Contacts of the helix formed by residues 131 - 153 (chain C) in PDB entry 1BRR
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 TYR 131 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71C PHE* 3.7 26.7 - + + -
72C GLY* 4.1 22.6 - - - +
129C LYS 3.3 5.4 + - - -
130C VAL* 1.3 72.4 - - - +
132C SER* 1.3 66.9 + - - +
134C ARG* 3.3 29.7 + - - +
135C PHE* 3.5 32.8 - + - -
195C GLY 3.2 28.5 + - - -
196C ALA* 3.3 16.5 - - - +
197C GLY 4.7 0.7 + - - -
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Residues in contact with SER 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C VAL* 3.5 5.8 - - - +
131C TYR* 1.3 82.8 - - - +
133C TYR* 1.3 74.1 + - - +
134C ARG 3.3 0.5 + - - -
135C PHE* 3.3 24.4 + - - +
136C VAL* 3.8 7.4 + - - +
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Residues in contact with TYR 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 3.4 65.7 - - + +
128C THR* 3.8 12.3 - - + -
129C LYS* 6.1 0.2 - - - -
130C VAL* 3.4 40.8 + - + +
131C TYR 3.3 0.4 - - - -
132C SER* 1.3 83.3 - - - +
134C ARG* 1.3 65.6 + - - +
136C VAL* 2.9 25.6 + - + +
137C TRP* 3.2 17.6 + - - +
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Residues in contact with ARG 134 (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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69C VAL* 4.3 0.4 - - - +
71C PHE* 3.5 29.5 - - - -
78C ILE* 4.0 2.0 - - - +
125C GLY* 2.8 33.9 + - - +
126C ALA* 2.6 41.2 + - - +
127C LEU 3.9 0.6 - - - -
128C THR* 2.8 28.4 + - - +
130C VAL 3.5 12.3 - - - +
131C TYR* 3.5 33.7 - - - +
132C SER 3.2 0.6 - - - -
133C TYR* 1.3 75.4 - - - +
135C PHE* 1.3 62.6 + - + +
137C TRP* 3.4 6.0 + - - +
138C TRP* 3.0 23.6 + - - +
189C TRP* 3.8 13.7 - - + -
194C GLU* 3.1 37.5 + - - +
195C GLY* 5.1 0.2 - - - -
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Residues in contact with PHE 135 (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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131C TYR* 3.5 59.2 - + - -
132C SER* 3.7 11.4 - - - +
133C TYR 3.1 0.6 - - - -
134C ARG* 1.3 78.3 - - + +
136C VAL* 1.3 60.8 + - + +
138C TRP* 3.3 12.9 - + + +
139C ALA* 2.8 31.0 + - - +
189C TRP* 4.8 7.0 - + - -
190C LEU* 3.6 32.3 - - + -
195C GLY* 4.0 15.3 - - - -
196C ALA* 4.1 10.5 - - + -
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Residues in contact with VAL 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 4.0 28.0 - - + -
62B LEU* 4.5 10.8 - - + -
132C SER 4.3 9.0 - - - +
133C TYR* 2.9 22.2 + - + +
135C PHE* 1.3 77.9 - - - +
137C TRP* 1.3 64.1 + - + +
139C ALA* 3.5 6.1 + - - +
140C ILE* 3.2 26.0 + - + +
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Residues in contact with TRP 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B THR* 3.4 41.7 - - + -
58B LEU* 3.7 21.8 - - + -
59B SER* 3.7 23.6 - - - -
62B LEU* 4.0 23.7 - - + +
64B TYR* 5.5 2.7 - - + +
121C THR* 3.1 34.5 - - + +
122C GLY* 5.6 1.3 - - - -
124C VAL* 3.3 25.1 - - + +
125C GLY* 3.6 21.1 - - - -
128C THR* 3.6 21.2 + - - +
133C TYR* 3.2 25.0 + - - +
134C ARG 3.6 6.3 - - - +
136C VAL* 1.3 75.1 - - - +
138C TRP* 1.3 59.0 + - - +
140C ILE* 3.3 9.8 + - + -
141C SER* 2.8 27.6 + - - -
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Residues in contact with TRP 138 (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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122C GLY* 6.3 0.7 - - - -
134C ARG 3.0 15.1 + - - +
135C PHE* 3.1 21.3 + + + +
137C TRP* 1.3 75.8 - - - +
139C ALA* 1.3 91.6 + - + +
141C SER* 3.1 7.1 + - - -
142C THR* 2.9 48.9 + - + -
186C PRO* 2.9 35.7 + - + +
187C VAL* 5.7 0.2 - - - -
189C TRP* 3.5 33.8 - + + -
190C LEU* 3.8 33.8 - - + +
999C RET 3.9 15.9 - - + -
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Residues in contact with ALA 139 (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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135C PHE 2.8 18.4 + - - +
136C VAL* 3.5 8.1 - - - +
138C TRP* 1.3 92.3 - - + +
140C ILE* 1.3 64.5 + - + +
142C THR* 3.2 3.7 + - - -
143C ALA* 3.0 22.6 + - - +
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Residues in contact with ILE 140 (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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54B PHE* 4.0 26.9 - - + -
55B THR* 5.1 4.0 - - - +
58B LEU* 3.4 33.2 - - + -
117C ILE* 5.0 9.9 - - + -
121C THR* 4.1 18.2 - - + +
136C VAL* 3.2 20.2 + - + +
137C TRP* 3.6 15.5 - - + +
139C ALA* 1.3 77.9 - - + +
141C SER* 1.3 62.7 + - - +
143C ALA* 3.2 9.3 + - - +
144C ALA* 3.0 20.3 + - - +
1001C ARC 5.5 8.7 - - + +
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Residues in contact with SER 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C MET* 2.6 29.2 + - - +
121C THR* 3.7 13.7 - - - +
122C GLY* 4.2 3.4 - - - -
137C TRP 2.8 20.5 + - - -
138C TRP 3.6 4.0 - - - -
140C ILE* 1.3 73.7 - - - +
142C THR* 1.3 57.3 + - - +
144C ALA* 3.3 8.6 + - - +
145C MET* 3.0 22.2 + - - +
999C RET 3.2 35.2 - - - +
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Residues in contact with THR 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C TRP* 2.9 47.6 + - + -
139C ALA* 3.5 6.5 - - - -
141C SER* 1.3 74.7 - - - +
143C ALA* 1.3 59.8 + - - +
145C MET* 3.1 13.7 + - + +
146C LEU* 2.8 48.3 + - + +
186C PRO* 3.7 8.2 - - + +
999C RET 3.5 17.7 - - - +
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Residues in contact with ALA 143 (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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139C ALA 3.0 12.4 + - - +
140C ILE* 3.2 12.3 + - - +
142C THR* 1.3 76.4 - - - +
144C ALA* 1.3 61.7 + - - +
146C LEU* 3.6 12.8 + - - +
147C TYR* 3.1 22.5 + - - +
1001C ARC 4.1 20.4 - - + +
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Residues in contact with ALA 144 (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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114C ALA* 3.8 22.7 - - + +
117C ILE* 4.7 11.0 - - + -
118C MET* 4.0 12.6 - - + +
140C ILE* 3.0 12.7 + - + +
141C SER* 3.4 9.2 - - - +
143C ALA* 1.3 73.6 - - - +
145C MET* 1.3 68.1 + - - +
147C TYR* 3.2 8.8 + - - +
148C ILE* 3.1 24.0 + - - +
1001C ARC 4.7 13.2 - - + +
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Residues in contact with MET 145 (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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118C MET* 3.5 29.1 - - - -
141C SER 3.0 6.3 + - - -
142C THR* 3.1 17.2 + - + +
144C ALA* 1.3 75.2 - - - +
146C LEU* 1.3 72.1 + - + +
148C ILE* 2.7 29.5 + - + +
149C LEU* 2.9 31.8 + - + +
182C TRP* 3.5 35.9 - - + +
183C SER* 3.9 14.4 - - - +
186C PRO* 3.8 25.1 - - + -
999C RET 3.7 17.0 - - + -
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Residues in contact with LEU 146 (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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142C THR* 2.8 41.2 + - + +
143C ALA* 3.7 10.1 - - - +
145C MET* 1.3 81.7 - - + +
147C TYR* 1.3 61.9 + - - +
149C LEU* 3.3 11.3 + - + +
150C TYR* 3.0 21.3 + - - +
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Residues in contact with TYR 147 (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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28B LEU* 4.9 5.6 - - + -
110C ALA* 3.3 31.9 + - - +
111C LEU* 4.5 4.6 - - + +
114C ALA* 3.8 19.7 - - + -
143C ALA 3.1 13.3 + - - +
144C ALA* 3.4 7.4 - - - +
145C MET 3.1 0.6 - - - -
146C LEU* 1.3 73.4 - - - +
148C ILE* 1.3 69.1 + - + +
150C TYR* 2.7 35.0 + + + +
151C VAL* 3.2 32.5 + - + +
1001C ARC 3.2 74.0 - - + +
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Residues in contact with ILE 148 (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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94C LEU* 4.0 20.0 - - + -
111C LEU* 4.1 15.3 - - + +
114C ALA* 3.7 18.6 - - + +
115C ASP* 3.5 47.3 - - + +
118C MET* 4.4 10.3 - - - -
144C ALA 3.4 13.0 - - - +
145C MET* 2.7 14.5 + - - +
147C TYR* 1.3 80.3 - - + +
149C LEU* 1.3 61.6 + - + +
151C VAL* 3.7 4.9 + - - +
152C LEU* 3.2 29.7 + - + +
182C TRP* 4.1 15.3 - - + -
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Residues in contact with LEU 149 (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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145C MET* 2.9 43.4 + - + +
146C LEU* 3.9 12.3 - - + +
147C TYR 3.1 0.2 - - - -
148C ILE* 1.3 75.6 - - + +
150C TYR* 1.3 59.9 + - - +
152C LEU* 3.4 20.1 - - + +
153C PHE* 2.8 33.4 + - + +
178C THR 4.9 0.7 - - - -
179C VAL* 4.2 45.6 - - + +
182C TRP* 4.4 24.9 - - + -
183C SER* 4.4 7.2 - - - +
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Residues in contact with TYR 150 (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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146C LEU 3.0 12.2 + - - +
147C TYR* 2.7 17.5 + + + +
149C LEU* 1.3 77.1 - - - +
151C VAL* 1.3 65.4 + - + +
152C LEU 3.0 0.2 + - - -
153C PHE* 4.8 2.0 - - - -
154C PHE* 2.8 76.1 + + + +
155C GLY 3.5 1.9 + - - -
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Residues in contact with VAL 151 (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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107C THR* 5.6 4.5 - - - +
111C LEU* 3.2 40.6 - - + -
147C TYR* 3.2 47.5 + - + +
148C ILE 3.7 3.1 - - - +
150C TYR* 1.3 79.6 - - + +
152C LEU* 1.3 60.6 + - - +
155C GLY* 3.3 8.1 - - - -
156C PHE* 2.9 35.1 + - + -
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Residues in contact with LEU 152 (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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94C LEU* 4.5 15.3 - - + -
97C LEU* 4.4 21.1 - - + -
111C LEU* 4.7 9.2 - - + -
148C ILE* 3.2 28.5 - - + +
149C LEU* 3.2 27.3 + - + +
150C TYR 3.0 0.6 - - - -
151C VAL* 1.3 79.3 - - + +
153C PHE* 1.3 67.2 + - - +
156C PHE* 3.3 40.2 + - + -
157C THR* 3.6 0.7 + - - -
171C PHE* 3.3 22.0 - - + -
175C ARG* 3.9 8.5 - - + -
178C THR* 4.3 16.6 - - - +
179C VAL* 5.3 2.9 - - + -
182C TRP* 5.7 1.1 - - + -
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Residues in contact with PHE 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C LEU* 2.8 20.5 + - + +
150C TYR* 4.0 0.9 - - - +
152C LEU* 1.3 71.3 - - - +
154C PHE* 1.3 102.4 + + + +
155C GLY 2.8 9.6 + - - -
157C THR* 2.7 26.6 + - - -
175C ARG* 3.2 48.7 - - + +
176C ASN* 5.0 1.1 - - - -
179C VAL* 4.6 17.7 - - + -
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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
------------------------------------------------------------
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