Contacts of the helix formed by residues 160 - 180 (chain E) in PDB entry 1XFB
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 160 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E THR* 4.3 3.8 - - - +
122E GLU* 2.6 31.2 + - - -
157E ARG 4.9 5.4 - - - -
158E THR 2.2 16.5 + - - +
159E PRO* 1.3 69.6 - - - +
161E ALA* 1.3 69.3 + - - +
162E LEU* 3.9 8.5 + - - +
163E ALA* 2.7 23.2 + - - +
164E ILE* 2.8 15.3 + - - +
3F HIS* 6.3 2.7 - - - -
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Residues in contact with ALA 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E PRO 4.1 1.0 + - - -
160E SER* 1.3 70.7 - - - +
162E LEU* 1.3 52.1 - - - +
164E ILE* 3.3 8.0 + - - +
165E LEU* 2.7 42.0 + - + +
161G ALA* 5.0 16.8 - - + -
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Residues in contact with LEU 162 (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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116E LEU* 4.0 14.4 - - + -
117E ALA 4.5 3.8 - - - +
119E THR* 3.9 13.5 - - + -
160E SER* 2.9 8.9 + - - +
161E ALA* 1.3 78.8 - - - +
163E ALA* 1.3 56.2 + - - +
165E LEU* 3.1 11.8 + - + +
166E GLU* 2.7 38.5 + - + +
219F ASP* 3.3 33.9 - - + +
220F HIS* 3.6 42.0 - - + +
221F HIS* 3.8 26.2 - - + +
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Residues in contact with ALA 163 (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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116E LEU* 3.8 17.7 - - + +
122E GLU* 2.9 33.9 - - + +
123E THR 4.7 0.9 - - - +
152E LEU* 3.8 13.2 - - + +
159E PRO 4.6 1.1 - - - -
160E SER* 2.7 17.8 + - - +
162E LEU* 1.3 75.9 - - - +
164E ILE* 1.3 53.1 + - - +
166E GLU 2.6 20.6 - - - +
167E ASN* 2.6 25.1 + - - +
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Residues in contact with ILE 164 (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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152E LEU* 4.6 6.5 - - + -
159E PRO* 3.6 35.4 - - + +
160E SER 2.8 20.1 + - - +
161E ALA* 3.8 6.1 - - - +
163E ALA* 1.3 69.0 - - - +
165E LEU* 1.3 59.1 + - - +
166E GLU 2.5 18.8 - - - +
167E ASN* 4.2 0.6 - - - +
168E ALA* 3.0 20.2 + - + +
205E VAL* 6.0 0.4 - - + -
208E LYS* 4.7 9.9 - - + +
209E VAL* 4.4 30.3 - - + +
212E ALA* 3.5 28.5 - - + -
3H HIS* 5.9 1.8 - - + -
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Residues in contact with LEU 165 (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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161E ALA* 2.7 24.0 + - + +
162E LEU* 3.4 9.2 - - + +
164E ILE* 1.3 71.1 - - - +
166E GLU* 1.3 88.4 + - + +
168E ALA* 3.6 3.5 - - - +
169E ASN* 3.1 24.7 + - + +
212E ALA* 6.1 0.9 - - - -
169F ASN* 3.4 28.3 - - - +
219F ASP* 3.8 30.5 - - + +
220F HIS* 4.2 4.5 - - - +
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Residues in contact with GLU 166 (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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116E LEU* 4.4 10.8 - - + -
124E THR* 3.0 34.8 + - - +
125E THR 5.4 0.3 - - - +
162E LEU* 2.7 19.9 + - + +
163E ALA 2.6 13.7 - - - +
164E ILE 2.5 20.1 - - - +
165E LEU* 1.3 81.9 - - + +
167E ASN* 1.3 58.0 + - - +
169E ASN* 4.3 4.4 - - - +
170E VAL* 3.3 16.4 - - - +
128F LEU* 5.3 1.7 - - - +
169F ASN* 2.8 31.2 + - - -
173F ARG* 3.1 28.3 + - - +
220F HIS* 3.9 10.0 - - + -
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Residues in contact with ASN 167 (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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116E LEU* 4.7 0.4 - - - +
123E THR 3.0 23.6 + - - +
124E THR* 3.5 18.3 - - - +
150E CYS* 3.3 30.7 - - + +
151E VAL 4.2 2.9 + - - -
152E LEU* 3.5 23.3 - - + +
163E ALA* 2.6 23.9 + - - +
164E ILE* 4.2 1.1 - - - +
166E GLU* 1.3 80.9 + - - +
168E ALA* 1.3 56.7 + - - +
169E ASN 3.0 0.2 - - - -
170E VAL* 3.1 15.2 - - - +
171E LEU* 2.7 41.6 + - + +
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Residues in contact with ALA 168 (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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164E ILE* 3.0 19.7 + - + +
165E LEU* 3.6 3.6 - - - +
166E GLU 2.8 7.1 + - - -
167E ASN* 1.3 74.5 - - - +
169E ASN* 1.3 62.0 + - - +
171E LEU* 3.6 12.3 + - - +
172E ALA 3.2 16.5 + - - -
212E ALA* 4.1 11.9 - - + +
213E VAL* 4.0 32.6 - - + +
216E ALA* 3.4 15.5 - - + +
217E LEU* 5.8 0.2 - - - +
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Residues in contact with ASN 169 (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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165E LEU* 3.1 19.6 + - + +
166E GLU* 4.3 8.9 + - - +
167E ASN 3.0 0.4 - - - -
168E ALA* 1.3 75.2 - - - +
170E VAL* 1.3 65.6 + - - +
172E ALA* 3.1 6.9 + - - +
173E ARG* 2.9 24.4 + - - +
216E ALA* 4.3 4.9 - - + +
220E HIS* 2.8 25.1 + - - -
165F LEU* 3.5 17.2 - - - +
166F GLU* 2.8 27.1 + - - -
169F ASN* 3.6 21.3 - - - +
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Residues in contact with VAL 170 (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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124E THR* 3.5 10.1 - - - +
125E THR 3.5 10.8 - - - +
128E LEU* 4.3 14.6 - - + -
148E TRP* 3.3 39.3 - - + +
150E CYS* 4.6 1.6 - - - -
166E GLU* 3.3 24.0 - - - +
167E ASN* 3.0 28.2 + - - +
169E ASN* 1.3 75.3 - - - +
171E LEU* 1.3 65.7 + - - +
173E ARG* 3.1 7.9 + - - +
174E TYR* 2.9 22.9 + - - +
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Residues in contact with LEU 171 (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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148E TRP* 3.6 27.6 - - + +
150E CYS* 3.6 23.6 - - + -
167E ASN* 2.7 25.9 + - + +
168E ALA* 3.7 4.0 - - - +
170E VAL* 1.3 74.6 - - - +
172E ALA* 1.3 53.0 + - - +
174E TYR* 3.2 9.1 + - + -
175E ALA* 2.8 37.3 + - - +
187E VAL* 3.5 35.7 - - + -
188E GLU 4.0 5.2 - - - +
189E PRO* 3.8 26.9 - - + -
213E VAL* 4.2 15.3 - - + -
217E LEU* 4.7 1.8 - - + -
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Residues in contact with ALA 172 (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 3.2 11.2 + - - +
169E ASN 3.1 7.7 + - - +
171E LEU* 1.3 79.9 - - - +
173E ARG* 1.3 62.1 + - - +
176E SER* 2.9 25.6 + - - -
216E ALA* 3.8 16.6 - - + +
217E LEU* 3.7 16.8 - - + +
220E HIS* 3.4 34.9 - - + +
222E VAL* 3.6 4.0 - - - +
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Residues in contact with ARG 173 (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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128E LEU* 3.7 28.9 - - + +
169E ASN* 2.9 17.8 + - - +
170E VAL* 3.1 8.0 + - - +
172E ALA* 1.3 76.7 - - - +
174E TYR* 1.3 64.4 + - - +
176E SER* 3.1 12.1 + - - -
177E ILE* 3.0 60.3 + - - +
220E HIS* 3.8 18.3 + - + -
114F VAL* 3.9 10.3 - - - +
115F PRO 3.5 23.4 + - - -
116F LEU* 4.0 12.0 - - - +
117F ALA 5.3 0.6 - - - +
124F THR* 3.3 24.5 - - - +
125F THR 5.6 1.4 + - - -
126F GLN* 6.1 1.4 - - - +
166F GLU* 3.1 31.6 + - - +
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Residues in contact with TYR 174 (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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109E VAL* 3.6 16.4 - - + -
128E LEU* 3.7 8.8 - - - +
131E LEU* 4.0 7.6 - - + +
146E ALA* 3.0 25.3 + - + -
147E LYS* 3.3 1.6 - - - -
148E TRP* 3.3 58.8 - + + -
170E VAL 2.9 11.8 + - - +
171E LEU* 3.4 16.4 - - + +
173E ARG* 1.3 76.2 - - - +
175E ALA* 1.3 71.9 + - + +
177E ILE* 3.2 4.0 + - - +
178E CYS* 3.0 45.6 + - - -
185E PRO* 3.5 14.9 - - + +
186E ILE 2.9 31.4 + - - -
187E VAL* 4.4 7.0 - - + -
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Residues in contact with ALA 175 (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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171E LEU 2.8 20.4 + - - +
172E ALA 3.7 0.2 - - - +
174E TYR* 1.3 75.4 - - + +
176E SER* 1.3 64.8 + - - +
178E CYS* 3.2 3.5 + - - +
179E GLN* 3.1 27.2 + - - +
185E PRO* 3.8 27.8 - - + +
187E VAL* 4.5 5.8 - - + -
217E LEU* 3.9 11.7 - - + -
222E VAL* 3.6 22.9 - - + -
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Residues in contact with SER 176 (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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172E ALA 2.9 18.9 + - - -
173E ARG* 3.4 13.1 + - - -
175E ALA* 1.3 76.4 - - - +
177E ILE* 1.3 64.3 + - - +
179E GLN* 3.5 6.7 + - - +
180E GLN* 3.3 23.0 + - - +
220E HIS* 3.7 21.0 + - - -
221E HIS 5.5 0.7 + - - -
222E VAL* 3.7 8.6 - - - +
117F ALA* 3.2 30.3 + - - +
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Residues in contact with ILE 177 (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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128E LEU* 3.9 28.7 - - + +
131E LEU* 4.0 19.3 - - + -
132E SER* 3.5 42.0 - - - +
135E CYS* 4.8 0.4 - - - -
173E ARG* 3.0 44.3 + - - +
174E TYR 3.6 5.2 - - - +
176E SER* 1.3 72.5 - - - +
178E CYS* 1.3 67.7 + - - +
180E GLN* 3.1 27.5 - - - +
181E ASN* 3.1 9.7 + - - +
114F VAL* 6.3 0.4 - - + -
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Residues in contact with CYS 178 (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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109E VAL* 5.1 0.4 - - - -
131E LEU* 4.8 1.1 - - - -
135E CYS* 4.0 24.9 - - - -
146E ALA* 4.1 13.7 - - - -
174E TYR* 3.0 47.7 + - - -
175E ALA 3.6 7.4 - - - +
177E ILE* 1.3 76.3 - - - +
179E GLN* 1.3 58.3 + - - +
181E ASN* 2.8 20.6 + - - +
183E ILE* 3.1 34.9 + - + +
185E PRO* 3.8 10.1 - - + -
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Residues in contact with GLN 179 (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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8E LEU* 3.5 20.3 - - + +
12E GLN* 5.4 1.4 + - - +
16E LEU* 3.8 20.7 - - + +
175E ALA 3.1 13.5 + - - +
176E SER* 3.9 5.2 - - - +
178E CYS* 1.3 72.1 - - - +
180E GLN* 1.3 57.1 + - - +
181E ASN 2.9 9.9 + - - -
182E GLY* 3.1 12.1 + - - -
183E ILE 3.8 4.5 - - - +
185E PRO* 3.8 12.8 - - + -
221E HIS 4.8 0.7 - - - +
222E VAL* 3.7 12.4 - - - +
223E TYR* 2.8 58.4 + - - +
226E GLY* 3.0 23.4 + - - -
227E THR* 3.5 4.6 - - - +
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Residues in contact with GLN 180 (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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7E ALA 5.3 4.5 - - - +
8E LEU* 4.1 13.0 - - + +
12E GLN* 4.8 10.0 + - - +
132E SER* 3.5 18.0 + - - -
176E SER 3.3 10.6 + - - +
177E ILE* 3.1 27.6 - - - +
179E GLN* 1.3 76.9 - - - +
181E ASN* 1.3 61.6 + - - +
182E GLY 3.5 0.7 - - - -
115F PRO* 5.1 20.7 + - - +
117F ALA* 4.0 25.9 - - + +
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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