Contacts of the helix formed by residues 188 - 201 (chain E) in PDB entry 3SWD
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 GLU 188 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163E VAL* 3.5 30.2 - - + +
186E ALA* 3.5 14.0 + - - +
187E ARG* 1.3 85.9 + - - +
189E PRO* 1.3 69.7 - - - +
190E GLU* 3.1 11.2 - - + +
191E ILE* 2.9 25.5 + - + +
192E VAL* 3.4 4.3 + - - +
232E ARG* 3.6 23.9 + - - +
298E PRO* 3.8 9.2 - - - +
299E HIS* 2.8 35.2 + - + +
501E EPZ 4.4 9.6 + - - +
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Residues in contact with PRO 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E ARG 3.4 1.3 - - - +
188E GLU* 1.3 86.7 - - + +
190E GLU* 1.3 63.6 + - - +
192E VAL* 3.0 27.5 + - + +
193E ASP* 3.0 13.2 + - - +
229E LEU* 4.1 17.3 - - + +
232E ARG* 3.7 23.8 - - - +
255E GLN* 5.9 0.4 - - - +
258E THR* 3.8 24.0 - - - +
299E HIS* 3.6 34.1 - - + +
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Residues in contact with GLU 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ALA* 4.6 11.3 - - + +
23E ASN* 3.3 45.7 - - + +
24E ALA* 3.9 9.8 - - + +
27E PRO* 5.2 1.3 - - + +
163E VAL* 5.9 5.2 - - + +
167E VAL* 5.9 0.9 - - - -
188E GLU* 3.1 10.6 - - + +
189E PRO* 1.3 79.7 - - - +
191E ILE* 1.3 57.2 + - + +
193E ASP* 3.5 9.0 + - - +
194E THR* 2.9 31.5 + - - -
229E LEU* 4.7 4.3 - - + +
230E PRO 5.4 0.9 - - - +
232E ARG* 2.7 53.6 + - - +
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Residues in contact with ILE 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E VAL* 4.0 16.2 - - + +
166E THR* 3.7 27.6 - - + -
167E VAL* 3.9 15.0 - - + -
170E MET* 3.8 15.7 - - + +
186E ALA* 3.3 48.5 - - + +
187E ARG 5.0 0.4 - - - -
188E GLU* 2.9 19.0 + - + +
190E GLU* 1.3 74.3 - - - +
192E VAL* 1.3 65.3 + - - +
194E THR* 3.4 5.0 + - - -
195E ALA* 3.0 22.3 + - - +
208E GLN* 5.1 4.3 - - + -
209E GLY 5.3 2.5 - - - +
213E ILE* 4.3 10.1 - - + -
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Residues in contact with VAL 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E ARG 4.6 1.1 - - - +
188E GLU 3.4 6.9 + - - +
189E PRO* 3.0 16.5 + - + +
191E ILE* 1.3 77.6 - - - +
193E ASP* 1.3 57.6 + - - +
195E ALA* 3.2 2.9 + - - +
196E ASN* 2.9 46.2 + - - +
208E GLN* 3.9 18.6 - - + +
209E GLY* 3.6 34.3 - - - +
229E LEU* 6.6 0.2 - - + -
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Residues in contact with ASP 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E ALA* 4.0 7.0 - - + +
28E ILE* 4.1 4.3 - - - +
189E PRO 3.0 11.5 + - - +
190E GLU 3.8 8.1 - - - +
191E ILE 3.3 0.2 - - - -
192E VAL* 1.3 78.7 - - - +
194E THR* 1.3 55.8 + - - +
196E ASN* 4.7 2.0 + - - -
197E PHE* 3.1 22.3 + - - +
226E TYR* 2.8 40.4 + - - -
227E ARG 4.5 1.2 - - - +
228E VAL* 3.5 12.8 - - - +
229E LEU* 2.9 53.6 + - + +
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Residues in contact with THR 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E ALA 4.5 1.0 + - - -
27E PRO* 3.4 38.7 - - + +
28E ILE* 4.1 16.6 - - + +
31E ALA* 4.6 4.9 - - + -
167E VAL* 4.7 5.0 - - + +
170E MET* 4.2 13.9 - - + -
171E CYS* 4.2 19.1 - - - -
190E GLU 2.9 19.1 + - - -
191E ILE* 3.8 6.2 - - - -
192E VAL 3.3 0.2 - - - -
193E ASP* 1.3 72.3 - - - +
195E ALA* 1.3 67.5 + - - +
197E PHE* 3.3 2.3 + - - +
198E LEU* 3.0 24.4 + - + +
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Residues in contact with ALA 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E MET* 3.8 19.9 - - + +
191E ILE 3.0 13.8 + - - +
192E VAL 3.6 7.0 - - - +
194E THR* 1.3 75.6 - - - +
196E ASN* 1.3 60.5 + - - +
198E LEU* 3.0 4.4 + - - +
199E ILE* 2.9 32.1 + - - +
205E ILE* 4.0 13.8 - - + +
208E GLN* 3.7 31.9 - - + +
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Residues in contact with ASN 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E VAL* 2.9 35.6 + - - +
193E ASP* 4.8 1.6 + - - +
195E ALA* 1.3 76.6 - - - +
197E PHE* 1.3 57.9 + - - +
199E ILE* 3.6 11.6 + - - +
200E THR* 2.9 27.9 + - - -
208E GLN* 3.2 22.5 + - - +
226E TYR* 3.2 27.8 + - + +
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Residues in contact with PHE 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E ILE* 3.7 47.6 - - + -
31E ALA* 3.9 20.6 - - + -
32E ALA* 4.1 11.7 - - - -
39E VAL* 3.6 29.8 - - + -
41E ILE* 4.0 7.6 - - + -
193E ASP 3.1 16.3 + - - +
194E THR* 3.7 5.4 - - + +
195E ALA 3.2 0.4 - - - -
196E ASN* 1.3 75.0 - - - +
198E LEU* 1.3 66.9 + - + +
200E THR* 3.2 18.3 + - + -
201E LEU* 3.3 38.5 + - + +
224E GLY 6.0 0.4 - - - -
226E TYR* 3.7 36.7 - - + -
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Residues in contact with LEU 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E ALA* 3.8 26.9 - - + +
34E LEU* 4.0 19.3 - - + -
170E MET* 4.5 9.9 - - + -
171E CYS* 3.8 24.7 - - - -
174E THR* 3.9 11.2 - - + -
194E THR* 3.0 19.6 + - + +
195E ALA 3.0 6.7 + - - +
197E PHE* 1.3 79.5 - - + +
199E ILE* 1.3 59.5 + - - +
201E LEU* 2.8 25.3 + - + +
202E GLY 3.3 0.3 + - - -
203E ALA* 3.1 22.6 + - + +
205E ILE* 3.7 24.7 - - + -
221E LEU* 4.5 10.1 - - + -
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Residues in contact with ILE 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E ALA 2.9 15.1 + - - +
196E ASN* 3.9 14.8 - - - +
198E LEU* 1.3 72.6 - - - +
200E THR* 1.3 58.4 + - - +
202E GLY* 2.7 25.1 + - - -
203E ALA 3.4 21.8 + - - +
205E ILE* 3.5 35.4 - - + +
208E GLN* 3.6 20.2 - - - +
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Residues in contact with THR 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E ASN 2.9 16.0 + - - -
197E PHE* 3.2 15.7 - - + +
198E LEU 3.2 0.2 - - - -
199E ILE* 1.3 79.5 - - - +
201E LEU* 1.3 61.3 + - + +
202E GLY 3.5 0.7 + - - -
223E GLY 4.1 6.2 - - - +
224E GLY* 4.7 7.4 - - - -
225E VAL 4.1 28.9 - - - +
226E TYR* 3.8 14.5 - - + -
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Residues in contact with LEU 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E ALA 5.1 2.7 - - - +
35E ALA* 3.9 17.9 - - + +
39E VAL* 4.2 11.0 - - + -
197E PHE* 3.3 43.3 + - + +
198E LEU* 2.8 18.0 + - + +
200E THR* 1.3 81.4 - - + +
202E GLY* 1.3 56.8 + - - +
203E ALA 3.6 0.4 - - - -
220E ARG 4.7 0.2 - - - +
221E LEU* 3.6 18.3 - - + +
222E GLY* 3.0 41.4 + - - +
223E GLY* 3.1 36.8 - - - +
224E GLY* 3.9 3.8 - - - +
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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