Contacts of the helix formed by residues 223 - 237 (chain E) in PDB entry 2BS3
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 PRO 223 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E GLU* 3.5 34.1 - - + +
148E LEU* 3.8 23.6 - - + -
177E ASN* 5.8 0.2 - - - -
215E HIS* 4.0 10.1 - - + -
221E ASN 3.7 3.3 - - - +
222E LEU* 1.3 81.4 - - + +
224E LEU* 1.3 64.3 + - - +
225E GLN 3.4 2.7 - - - -
226E SER* 3.5 14.8 + - - +
227E LYS* 3.1 36.2 + - - +
202F PRO* 6.0 2.7 - - + -
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Residues in contact with LEU 224 (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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157E CYS* 4.5 1.1 - - + -
173E ALA* 4.2 13.2 - - + +
177E ASN* 3.8 36.1 - - + +
214E CYS* 3.6 46.4 - - + +
215E HIS* 3.4 13.1 + - + +
218E CYS* 4.2 13.5 - - + -
222E LEU* 2.8 19.3 + - + +
223E PRO* 1.3 70.0 - - - +
225E GLN* 1.3 66.6 + - - +
227E LYS* 4.5 3.4 - - + -
228E ILE* 2.8 37.5 + - + +
1242E SF4 4.2 17.7 - - - -
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Residues in contact with GLN 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E LEU* 3.8 39.7 - - + +
215E HIS* 3.1 29.0 + - + +
224E LEU* 1.3 77.9 - - - +
226E SER* 1.3 63.2 + - - +
228E ILE* 4.1 2.9 - - - +
229E ALA* 3.3 16.5 + - - +
192F VAL* 3.1 38.0 + - + +
198F ASP* 3.2 31.8 + - - +
202F PRO* 3.7 25.1 - - - +
206F ARG* 4.8 9.0 - - - +
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Residues in contact with SER 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223E PRO* 3.5 19.1 + - - +
225E GLN* 1.3 81.2 - - - +
227E LYS* 1.3 70.1 + - - +
229E ALA* 3.8 1.7 - - - +
230E TYR* 3.0 27.9 + - - +
233E ARG* 5.0 1.0 + - - -
198F ASP* 3.4 27.3 - - - +
202F PRO* 3.8 28.6 - - - +
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Residues in contact with LYS 227 (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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147E GLU* 5.3 4.2 + - - -
148E LEU* 4.0 19.6 - - + +
177E ASN* 4.7 9.0 - - - +
180E VAL* 3.3 47.3 - - + +
184E ILE* 5.9 2.5 - - + +
223E PRO* 3.1 40.3 + - + +
224E LEU* 4.0 3.6 - - + +
226E SER* 1.3 86.0 + - - +
228E ILE* 1.3 65.8 + - + +
230E TYR* 3.3 12.2 - - + +
231E LEU* 3.0 22.5 + - - +
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Residues in contact with ILE 228 (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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173E ALA* 4.3 14.4 - - + +
176E LEU* 4.0 40.4 - - + -
177E ASN* 5.4 1.8 - - - +
180E VAL* 5.6 0.2 - - - -
205E VAL* 4.4 6.6 - - + +
208E CYS* 4.1 17.0 - - + -
212E LEU* 6.0 0.7 - - + -
214E CYS* 4.3 24.2 - - - -
224E LEU* 2.8 28.7 + - + +
225E GLN* 4.1 3.4 - - - +
227E LYS* 1.3 74.3 - - + +
229E ALA* 1.3 61.7 + - - +
231E LEU* 3.1 8.0 + - - +
232E ARG* 2.8 31.0 + - + +
1241E F3S 4.3 12.6 - - - -
193F LYS 5.8 0.9 - - - +
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Residues in contact with ALA 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E GLN 3.3 16.8 + - - +
226E SER 3.8 4.5 - - - +
228E ILE* 1.3 77.7 - - - +
230E TYR* 1.3 63.9 + - - +
232E ARG* 3.2 3.3 + - - +
233E ARG* 2.9 32.4 + - - +
192F VAL 3.8 4.7 - - - +
193F LYS 3.2 27.0 - - - +
194F TRP 3.7 1.5 - - - +
195F GLY* 3.6 25.6 - - - +
198F ASP* 4.2 1.8 - - - +
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Residues in contact with TYR 230 (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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180E VAL* 4.2 21.3 - - + -
183E MET* 3.8 17.1 - - + +
184E ILE* 4.7 12.8 - - + +
226E SER 3.0 19.0 + - - +
227E LYS* 3.3 15.3 - - + +
228E ILE 3.2 0.2 - - - -
229E ALA* 1.3 77.7 - - - +
231E LEU* 1.3 65.2 + - - +
233E ARG* 3.4 30.3 + - - +
234E LYS* 3.2 67.1 + - + +
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Residues in contact with LEU 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176E LEU* 3.8 50.5 - - + +
179E VAL* 3.8 16.4 - - + -
180E VAL* 4.0 6.3 - - + -
183E MET* 3.6 33.0 - - + -
199E ILE* 4.3 6.7 - - + -
205E VAL* 4.2 7.2 - - + -
227E LYS 3.0 12.9 + - - +
228E ILE* 3.1 8.9 + - - +
230E TYR* 1.3 81.6 - - - +
232E ARG* 1.3 57.3 + - - +
234E LYS* 3.2 3.4 + - - -
235E MET* 2.9 51.5 + - + +
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Residues in contact with ARG 232 (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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205E VAL* 3.5 32.3 + - + +
206E PHE* 3.7 18.7 + - + +
208E CYS* 3.1 37.6 + - - +
210E THR* 4.1 4.0 + - - -
228E ILE* 2.8 20.1 + - + +
229E ALA* 3.2 8.0 + - - +
231E LEU* 1.3 77.4 - - - +
233E ARG* 1.3 62.1 + - - +
235E MET* 3.4 2.3 + - - +
236E VAL* 3.0 27.9 + - - +
27F ASP* 2.8 37.7 + - - +
100F LYS* 5.4 2.2 - - - +
193F LYS* 3.4 44.1 + - - +
194F TRP* 3.6 23.3 - - + -
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Residues in contact with ARG 233 (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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226E SER 5.0 0.6 + - - -
229E ALA* 2.9 26.3 + - - +
230E TYR* 3.7 35.8 - - - +
231E LEU 3.3 0.2 - - - -
232E ARG* 1.3 75.4 - - - +
234E LYS* 1.3 62.2 + - + +
236E VAL* 3.2 13.0 - - - +
237E SER* 2.9 24.9 + - - -
194F TRP* 2.8 51.3 + - + +
195F GLY* 3.6 16.2 + - - -
196F TRP* 5.0 11.7 - - - +
198F ASP* 4.7 2.6 + - - +
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Residues in contact with LYS 234 (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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183E MET* 4.0 15.7 - - - +
192E ASP* 2.9 44.9 + - - +
230E TYR* 3.2 59.6 + - + +
231E LEU* 3.8 4.7 - - - +
233E ARG* 1.3 78.3 - - + +
235E MET* 1.3 73.6 + - + +
237E SER* 3.4 13.3 + - - -
238E VAL* 3.4 15.4 + - - +
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Residues in contact with MET 235 (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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183E MET* 4.2 16.4 - - + -
192E ASP* 3.5 25.1 - - + +
195E TYR* 4.0 2.0 - - + -
196E TYR* 3.5 57.2 - - + -
199E ILE* 3.6 27.4 - - + -
205E VAL* 4.0 9.0 - - + -
206E PHE* 3.8 17.9 - - + -
231E LEU* 2.9 23.8 + - + +
232E ARG 4.1 0.7 - - - +
234E LYS* 1.3 91.1 - - + +
236E VAL* 1.3 64.9 + - - +
237E SER 3.1 1.0 + - - -
238E VAL* 3.4 13.0 + - + +
24F ALA* 4.3 1.2 - - - +
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Residues in contact with VAL 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206E PHE* 4.0 11.4 - - + -
232E ARG 3.0 16.2 + - - +
233E ARG* 3.2 18.2 - - - +
235E MET* 1.3 76.9 - - - +
237E SER* 1.3 63.5 - - - +
238E VAL 3.4 3.1 + - - +
24F ALA* 3.5 32.4 - - - +
27F ASP* 4.9 0.2 - - - +
28F TRP* 4.1 29.3 - - + +
194F TRP* 3.9 27.1 - - + -
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Residues in contact with SER 237 (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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233E ARG 2.9 18.5 + - - -
234E LYS* 3.4 7.7 + - - -
235E MET 3.1 1.0 - - - -
236E VAL* 1.3 83.8 - - - +
238E VAL* 1.3 62.1 + - - +
239E ASN 3.4 11.4 + - - +
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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