - +
188A THR* 1.3 74.8 - - - +
190A ALA* 1.3 58.1 + - - +
192A TYR* 3.3 7.0 + - - +
193A ALA* 2.9 28.4 + - - +
213A TYR* 3.6 43.5 - - + -
261A GLN* 3.5 45.5 - - + +
262A VAL 3.7 2.9 - - - +
263A GLY* 3.6 15.6 - - - +
280A SER* 3.6 20.1 - - - +
282A ASP* 4.0 11.9 - - + +
302A DIO 3.8 14.8 - - - -
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Residues in contact with ALA 190 (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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185A TRP* 3.9 24.5 - - + +
186A SER 3.0 16.2 + - - +
187A ASP* 3.9 6.1 - - - +
189A LEU* 1.3 75.8 - - - +
191A SER* 1.3 59.7 + - - +
193A ALA* 4.4 0.4 - - - -
194A GLN* 2.9 31.7 + - - +
264A CYS 3.8 25.6 - - - +
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Residues in contact with SER 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ASP* 3.0 19.0 + - - +
188A THR* 3.9 5.6 - - - -
189A LEU 3.3 0.2 - - - -
190A ALA* 1.3 73.2 - - - +
192A TYR* 1.3 66.2 + - - +
194A GLN* 4.2 2.9 - - - +
195A ASP* 3.0 38.3 + - - +
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Residues in contact with TYR 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A THR 3.2 11.0 + - - +
189A LEU 3.5 7.6 - - - +
191A SER* 1.3 80.1 - - - +
193A ALA* 1.3 65.7 + - - +
195A ASP* 3.4 7.5 + - + +
196A TYR* 3.2 23.4 + + + +
209A SER* 2.7 36.7 + - - -
211A GLY* 3.2 18.6 + - - -
212A PRO* 4.2 14.1 - - + -
213A TYR* 3.7 29.4 - + + -
215A GLU* 4.3 5.8 - - - -
278A ILE* 4.9 4.0 - - + -
280A SER* 3.7 17.7 - - - -
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Residues in contact with ALA 193 (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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189A LEU 2.9 17.1 + - - +
190A ALA 3.9 0.4 - - - +
192A TYR* 1.3 78.6 - - - +
194A GLN* 1.3 58.7 + - - +
196A TYR* 3.1 3.1 + - - +
197A ALA 3.0 23.2 + - - -
263A GLY 3.7 0.4 - - - +
264A CYS* 3.6 13.0 - - - -
265A GLY* 3.5 21.5 - - - +
278A ILE* 3.4 26.1 - - + +
280A SER* 3.7 17.5 - - - +
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Residues in contact with GLN 194 (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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162A PHE* 5.3 1.4 - - - -
190A ALA 2.9 18.3 + - - +
191A SER* 4.2 3.8 - - - +
193A ALA* 1.3 73.7 - - - +
195A ASP* 1.3 62.3 + - - +
197A ALA* 3.2 5.2 + - - +
198A ASP* 2.8 60.7 + - - +
264A CYS 4.7 1.0 - - - +
265A GLY* 3.3 9.8 - - - -
266A ILE* 3.0 46.5 + - - +
267A LYS* 5.3 0.6 - - - +
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Residues in contact with ASP 195 (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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191A SER* 3.0 29.8 + - - +
192A TYR* 3.6 7.2 - - - +
194A GLN* 1.3 79.7 - - - +
196A TYR* 1.3 60.8 + - - +
198A ASP* 3.5 20.5 + - - +
199A ASN* 3.5 19.0 + - - +
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Residues in contact with TYR 196 (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 TYR* 3.2 15.0 + + + +
193A ALA 3.1 9.0 + - - +
195A ASP* 1.3 76.0 - - - +
197A ALA* 1.3 66.2 + - - +
199A ASN* 3.1 23.1 + - + +
200A TYR* 3.5 8.3 + - - +
207A THR* 2.8 29.7 + - - +
208A HIS 3.4 10.6 + - - -
209A SER* 3.5 31.8 - - - -
215A GLU* 4.8 1.8 - - - -
217A LEU* 4.9 0.7 - - + -
276A TYR* 3.3 28.0 - - - -
278A ILE* 3.8 21.1 - - + -
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Residues in contact with ALA 197 (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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193A ALA 3.0 12.9 + - - +
194A GLN* 3.7 18.4 - - - +
196A TYR* 1.3 74.7 - - - +
198A ASP* 1.3 66.2 + - - +
200A TYR* 2.9 15.4 + - - +
266A ILE 4.1 21.3 - - - +
267A LYS* 3.2 17.0 - - + +
276A TYR* 3.8 28.9 - - + -
278A ILE* 4.1 3.3 - - + +
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Residues in contact with ASP 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A GLN* 2.8 48.7 + - - +
195A ASP* 3.5 16.9 - - - +
197A ALA* 1.3 72.4 - - - +
199A ASN* 1.3 61.7 + - - +
267A LYS* 3.3 23.9 + - - +
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Residues in contact with ASN 199 (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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195A ASP* 3.5 15.5 + - - +
196A TYR* 3.1 16.9 + - + +
197A ALA 3.0 1.4 - - - -
198A ASP* 1.3 82.0 - - - +
200A TYR* 1.3 63.8 + - - +
201A ASP* 3.5 3.6 + - - +
267A LYS* 4.6 0.2 - - - -
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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