Contacts of the helix formed by residues 181 - 201 (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 SER 181 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172E CYS* 4.6 3.8 - - - -
179E PHE* 3.4 8.7 - - - +
180E GLN* 1.3 79.0 - - - +
182E THR* 1.3 65.1 + - - +
183E ASP* 3.7 4.7 + - - -
184E THR* 2.8 34.6 + - - -
185E CYS* 3.6 7.1 + - - +
222E GLU* 2.8 33.6 + - - +
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Residues in contact with THR 182 (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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168E ALA* 4.0 1.6 - - - +
169E GLN* 4.4 30.6 - - + +
172E CYS* 4.0 30.1 - - + -
181E SER* 1.3 70.6 - - - +
183E ASP* 1.3 67.1 + - - +
185E CYS* 3.1 4.7 + - - +
186E TYR* 2.8 29.4 + - - +
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Residues in contact with ASP 183 (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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73A LYS* 2.7 44.9 + - + +
165E GLU* 4.4 5.9 - - - +
181E SER* 3.2 8.5 + - - +
182E THR* 1.3 85.7 + - - +
184E THR* 1.3 63.2 + - - +
186E TYR* 3.8 12.6 - - + +
187E VAL* 3.0 31.8 + - + +
220E ILE 5.1 0.2 - - - -
222E GLU* 4.4 8.1 - - - +
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Residues in contact with THR 184 (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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179E PHE* 4.2 19.7 - - + -
181E SER* 2.8 26.4 + - - -
183E ASP* 1.3 79.0 - - - +
185E CYS* 1.3 57.9 + - - +
187E VAL* 4.0 1.7 - - - -
188E LEU* 3.0 30.0 + - - +
220E ILE* 3.0 40.1 + - + +
221E ASN* 3.6 26.6 + - - +
222E GLU* 3.9 3.8 + - - +
226E LEU* 4.3 7.2 - - + -
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Residues in contact with CYS 185 (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* 3.7 26.5 - - - +
168E ALA* 3.8 22.4 - - + -
171E TYR* 3.8 18.4 - - - -
172E CYS* 3.4 22.4 - - - -
179E PHE* 3.7 16.0 - - + -
181E SER 3.6 1.4 + - - -
182E THR 3.1 9.3 + - - +
184E THR* 1.3 77.8 - - - +
186E TYR* 1.3 55.3 + - - +
188E LEU* 3.8 3.5 - - - +
189E SER* 2.7 39.0 + - - -
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Residues in contact with TYR 186 (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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71A GLN* 3.0 29.6 + - - +
73A LYS* 4.0 25.6 - - + +
74A ILE* 3.6 15.7 - - + +
161E ASP* 2.5 43.5 + - - -
164E MET* 4.0 5.3 - - + +
165E GLU* 3.5 34.3 - - + -
168E ALA* 3.5 22.4 - - + +
182E THR 2.8 12.3 + - - +
183E ASP* 3.8 19.1 - - - +
185E CYS* 1.3 75.5 - - - +
187E VAL* 1.3 63.8 + - + +
189E SER* 3.3 5.1 + - - -
190E TYR* 2.9 25.9 + - + +
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Residues in contact with VAL 187 (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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73A LYS* 4.0 25.6 - - + +
74A ILE* 4.4 8.5 - - + -
76A PRO* 6.4 0.9 - - + -
77A LEU* 3.6 22.6 - - + +
183E ASP* 3.0 25.0 + - + +
184E THR 4.1 2.9 - - - +
186E TYR* 1.3 91.9 - - + +
188E LEU* 1.3 58.3 + - - +
190E TYR* 3.2 3.3 + - - +
191E SER* 2.9 26.9 + - - -
220E ILE* 3.8 32.1 - - + +
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Residues in contact with LEU 188 (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* 3.5 22.9 - - + -
179E PHE* 3.8 25.4 - - + -
184E THR 3.0 18.6 + - - +
185E CYS 3.8 3.1 - - - +
187E VAL* 1.3 75.3 - - - +
189E SER* 1.4 57.9 + - - +
191E SER* 2.7 35.8 + - - +
192E VAL* 2.9 18.5 + - - +
213E PHE* 4.5 0.9 - - + -
217E ASN* 3.7 19.3 - - - +
220E ILE* 3.7 10.7 - - + +
226E LEU* 3.8 11.0 - - + -
230E LEU* 4.1 5.2 - - + -
231E LEU* 3.7 16.6 - - + -
234E LEU* 3.9 19.7 - - + -
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Residues in contact with SER 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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140E LEU* 3.6 14.6 - - - +
144E LEU* 4.3 7.4 - - - +
164E MET* 3.9 23.6 - - - +
167E PHE* 3.4 28.8 - - - -
185E CYS* 2.7 26.4 + - - -
186E TYR* 3.5 6.7 - - - -
188E LEU* 1.4 74.9 - - - +
190E TYR* 1.3 63.3 + - - +
192E VAL* 3.1 12.5 + - - +
193E ILE* 3.3 16.8 + - - +
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Residues in contact with TYR 190 (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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51A PHE* 3.3 26.8 - + - -
70A GLY 4.8 1.4 + - - -
74A ILE* 3.8 34.5 - - + +
77A LEU* 3.8 9.2 - - + -
78A TRP* 4.9 0.9 - - - -
403A AFB 2.7 29.0 + - - -
157E ALA* 3.5 10.2 + - - +
160E ILE* 4.0 9.9 - - + -
161E ASP* 3.7 40.4 - - + -
164E MET* 4.2 12.3 - - + +
186E TYR* 2.9 15.4 + + + +
187E VAL 3.6 7.0 - - - +
189E SER* 1.3 75.9 - - - +
191E SER* 1.3 57.1 + - - +
193E ILE* 3.1 6.7 + - - +
194E MET* 2.8 52.4 + - - +
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Residues in contact with SER 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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77A LEU* 4.0 16.7 - - - +
187E VAL 2.9 10.3 + - - -
188E LEU* 2.7 21.1 + - - +
190E TYR* 1.3 75.8 - - - +
192E VAL* 1.3 50.5 + - - +
194E MET* 3.2 10.5 + - - +
195E LEU* 2.7 34.7 + - - +
213E PHE* 3.5 8.3 - - - -
216E MET* 4.2 8.9 - - - +
217E ASN* 3.1 40.5 + - - -
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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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140E LEU* 4.7 2.7 - - + -
141E VAL* 4.0 17.5 - - + -
144E LEU* 3.7 25.1 - - + -
188E LEU 2.9 18.8 + - - +
189E SER* 3.1 9.1 + - - +
191E SER* 1.3 78.1 - - - +
193E ILE* 1.3 54.6 + - - +
195E LEU* 3.1 6.3 + - + +
196E ASN* 2.7 34.1 + - - +
213E PHE* 4.4 7.9 - - + -
234E LEU* 4.2 26.5 - - + -
238E ILE* 4.0 9.8 - - + +
243E PHE* 3.8 16.8 - - + -
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Residues in contact with ILE 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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49A ILE* 5.2 1.3 - - + +
50A GLY* 4.0 11.9 - - - -
51A PHE* 3.7 17.5 - - + -
144E LEU* 4.7 3.6 - - + -
148E LEU* 3.8 28.5 - - + -
153E LEU* 3.9 24.7 - - + -
160E ILE* 3.9 10.8 - - + -
164E MET* 3.7 28.3 - - + -
189E SER 3.5 13.7 - - - +
190E TYR 3.1 6.7 + - - +
192E VAL* 1.3 74.1 - - - +
194E MET* 1.3 63.7 + - - +
196E ASN* 3.3 5.7 + - + +
197E THR* 3.1 26.5 + - - -
243E PHE* 3.9 12.6 - - + -
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Residues in contact with MET 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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51A PHE* 3.7 20.2 - - + -
77A LEU* 3.8 28.5 - - + +
78A TRP* 4.5 2.9 - - + -
81A TYR* 3.7 19.3 - - + +
403A AFB 3.5 32.3 - - + +
190E TYR* 2.8 39.8 + - + +
191E SER* 3.2 9.6 + - - +
193E ILE* 1.3 75.3 - - - +
195E LEU* 1.3 51.0 + - - +
197E THR* 3.2 4.2 + - - -
198E ASP* 2.6 37.6 + - - +
208E MET* 4.7 0.7 - - - -
216E MET* 3.5 28.9 - - + -
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Residues in contact with LEU 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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191E SER 2.7 19.9 + - - +
192E VAL* 3.4 6.7 - - + +
194E MET* 1.3 72.6 - - - +
196E ASN* 1.3 64.6 + - - +
198E ASP* 4.1 0.7 - - + -
199E LEU* 2.9 37.3 + - + +
208E MET* 3.7 25.8 - - + +
213E PHE* 3.9 22.7 - - + -
234E LEU 4.8 0.2 - - - -
235E TYR* 3.7 57.9 - - + +
238E ILE* 3.9 23.6 - - + -
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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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48A THR* 4.1 4.3 - - - +
49A ILE* 2.8 32.3 + - - +
192E VAL 2.7 19.4 + - - +
193E ILE* 3.3 5.4 + - - +
195E LEU* 1.3 73.4 - - - +
197E THR* 1.4 56.5 + - - +
200E HIS* 2.9 44.0 + - - +
201E ASN 4.1 0.3 + - - -
238E ILE* 3.7 15.8 - - + +
242E PRO* 3.3 14.7 - - - +
243E PHE* 3.0 52.2 + - + +
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Residues in contact with THR 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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48A THR* 4.4 5.6 - - + -
49A ILE 4.4 3.8 - - - -
50A GLY* 3.2 6.8 - - - -
51A PHE* 3.0 40.7 + - + +
53A VAL* 3.6 31.6 - - + -
403A AFB 3.9 10.3 - - + -
193E ILE 3.1 13.3 + - - -
194E MET 3.5 7.4 - - - -
196E ASN* 1.4 76.4 + - - +
198E ASP* 1.3 65.4 + - - +
201E ASN* 3.1 32.1 + - + +
204E VAL* 3.8 1.6 - - + +
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Residues in contact with ASP 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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81A TYR* 2.7 36.3 + - - +
403A AFB 3.8 11.0 - - + +
194E MET 2.6 22.0 + - - +
195E LEU* 3.6 8.3 - - - +
197E THR* 1.3 75.4 - - - +
199E LEU* 1.3 56.7 + - + +
204E VAL* 3.6 14.6 - - - +
206E ASP 4.3 1.7 - - - +
207E LYS* 2.7 40.8 + - - +
208E MET* 2.8 40.6 + - + +
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Residues in contact with LEU 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 LEU* 2.9 39.5 + - + +
198E ASP* 1.3 88.2 - - - +
200E HIS* 1.3 76.0 + - + +
207E LYS* 3.4 29.3 + - + +
208E MET 3.5 24.7 - - - +
235E TYR* 4.3 8.7 - - + +
238E ILE* 4.4 2.5 - - + -
239E ARG* 3.6 42.0 - - + +
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Residues in contact with HIS 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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46A ILE* 4.5 6.4 - - - +
48A THR* 3.4 17.0 + - + -
196E ASN* 2.9 43.7 + - - +
199E LEU* 1.3 94.0 + - + +
201E ASN* 1.3 61.2 + - - +
202E PRO* 3.3 13.4 - - - +
207E LYS* 4.8 0.2 - - - -
238E ILE* 2.7 27.1 + - + -
239E ARG* 3.4 21.5 - - + -
242E PRO* 3.6 30.1 - - + +
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Residues in contact with ASN 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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46A ILE 5.9 0.4 + - - -
48A THR* 3.6 23.5 + - + +
51A PHE 4.1 10.5 + - - -
52A ASN* 5.6 0.2 - - - +
53A VAL* 3.8 26.9 + - - +
197E THR* 3.1 23.0 + - + +
200E HIS* 1.3 75.5 - - - +
202E PRO* 1.3 68.4 - - - +
203E ASN* 2.9 48.8 + - - +
204E VAL* 3.0 14.1 + - + +
207E LYS* 3.1 12.3 + - - -
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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