Contacts of the helix formed by residues 227 - 241 (chain E) in PDB entry 1S9D
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 227 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221E ASN* 6.0 0.2 - - - +
225E ASP 4.6 1.1 - - - +
226E LEU* 1.3 97.2 - - + +
228E GLU* 1.3 66.1 + - - +
229E GLU* 4.5 7.0 - - + +
230E LEU* 3.1 32.3 + - + +
231E LEU* 3.4 10.0 + - - +
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Residues in contact with GLU 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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210E LEU* 4.8 2.8 - - - +
211E GLU* 5.1 3.6 - - - +
214E VAL* 4.4 29.8 - - + +
218E ARG* 5.3 5.8 + - - +
226E LEU 3.3 4.5 + - - -
227E PRO* 1.3 72.0 - - - +
229E GLU* 1.3 57.0 + - - +
231E LEU* 3.2 10.2 + - - +
232E ARG* 2.8 54.0 + - + +
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Residues in contact with GLU 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227E PRO* 3.2 5.4 + - + +
228E GLU* 1.3 75.5 - - - +
230E LEU* 1.3 65.4 - - - +
232E ARG* 3.9 21.6 + - - +
233E ASN* 3.0 58.7 + - - +
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Residues in contact with LEU 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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140E LEU* 6.4 0.2 - - + -
178E VAL* 5.4 10.3 - - + +
179E PHE* 4.5 19.7 - - + -
188E LEU* 4.1 15.5 - - + -
226E LEU* 4.6 6.7 - - + -
227E PRO* 3.1 32.6 + - + +
229E GLU* 1.3 78.0 - - - +
231E LEU* 1.3 71.3 + - + +
233E ASN* 3.3 9.2 + - - +
234E LEU* 3.1 48.4 + - + +
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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
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188E LEU* 3.7 30.3 - - + -
210E LEU* 4.8 0.4 - - - -
213E PHE* 3.5 21.3 - - + -
214E VAL* 4.1 38.1 - - + +
217E ASN* 4.2 16.4 - - + +
226E LEU* 4.4 26.2 - - + +
227E PRO 3.4 11.6 + - - +
228E GLU* 3.2 8.1 + - - +
230E LEU* 1.3 85.5 - - + +
232E ARG* 1.3 58.8 + - - +
234E LEU* 3.2 3.5 + - + +
235E TYR* 2.9 29.5 + - - +
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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
----------------------------------------------------------
210E LEU* 3.3 49.9 - - + +
211E GLU* 4.6 4.8 + - - -
228E GLU* 2.8 36.1 + - + +
229E GLU* 3.8 25.5 + - - +
230E LEU 3.3 0.2 - - - -
231E LEU* 1.3 77.4 - - - +
233E ASN* 1.3 58.1 + - - +
235E TYR* 3.6 0.7 - - - +
236E ASP* 2.8 48.8 + - - +
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Residues in contact with ASN 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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139E ASN* 5.8 7.2 - - - +
229E GLU* 3.0 50.3 + - - +
230E LEU* 3.6 7.7 - - - +
232E ARG* 1.3 78.4 - - - +
234E LEU* 1.3 65.1 + - + +
236E ASP* 4.1 4.7 - - - +
237E SER* 3.1 23.6 + - - -
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Residues in contact with LEU 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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139E ASN* 4.4 11.9 - - + +
140E LEU* 4.2 11.4 - - + +
141E VAL* 3.5 37.5 - - + +
188E LEU* 3.9 38.6 - - + -
192E VAL* 4.2 14.8 - - + -
195E LEU* 4.8 1.1 - - - -
213E PHE* 4.4 8.1 - - + -
230E LEU* 3.1 25.3 + - + +
231E LEU* 3.6 8.1 - - + +
233E ASN* 1.3 75.2 - - + +
235E TYR* 1.3 67.1 + - - +
237E SER* 3.2 3.6 + - - -
238E ILE* 3.1 28.7 + - - +
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Residues in contact with TYR 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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195E LEU* 3.7 36.9 - - + +
199E LEU* 4.3 12.9 - - + +
208E MET 2.6 29.2 + - - -
209E GLY* 3.3 15.5 - - - -
210E LEU* 3.3 35.2 + - + -
213E PHE* 3.7 19.9 - - + -
231E LEU 2.9 16.3 + - - +
232E ARG 3.6 3.4 - - - +
234E LEU* 1.3 79.6 - - - +
236E ASP* 1.3 70.7 + - - +
238E ILE* 3.4 2.1 + - - +
239E ARG* 2.8 53.1 + - - +
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Residues in contact with ASP 236 (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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210E LEU* 5.5 1.7 - - - +
232E ARG* 2.8 45.2 + - - +
233E ASN* 4.2 4.5 - - - +
235E TYR* 1.3 90.1 - - - +
237E SER* 1.3 62.7 + - - +
239E ARG* 4.3 8.8 - - - -
240E ASN* 3.1 36.8 + - - +
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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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139E ASN* 6.3 0.9 - - - -
141E VAL* 3.5 19.2 - - - +
142E GLN* 6.1 0.7 - - - +
145E ARG* 2.9 28.6 + - - -
233E ASN 3.1 19.5 + - - -
234E LEU 3.2 5.1 + - - -
236E ASP* 1.3 77.9 - - - +
238E ILE* 1.3 57.9 + - - +
240E ASN* 3.8 1.3 - - - +
241E GLU* 3.0 25.8 + - - +
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Residues in contact with ILE 238 (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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141E VAL* 3.8 18.2 - - + -
145E ARG* 4.1 5.2 - - - +
192E VAL* 4.0 15.9 - - + -
195E LEU* 3.9 20.4 - - + +
196E ASN* 3.7 39.9 - - - +
199E LEU* 4.4 1.6 - - + -
200E HIS* 2.7 31.0 + - + +
234E LEU 3.1 15.9 + - - +
237E SER* 1.3 71.7 - - - +
239E ARG* 1.3 61.0 + - - +
240E ASN 3.2 0.5 + - - -
241E GLU 3.2 13.4 + - - +
243E PHE* 3.8 36.8 - - + -
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Residues in contact with ARG 239 (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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199E LEU* 3.6 22.8 - - + +
200E HIS* 3.4 15.5 - - - -
235E TYR* 2.8 43.0 + - + +
236E ASP* 3.8 9.9 - - - +
237E SER 3.4 0.2 - - - -
238E ILE* 1.3 79.1 - - - +
240E ASN* 1.3 86.3 + - - +
242E PRO* 5.1 0.2 - - - +
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Residues in contact with ASN 240 (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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236E ASP* 3.1 28.8 + - - +
237E SER* 3.8 1.1 - - - +
239E ARG* 1.3 115.6 + - - +
241E GLU* 1.4 63.1 + - + +
242E PRO* 4.3 3.4 - - - +
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Residues in contact with GLU 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E ARG* 2.7 62.1 + - - +
237E SER* 3.0 7.5 + - - +
238E ILE* 3.2 11.5 + - - +
240E ASN* 1.4 82.8 - - - +
242E PRO* 1.3 71.5 - - + +
243E PHE 3.7 0.2 + - - -
244E LYS* 4.4 20.1 - - + +
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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