Contacts of the helix formed by residues 160 - 180 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C HIS* 6.1 4.9 - - - -
119D THR* 4.3 3.8 - - - +
122D GLU* 2.6 31.5 + - - -
157D ARG 4.9 6.1 - - - -
158D THR 2.2 17.9 + - - -
159D PRO* 1.3 69.0 - - - +
161D ALA* 1.3 68.0 + - - +
162D LEU* 3.9 8.1 + - - +
163D ALA* 2.8 23.1 + - - +
164D ILE* 2.8 13.8 + - - +
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Residues in contact with ALA 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B ALA* 5.8 8.5 - - + -
159D PRO 4.1 0.8 + - - -
160D SER* 1.3 71.5 - - - +
162D LEU* 1.3 52.2 + - - +
164D ILE* 3.3 8.0 + - - +
165D LEU* 2.7 42.1 + - + +
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Residues in contact with LEU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C ASP* 3.5 28.7 - - - +
220C HIS* 3.6 44.6 - - + +
221C HIS* 3.6 29.8 - - + +
116D LEU* 4.0 14.4 - - + -
117D ALA 4.5 4.3 - - - +
119D THR* 3.9 14.1 - - + -
160D SER* 2.9 8.7 + - - +
161D ALA* 1.3 78.7 - - - +
163D ALA* 1.3 56.1 + - - +
165D LEU* 3.1 11.2 + - + +
166D GLU* 2.7 38.9 + - + +
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Residues in contact with ALA 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D LEU* 3.8 18.3 - - + +
122D GLU* 2.9 34.5 - - + +
123D THR 4.7 0.4 - - - +
152D LEU* 3.8 14.0 - - + +
159D PRO 4.6 0.9 - - - -
160D SER* 2.8 17.0 + - - +
162D LEU* 1.3 76.1 - - - +
164D ILE* 1.3 52.1 + - - +
166D GLU 2.6 21.1 - - - +
167D ASN* 2.6 24.7 + - - +
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Residues in contact with ILE 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A HIS* 6.2 0.9 - - + -
152D LEU* 4.6 7.0 - - + -
159D PRO* 3.6 35.0 - - + +
160D SER 2.8 19.9 + - - +
161D ALA* 3.8 5.8 - - - +
163D ALA* 1.3 68.3 - - - +
165D LEU* 1.3 58.7 + - - +
166D GLU 2.5 18.4 - - - +
167D ASN* 5.0 0.4 - - - -
168D ALA* 3.0 20.7 + - + +
205D VAL* 6.0 0.2 - - + -
208D LYS* 4.7 10.1 - - + +
209D VAL* 4.4 29.2 - - + +
212D ALA* 3.5 29.4 - - + -
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Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C ASN* 3.3 28.3 - - - +
219C ASP* 3.7 35.4 - - + +
220C HIS* 3.9 7.9 - - + +
161D ALA* 2.7 23.3 + - + +
162D LEU* 3.4 8.3 - - + +
164D ILE* 1.3 70.9 - - - +
166D GLU* 1.3 87.5 + - + +
168D ALA* 3.6 3.5 - - - +
169D ASN* 3.1 24.4 + - + +
212D ALA* 6.1 0.7 - - - -
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Residues in contact with GLU 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C LEU* 5.3 1.7 - - - +
169C ASN* 3.0 29.1 + - - -
173C ARG* 3.0 31.5 + - - +
220C HIS* 3.8 9.6 - - + -
116D LEU* 4.4 9.4 - - + -
124D THR* 3.0 35.9 + - - +
125D THR 5.4 0.7 - - - +
162D LEU* 2.7 20.3 + - + +
163D ALA 2.6 13.7 - - - +
164D ILE 2.5 20.1 - - - +
165D LEU* 1.3 81.8 - - + +
167D ASN* 1.3 58.3 + - - +
169D ASN* 4.3 4.0 - - - +
170D VAL* 3.3 15.8 - - - +
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Residues in contact with ASN 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D LEU* 4.7 0.4 - - - +
123D THR 3.0 23.8 + - - +
124D THR* 3.5 17.4 - - - +
150D CYS* 3.3 30.3 - - + +
151D VAL 4.2 2.8 + - - -
152D LEU* 3.5 23.7 - - + +
163D ALA* 2.6 25.4 + - - +
164D ILE 4.2 0.9 - - - +
166D GLU* 1.3 82.1 + - - +
168D ALA* 1.3 56.8 + - - +
169D ASN 3.0 0.4 - - - -
170D VAL* 3.1 15.2 - - - +
171D LEU* 2.7 42.0 + - + +
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Residues in contact with ALA 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ILE* 3.0 19.5 + - + +
165D LEU* 3.6 4.0 - - - +
166D GLU 2.8 6.9 + - - -
167D ASN* 1.3 74.7 - - - +
169D ASN* 1.3 61.4 + - - +
171D LEU* 3.6 11.7 + - - +
172D ALA 3.2 16.3 + - - -
212D ALA* 4.1 11.9 - - + +
213D VAL* 4.0 32.2 - - + +
216D ALA* 3.4 16.2 - - + +
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Residues in contact with ASN 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C LEU* 3.4 16.1 - - - +
166C GLU* 2.9 25.5 + - - -
169C ASN* 3.3 29.8 - - - +
165D LEU* 3.1 18.9 + - + +
166D GLU* 4.3 4.9 + - - +
167D ASN 3.0 0.4 - - - -
168D ALA* 1.3 76.6 - - - +
170D VAL* 1.3 66.7 + - - +
172D ALA* 3.1 7.4 + - - +
173D ARG* 2.9 24.3 + - - +
216D ALA* 4.5 4.1 - - - +
220D HIS* 2.8 25.3 + - - -
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Residues in contact with VAL 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D THR* 3.5 10.3 - - - +
125D THR 3.5 10.8 - - - +
128D LEU* 4.3 14.3 - - + +
148D TRP* 3.3 37.9 - - + +
150D CYS* 4.6 1.3 - - - -
166D GLU* 3.3 24.2 - - - +
167D ASN* 3.0 27.6 + - - +
169D ASN* 1.3 74.9 - - - +
171D LEU* 1.3 64.8 + - - +
173D ARG* 3.1 7.4 + - - +
174D TYR* 2.9 22.6 + - - +
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Residues in contact with LEU 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D TRP* 3.6 27.1 - - + +
150D CYS* 3.6 23.6 - - + -
167D ASN* 2.7 25.9 + - + +
168D ALA* 3.7 4.3 - - - +
170D VAL* 1.3 74.7 - - - +
172D ALA* 1.3 52.9 + - - +
174D TYR* 3.2 9.1 + - + -
175D ALA* 2.8 36.7 + - - +
187D VAL* 3.5 36.6 - - + -
188D GLU 4.0 4.9 - - - +
189D PRO* 3.8 27.4 - - + -
213D VAL* 4.2 15.3 - - + -
217D LEU* 4.7 1.6 - - + -
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Residues in contact with ALA 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ALA 3.2 11.2 + - - +
169D ASN 3.1 6.6 + - - +
171D LEU* 1.3 79.3 - - - +
173D ARG* 1.3 62.7 + - - +
176D SER* 2.9 25.6 + - - -
216D ALA* 3.8 17.0 - - + +
217D LEU* 3.7 16.3 - - - +
220D HIS* 3.4 35.5 - - + +
222D VAL* 3.6 4.2 - - - +
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Residues in contact with ARG 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C VAL* 4.0 10.9 - - - +
115C PRO 3.6 22.0 + - - -
116C LEU* 4.0 12.9 - - - +
117C ALA 5.4 0.6 - - - +
124C THR* 3.4 23.5 - - - +
125C THR 5.6 1.6 + - - -
126C GLN* 6.1 1.2 - - - +
166C GLU* 3.0 31.1 + - - +
128D LEU* 3.7 29.7 - - + +
169D ASN* 2.9 17.6 + - - +
170D VAL* 3.1 8.7 + - - +
172D ALA* 1.3 76.1 - - - +
174D TYR* 1.3 64.5 + - - +
176D SER* 3.1 13.3 + - - -
177D ILE* 3.0 59.2 + - - +
220D HIS* 3.8 17.9 + - + -
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Residues in contact with TYR 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D VAL* 3.6 16.2 - - + -
128D LEU* 3.7 8.9 - - + +
131D LEU* 4.0 7.8 - - + +
146D ALA* 3.0 25.9 + - + -
147D LYS* 3.3 1.4 - - - -
148D TRP* 3.3 60.6 - + + -
170D VAL 2.9 11.7 + - - +
171D LEU* 3.4 17.0 - - + +
173D ARG* 1.3 75.5 - - - +
175D ALA* 1.3 69.6 + - + -
177D ILE* 3.2 4.0 + - - +
178D CYS* 3.0 46.6 + - - -
185D PRO* 3.5 15.1 - - + +
186D ILE 2.9 31.8 + - - -
187D VAL* 4.4 6.5 - - + -
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Residues in contact with ALA 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D LEU 2.8 20.3 + - - +
172D ALA 3.7 0.4 - - - +
174D TYR* 1.3 74.7 - - + +
176D SER* 1.3 63.8 + - - +
178D CYS* 3.2 2.9 + - - +
179D GLN* 3.1 28.3 + - - +
185D PRO* 3.8 27.6 - - + -
187D VAL* 4.5 5.8 - - + -
217D LEU* 3.9 11.4 - - + -
222D VAL* 3.6 23.1 - - + -
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Residues in contact with SER 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C ALA* 3.3 28.5 + - - +
172D ALA 2.9 18.3 + - - -
173D ARG* 3.4 13.2 + - - -
175D ALA* 1.3 76.9 - - - +
177D ILE* 1.3 64.9 + - - +
179D GLN* 3.5 6.5 + - - +
180D GLN* 3.3 22.5 + - - +
220D HIS* 3.7 23.4 + - - -
221D HIS 5.5 0.9 + - - -
222D VAL* 3.7 9.3 - - - +
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Residues in contact with ILE 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D LEU* 3.9 28.5 - - + +
131D LEU* 4.0 20.4 - - + +
132D SER* 3.5 42.0 - - - +
135D CYS* 4.8 0.4 - - - -
173D ARG* 3.0 44.5 + - - +
174D TYR 3.6 4.9 - - - +
176D SER* 1.3 73.0 - - - +
178D CYS* 1.3 67.7 + - - +
180D GLN* 3.1 26.7 - - - +
181D ASN* 3.1 9.3 + - - +
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Residues in contact with CYS 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D VAL* 5.1 0.2 - - - -
131D LEU* 4.8 1.8 - - - -
135D CYS* 4.0 24.0 - - - -
146D ALA* 4.1 13.2 - - - -
174D TYR* 3.0 47.2 + - - -
175D ALA 3.6 7.2 - - - +
177D ILE* 1.3 77.1 - - - +
179D GLN* 1.3 57.9 + - - +
181D ASN* 2.8 20.6 + - - +
183D ILE* 3.1 35.1 + - + +
185D PRO* 3.8 10.5 - - + -
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Residues in contact with GLN 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 3.5 21.4 - - + +
12D GLN* 5.4 1.9 + - - +
16D LEU* 3.8 20.0 - - + +
175D ALA 3.1 15.2 + - - +
176D SER* 3.9 5.2 - - - +
177D ILE 3.3 0.2 - - - -
178D CYS* 1.3 71.8 - - - +
180D GLN* 1.3 58.2 + - - +
181D ASN 2.9 9.5 + - - -
182D GLY* 3.1 12.1 + - - -
183D ILE 3.8 4.9 - - - +
185D PRO* 3.8 12.3 - - + -
221D HIS 4.8 0.7 - - - +
222D VAL* 3.7 12.3 - - - +
223D TYR* 2.8 59.1 + - - +
226D GLY* 3.0 23.8 + - - -
227D THR* 3.5 4.0 - - - +
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Residues in contact with GLN 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C PRO* 5.0 19.9 + - - +
117C ALA* 3.8 28.3 - - + +
7D ALA 5.3 3.6 - - - +
8D LEU* 4.1 12.5 - - + +
12D GLN* 4.8 10.4 + - - +
132D SER* 3.5 18.2 + - - -
176D SER 3.3 11.1 + - - +
177D ILE* 3.1 27.5 - - - +
179D GLN* 1.3 76.3 - - - +
181D ASN* 1.3 62.4 + - - +
182D GLY 3.5 0.8 + - - -
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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