Contacts of the helix formed by residues 160 - 180 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C THR* 4.3 3.6 - - - +
122C GLU* 2.6 31.2 + - - -
157C ARG 4.9 5.4 - - - -
158C THR 2.2 17.3 + - - -
159C PRO* 1.3 69.9 - - - +
161C ALA* 1.3 69.2 + - - +
162C LEU* 3.9 8.3 + - - +
163C ALA* 2.8 23.2 + - - +
164C ILE* 2.8 14.2 + - - +
3D HIS* 6.0 6.5 - - - -
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Residues in contact with ALA 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ALA* 5.8 9.0 - - + -
159C PRO 4.1 0.2 + - - -
160C SER* 1.3 71.4 - - - +
162C LEU* 1.3 52.6 + - - +
164C ILE* 3.3 7.8 + - - +
165C LEU* 2.7 41.8 + - + +
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Residues in contact with LEU 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C LEU* 4.0 14.4 - - + -
117C ALA 4.5 3.4 - - - +
119C THR* 3.9 12.8 - - + -
160C SER* 2.9 9.2 + - - +
161C ALA* 1.3 78.7 - - - +
163C ALA* 1.3 56.2 + - - +
165C LEU* 3.1 11.5 + - + +
166C GLU* 2.7 38.9 + - + +
219D ASP* 3.3 32.5 - - + +
220D HIS* 3.7 42.0 - - + +
221D HIS* 3.5 30.5 - - + +
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Residues in contact with ALA 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C LEU* 3.8 17.7 - - + +
122C GLU* 2.9 34.1 - - + +
123C THR 4.7 0.4 - - - +
152C LEU* 3.8 13.3 - - + +
159C PRO* 4.6 1.1 - - + -
160C SER* 2.8 17.6 + - - +
162C LEU* 1.3 76.4 - - - +
164C ILE* 1.3 53.2 + - - +
166C GLU 2.6 21.1 - - - +
167C ASN* 2.6 24.9 + - - +
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Residues in contact with ILE 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B HIS* 6.2 1.3 - - + -
152C LEU* 4.6 7.4 - - + -
159C PRO* 3.6 35.4 - - + +
160C SER 2.8 21.4 + - - +
161C ALA* 3.8 5.8 - - - +
163C ALA* 1.3 67.0 - - - +
165C LEU* 1.3 58.8 + - - +
166C GLU 2.5 17.9 - - - +
167C ASN* 5.0 0.4 - - - -
168C ALA* 3.0 20.7 + - + +
205C VAL* 6.0 0.2 - - + -
208C LYS* 4.7 10.5 - - + +
209C VAL* 4.4 29.4 - - + +
212C ALA* 3.5 28.7 - - + -
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Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ALA* 2.7 24.2 + - + +
162C LEU* 3.4 8.1 - - + +
164C ILE* 1.3 72.7 - - - +
166C GLU* 1.3 85.6 + - + +
168C ALA* 3.6 3.1 - - - +
169C ASN* 3.1 23.9 + - + +
212C ALA* 6.1 0.9 - - - -
169D ASN* 3.4 27.8 - - - +
219D ASP* 3.5 36.6 - - + +
220D HIS* 4.0 7.6 - - + +
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Residues in contact with GLU 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C LEU* 4.4 11.0 - - + -
124C THR* 3.0 35.9 + - - +
125C THR 5.4 0.5 - - - +
162C LEU* 2.7 19.3 + - + +
163C ALA 2.6 13.4 - - - +
164C ILE 2.5 21.0 - - - +
165C LEU* 1.3 82.2 - - + +
167C ASN* 1.3 57.4 + - - +
168C ALA 3.1 0.2 - - - -
169C ASN* 4.3 3.2 - - - +
170C VAL* 3.3 16.4 - - - +
128D LEU* 5.4 1.0 - - - +
169D ASN* 2.9 29.4 + - - -
173D ARG* 3.0 28.8 + - - +
220D HIS* 3.7 11.9 - - + -
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Residues in contact with ASN 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C LEU* 4.7 0.8 - - - +
123C THR 3.0 22.8 + - - +
124C THR* 3.5 17.6 - - - +
150C CYS* 3.3 31.4 - - + +
151C VAL 4.2 2.8 + - - -
152C LEU* 3.5 23.7 - - + +
163C ALA* 2.6 24.9 + - - +
164C ILE* 4.2 1.1 - - - +
166C GLU* 1.3 81.3 + - - +
168C ALA* 1.3 56.5 + - - +
169C ASN 3.0 0.2 - - - -
170C VAL* 3.1 14.7 - - - +
171C LEU* 2.7 42.7 + - + +
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Residues in contact with ALA 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C ILE* 3.0 19.2 + - + +
165C LEU* 3.6 4.5 - - - +
166C GLU 2.8 7.3 + - - -
167C ASN* 1.3 74.5 - - - +
169C ASN* 1.3 62.7 + - - +
171C LEU* 3.6 11.2 + - - +
172C ALA 3.2 16.6 + - - -
212C ALA* 4.1 11.7 - - + +
213C VAL* 4.0 33.1 - - + +
216C ALA* 3.4 16.5 - - + +
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Residues in contact with ASN 169 (chain C).
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* 3.1 18.7 + - + +
166C GLU* 4.3 8.2 + - - +
167C ASN 3.0 0.6 - - - -
168C ALA* 1.3 76.0 - - - +
170C VAL* 1.3 66.1 + - - +
172C ALA* 3.1 6.8 + - - +
173C ARG* 2.9 24.4 + - - +
216C ALA* 4.5 4.4 - - - +
220C HIS* 2.8 25.7 + - - -
165D LEU* 3.3 15.8 - - - +
166D GLU* 3.0 25.3 + - - -
169D ASN* 3.3 26.5 - - - +
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Residues in contact with VAL 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C THR* 3.5 9.4 - - - +
125C THR 3.5 11.0 - - - +
128C LEU* 4.3 14.8 - - + +
148C TRP* 3.3 37.7 - - + +
150C CYS* 4.6 1.6 - - - -
166C GLU* 3.3 24.0 - - - +
167C ASN* 3.0 28.2 + - - +
169C ASN* 1.3 76.1 - - + +
171C LEU* 1.3 64.6 + - - +
173C ARG* 3.1 7.4 + - - +
174C TYR* 2.9 22.9 + - - +
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Residues in contact with LEU 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C TRP* 3.6 27.4 - - + +
150C CYS* 3.6 22.2 - - + -
167C ASN* 2.7 25.9 + - + +
168C ALA 3.7 3.8 - - - +
170C VAL* 1.3 74.5 - - - +
172C ALA* 1.3 53.8 + - - +
174C TYR* 3.2 9.3 + - + -
175C ALA* 2.8 36.6 + - - +
187C VAL* 3.5 36.1 - - + -
188C GLU 4.0 5.4 - - - +
189C PRO* 3.8 26.7 - - + -
213C VAL* 4.2 15.5 - - + -
217C LEU* 4.7 1.8 - - + -
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Residues in contact with ALA 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C ALA 3.2 10.7 + - - +
169C ASN 3.1 7.0 + - - +
171C LEU* 1.3 78.4 - - - +
173C ARG* 1.3 62.7 + - - +
176C SER* 2.9 25.3 + - - -
216C ALA* 3.8 17.7 - - + +
217C LEU* 3.7 17.0 - - + +
220C HIS* 3.4 34.7 - - + +
222C VAL* 3.6 4.3 - - - +
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Residues in contact with ARG 173 (chain C).
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* 3.7 30.0 - - + +
169C ASN* 2.9 17.8 + - - +
170C VAL* 3.1 8.5 + - - +
172C ALA* 1.3 75.0 - - - +
174C TYR* 1.3 63.5 + - - +
176C SER* 3.1 12.4 + - - -
177C ILE* 3.0 59.5 + - - +
220C HIS* 3.8 18.6 + - + -
114D VAL* 4.1 9.5 - - - +
115D PRO 3.6 21.4 + - - -
116D LEU* 3.9 14.4 - - - +
117D ALA 5.3 0.6 - - - +
124D THR* 3.3 24.4 - - - +
125D THR 5.6 0.8 + - - -
126D GLN* 6.3 0.2 - - - +
166D GLU* 3.0 30.9 + - - +
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Residues in contact with TYR 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C VAL* 3.6 16.4 - - + -
128C LEU* 3.7 9.3 - - + +
131C LEU* 4.0 7.4 - - + +
146C ALA* 3.0 25.7 + - + -
147C LYS* 3.3 1.2 - - - -
148C TRP* 3.3 57.9 - + + -
170C VAL 2.9 10.9 + - - +
171C LEU* 3.4 17.0 - - + +
173C ARG* 1.3 77.0 - - - +
175C ALA* 1.3 72.3 + - + +
177C ILE* 3.2 3.8 + - - +
178C CYS* 3.0 46.1 + - - -
185C PRO* 3.5 15.8 - - + +
186C ILE 2.9 31.8 + - - -
187C VAL* 4.4 6.5 - - + -
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Residues in contact with ALA 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C LEU 2.8 19.9 + - - +
172C ALA 3.7 0.2 - - - +
174C TYR* 1.3 75.7 - - + +
176C SER* 1.3 63.9 + - - +
178C CYS* 3.2 3.3 + - - +
179C GLN* 3.1 27.5 + - - +
185C PRO* 3.8 28.0 - - + -
187C VAL* 4.5 6.3 - - + -
217C LEU* 3.9 11.4 - - + -
222C VAL* 3.6 22.9 - - + -
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Residues in contact with SER 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C ALA 2.9 18.1 + - - -
173C ARG* 3.4 13.3 + - - -
175C ALA* 1.3 77.1 - - - +
177C ILE* 1.3 63.2 + - - +
179C GLN* 3.5 5.9 + - - +
180C GLN* 3.3 23.2 + - - +
220C HIS* 3.7 23.3 + - - -
221C HIS 5.5 0.5 + - - -
222C VAL* 3.7 9.8 - - - +
117D ALA* 3.4 27.3 + - - +
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Residues in contact with ILE 177 (chain C).
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* 3.9 28.5 - - + +
131C LEU* 4.0 20.4 - - + +
132C SER* 3.5 41.7 - - - +
135C CYS* 4.8 0.7 - - - -
173C ARG* 3.0 44.7 + - - +
174C TYR 3.2 5.1 + - - +
176C SER* 1.3 72.8 - - - +
178C CYS* 1.3 67.3 + - - +
180C GLN* 3.1 27.6 - - - +
181C ASN* 3.1 9.8 + - - +
114D VAL* 6.4 0.4 - - + -
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Residues in contact with CYS 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C VAL* 5.1 0.4 - - - -
131C LEU* 4.8 1.8 - - - -
135C CYS* 4.0 24.7 - - - -
146C ALA* 4.1 13.0 - - - -
174C TYR* 3.0 46.7 + - - -
175C ALA 3.2 7.8 + - - +
177C ILE* 1.3 76.7 - - - +
179C GLN* 1.3 58.6 + - - +
181C ASN* 2.8 21.1 + - - +
183C ILE* 3.1 35.0 + - + +
185C PRO* 3.8 10.1 - - + -
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Residues in contact with GLN 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 3.5 20.9 - - + +
12C GLN* 5.4 1.6 + - - +
16C LEU* 3.8 20.8 - - + +
175C ALA 3.1 14.3 + - - +
176C SER* 3.9 5.5 - - - +
178C CYS* 1.3 71.7 - - - +
180C GLN* 1.3 57.8 + - - +
181C ASN 2.9 10.0 + - - -
182C GLY* 3.1 12.0 + - - -
183C ILE 3.8 4.7 - - - +
185C PRO* 3.8 13.2 - - + -
221C HIS 4.8 0.7 - - - +
222C VAL* 3.7 12.0 - - - +
223C TYR* 2.8 58.4 + - - +
226C GLY* 3.0 24.0 + - - -
227C THR* 3.5 4.8 - - - +
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Residues in contact with GLN 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ALA 5.3 3.8 - - - +
8C LEU* 4.1 12.3 - - + +
12C GLN* 4.8 10.7 + - - +
132C SER* 3.5 18.2 + - - -
176C SER 3.3 10.0 + - - +
177C ILE* 3.1 27.2 - - - +
179C GLN* 1.3 76.8 - - - +
181C ASN* 1.3 62.9 + - - +
182C GLY 3.5 0.8 + - - -
115D PRO* 4.9 19.0 - - - +
117D ALA* 3.5 31.5 - - + +
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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
------------------------------------------------------------
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