Contacts of the helix formed by residues 160 - 180 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E HIS* 6.4 2.0 - - - -
119F THR* 4.3 4.1 - - - +
122F GLU* 2.6 31.2 + - - -
157F ARG 4.9 5.4 - - - -
158F THR 2.2 17.7 + - - -
159F PRO* 1.3 68.7 - - - +
161F ALA* 1.3 70.1 + - - +
162F LEU* 3.9 7.9 + - - +
163F ALA* 2.8 24.0 + - - +
164F ILE* 2.8 14.2 + - - +
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Residues in contact with ALA 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F PRO 4.1 0.8 + - - -
160F SER* 1.3 70.7 - - - +
162F LEU* 1.3 54.0 + - - +
164F ILE* 3.3 7.8 + - - +
165F LEU* 2.7 41.2 + - + +
161H ALA* 5.3 13.2 - - + -
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Residues in contact with LEU 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E ASP* 3.4 29.2 - - + +
220E HIS* 3.7 41.7 - - + +
221E HIS* 3.8 25.1 - - + +
116F LEU* 4.0 14.4 - - + -
117F ALA 4.5 3.8 - - - +
119F THR* 3.9 14.6 - - + -
160F SER* 2.9 9.6 + - - +
161F ALA* 1.3 79.0 - - - +
163F ALA* 1.3 56.7 + - - +
165F LEU* 3.1 15.0 + - + +
166F GLU* 2.7 37.7 + - + +
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Residues in contact with ALA 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F LEU* 3.8 17.4 - - + +
122F GLU* 2.9 34.3 - - + +
123F THR 4.7 0.7 - - - +
152F LEU* 3.8 12.0 - - + +
159F PRO* 4.6 1.1 - - + -
160F SER* 2.8 17.8 + - - +
162F LEU* 1.3 75.7 - - - +
164F ILE* 1.3 51.7 + - - +
166F GLU 2.6 21.7 - - - +
167F ASN* 2.6 24.0 + - - +
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Residues in contact with ILE 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F LEU* 4.6 6.7 - - + -
159F PRO* 3.6 35.0 - - + +
160F SER 2.8 21.8 + - - +
161F ALA* 3.8 5.4 - - - +
163F ALA* 1.3 68.7 - - - +
165F LEU* 1.3 59.0 + - - +
166F GLU 2.5 18.7 - - - +
167F ASN* 5.0 0.4 - - - -
168F ALA* 3.0 20.8 + - + +
205F VAL* 6.0 0.4 - - + -
208F LYS* 4.7 9.9 - - + +
209F VAL* 4.4 29.6 - - + +
212F ALA* 3.5 28.3 - - + -
3G HIS* 6.1 1.3 - - + -
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Residues in contact with LEU 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E ASN* 3.5 28.7 - - - +
219E ASP* 3.9 31.0 - - + +
220E HIS* 4.3 4.7 - - - +
161F ALA* 2.7 24.6 + - + +
162F LEU* 3.4 9.2 - - + +
164F ILE* 1.3 72.0 - - - +
166F GLU* 1.3 88.5 + - + +
168F ALA* 3.6 3.3 - - - +
169F ASN* 3.1 24.3 + - + +
212F ALA* 6.1 0.7 - - - -
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Residues in contact with GLU 166 (chain F).
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* 5.3 1.6 - - - +
169E ASN* 2.8 30.9 + - - -
173E ARG* 3.1 27.6 + - - +
220E HIS* 4.0 10.3 - - + -
116F LEU* 4.4 10.8 - - + -
124F THR* 3.0 35.9 + - - +
125F THR 5.4 0.5 - - - +
162F LEU* 2.7 19.9 + - + +
163F ALA 2.6 13.5 - - - +
164F ILE 2.5 20.1 - - - +
165F LEU* 1.3 81.6 - - + +
167F ASN* 1.3 58.2 + - - +
168F ALA 3.1 0.4 - - - -
169F ASN* 3.9 4.2 - - - +
170F VAL* 3.3 16.4 - - - +
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Residues in contact with ASN 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F LEU* 4.7 0.8 - - - +
123F THR 3.0 23.4 + - - +
124F THR* 3.5 18.1 - - - +
150F CYS* 3.3 30.5 - - + +
151F VAL 4.2 2.8 + - - -
152F LEU* 3.5 23.1 - - + +
163F ALA* 2.6 24.7 + - - +
164F ILE* 4.2 0.9 - - - +
166F GLU* 1.3 81.4 + - - +
168F ALA* 1.3 55.2 + - - +
169F ASN 3.0 0.4 - - - -
170F VAL* 3.1 15.4 - - - +
171F LEU* 2.7 42.5 + - + +
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Residues in contact with ALA 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F ILE* 3.0 19.2 + - + +
165F LEU* 3.6 4.0 - - - +
166F GLU 2.8 6.9 + - - -
167F ASN* 1.3 74.3 - - - +
169F ASN* 1.3 62.7 + - - +
171F LEU* 3.6 12.2 + - - +
172F ALA* 3.2 16.8 + - - +
212F ALA* 4.1 11.7 - - + +
213F VAL* 4.0 32.7 - - + +
216F ALA* 3.4 15.8 - - + +
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Residues in contact with ASN 169 (chain F).
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* 3.4 17.0 - - - +
166E GLU* 2.8 26.5 + - - -
169E ASN* 3.6 23.2 - - - +
165F LEU* 3.1 19.8 + - + +
166F GLU* 4.3 8.0 + - - +
167F ASN 3.0 0.4 - - - -
168F ALA* 1.3 76.2 - - - +
170F VAL* 1.3 66.2 + - - +
172F ALA* 3.1 7.5 + - - +
173F ARG* 2.9 24.4 + - - +
216F ALA* 4.3 5.1 - - - +
220F HIS* 2.8 25.2 + - - -
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Residues in contact with VAL 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F THR* 3.5 10.3 - - - +
125F THR 3.5 10.8 - - - +
128F LEU* 4.3 13.9 - - + -
148F TRP* 3.3 38.4 - - + +
150F CYS* 4.6 0.7 - - - -
166F GLU* 3.3 24.0 - - - +
167F ASN* 3.0 27.8 + - - +
169F ASN* 1.3 75.5 - - - +
171F LEU* 1.3 65.8 + - - +
173F ARG* 3.1 8.3 + - - +
174F TYR* 2.9 22.6 + - - +
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Residues in contact with LEU 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F TRP* 3.6 27.8 - - + +
150F CYS* 3.6 22.9 - - + -
167F ASN* 2.7 25.9 + - + +
168F ALA* 3.7 3.8 - - - +
170F VAL* 1.3 74.9 - - - +
172F ALA* 1.3 52.9 + - - +
174F TYR* 3.2 9.0 + - + -
175F ALA* 2.8 37.3 + - - +
187F VAL* 3.5 36.1 - - + -
188F GLU 4.0 5.6 - - - +
189F PRO* 3.8 25.8 - - + -
213F VAL* 4.2 15.7 - - + -
217F LEU* 4.7 2.0 - - + -
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Residues in contact with ALA 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F ALA 3.2 10.7 + - - +
169F ASN 3.1 7.0 + - - +
171F LEU* 1.3 78.9 - - - +
173F ARG* 1.3 61.8 + - - +
176F SER* 2.9 25.5 + - - -
216F ALA* 3.8 17.9 - - + +
217F LEU* 3.7 16.9 - - - +
220F HIS* 3.4 34.8 - - + +
222F VAL* 3.6 3.8 - - - +
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Residues in contact with ARG 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E VAL* 3.8 11.3 - - - +
115E PRO 3.4 23.8 + - - -
116E LEU* 3.9 12.8 - - - +
117E ALA 5.2 0.4 - - - +
124E THR* 3.2 25.1 - - - +
125E THR 5.6 1.6 + - - -
126E GLN* 6.1 0.8 - - - +
166E GLU* 3.1 32.1 + - - +
128F LEU* 3.7 28.8 - - + +
169F ASN* 2.9 17.4 + - - +
170F VAL* 3.4 7.9 - - - +
172F ALA* 1.3 75.9 - - - +
174F TYR* 1.3 65.1 + - - +
176F SER* 3.1 12.2 + - - -
177F ILE* 3.0 59.7 + - - +
220F HIS* 3.8 17.7 + - + -
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Residues in contact with TYR 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F VAL* 3.6 16.8 - - + -
128F LEU* 3.7 8.9 - - - +
131F LEU* 4.0 7.1 - - + +
146F ALA* 3.0 26.1 + - + -
147F LYS* 3.3 1.2 - - - -
148F TRP* 3.3 60.6 - + + -
170F VAL 2.9 11.8 + - - +
171F LEU* 3.4 16.2 - - + +
173F ARG* 1.3 76.0 - - - +
175F ALA* 1.3 72.0 + - + +
177F ILE* 3.2 3.8 + - - +
178F CYS* 3.0 44.8 + - - -
185F PRO* 3.5 15.6 - - + +
186F ILE 2.9 31.8 + - - -
187F VAL* 4.4 6.1 - - + -
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Residues in contact with ALA 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F LEU 2.8 20.1 + - - +
174F TYR* 1.3 74.5 - - + +
176F SER* 1.3 66.0 + - - +
178F CYS* 3.2 3.3 + - - +
179F GLN* 3.1 27.6 + - - +
185F PRO* 3.8 27.8 - - + -
187F VAL* 4.5 5.8 - - + -
217F LEU* 3.9 11.4 - - + -
222F VAL* 3.6 23.1 - - + -
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Residues in contact with SER 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E ALA* 3.1 31.8 + - - +
172F ALA 2.9 17.9 + - - -
173F ARG* 3.4 12.2 + - - -
175F ALA* 1.3 76.5 - - - +
177F ILE* 1.3 64.9 + - - +
179F GLN* 3.5 6.1 + - - +
180F GLN* 3.3 22.8 + - - +
220F HIS* 3.7 22.2 + - - -
221F HIS 5.5 0.6 + - - -
222F VAL* 3.7 8.6 - - - +
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Residues in contact with ILE 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E VAL* 6.2 0.9 - - + -
128F LEU* 3.9 28.9 - - + +
131F LEU* 4.0 19.7 - - + -
132F SER* 3.5 42.2 - - - +
135F CYS* 4.8 0.7 - - - -
173F ARG* 3.0 44.7 + - - +
174F TYR 3.6 5.2 - - - +
176F SER* 1.3 73.2 - - - +
178F CYS* 1.3 66.5 + - - +
180F GLN* 3.1 26.4 - - - +
181F ASN* 3.1 10.0 + - - +
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Residues in contact with CYS 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F VAL* 5.1 0.4 - - - -
131F LEU* 4.8 1.6 - - - -
135F CYS* 4.0 24.5 - - - -
146F ALA* 4.1 12.8 - - - -
174F TYR* 3.0 47.4 + - - -
175F ALA 3.6 6.5 - - - +
177F ILE* 1.3 76.3 - - - +
179F GLN* 1.3 58.7 + - - +
181F ASN* 2.8 21.1 + - - +
183F ILE* 3.1 33.5 + - + +
185F PRO* 3.8 10.5 - - + -
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Residues in contact with GLN 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LEU* 3.5 21.0 - - + +
12F GLN* 5.4 1.7 + - - +
16F LEU* 3.8 19.8 - - + +
175F ALA 3.1 15.2 + - - +
176F SER* 3.9 5.0 - - - +
177F ILE 3.3 0.2 - - - -
178F CYS* 1.3 72.2 - - - +
180F GLN* 1.3 58.6 + - - +
181F ASN 2.9 10.1 + - - -
182F GLY* 3.1 12.0 + - - -
183F ILE 3.8 4.7 - - - +
185F PRO* 3.8 12.6 - - + -
221F HIS 4.8 0.9 - - - +
222F VAL* 3.7 11.5 - - - +
223F TYR* 2.8 59.5 + - - +
226F GLY* 3.0 23.6 + - - -
227F THR* 3.5 4.2 - - - +
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Residues in contact with GLN 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E PRO* 4.9 22.5 - - - +
117E ALA* 4.0 26.8 - - + +
7F ALA 5.3 4.0 - - - +
8F LEU* 4.1 12.1 - - + +
12F GLN* 4.8 9.9 + - - +
132F SER* 3.5 18.2 + - - -
176F SER 3.3 10.8 + - - +
177F ILE* 3.1 27.8 - - - +
179F GLN* 1.3 77.7 - - - +
181F ASN* 1.3 63.4 + - - +
182F GLY 3.5 0.6 + - - -
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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