Contacts of the helix formed by residues 80 - 100 (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 TRP 80 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002A ARC 3.7 25.6 - - + -
56C MET* 5.0 2.0 - - - -
59C SER* 5.8 0.2 - - - -
64C TYR* 3.8 26.1 + + - -
65C GLY* 3.6 31.8 - - - -
67C THR* 3.7 27.4 - - + -
78C ILE* 3.5 8.0 + - + -
79C TYR* 1.3 69.0 - - - +
81C ALA* 1.3 75.0 + - + +
82C ARG 3.0 5.4 - - - -
83C TYR* 2.8 38.4 + - - +
84C ALA* 3.3 22.6 + - + -
123C LEU* 4.3 8.9 - - + +
127C LEU* 5.0 4.5 - - + -
1002C ARC 3.5 72.4 - - + +
2E MAN 3.8 9.4 + - - -
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Residues in contact with ALA 81 (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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56C MET* 3.2 25.7 - - - +
59C SER* 3.5 25.1 - - - +
60C MET* 3.7 17.7 - - + -
65C GLY* 3.7 11.4 + - - -
79C TYR 3.2 1.2 - - - -
80C TRP* 1.3 96.7 - - + +
82C ARG* 1.3 60.5 + - - +
83C TYR 3.3 0.2 - - - -
84C ALA* 3.4 1.6 + - - +
85C ASP 3.1 15.9 + - - -
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Residues in contact with ARG 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C TYR* 3.9 16.0 + - - -
60C MET* 3.6 33.2 - - + +
79C TYR* 3.4 32.1 - - - +
80C TRP 2.9 0.8 + - - -
81C ALA* 1.3 76.0 - - - +
83C TYR* 1.3 60.5 + - + +
85C ASP* 3.1 7.7 - - - +
86C TRP* 2.7 65.0 + - + +
194C GLU* 4.5 6.5 + - - -
204C GLU* 3.8 8.3 + - - -
205C THR* 3.5 42.4 + - - +
208C PHE* 3.5 35.4 - - - +
212C ASP* 4.4 3.6 + - - -
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Residues in contact with TYR 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ILE* 5.1 0.7 - - + -
79C TYR 3.8 16.2 - - - -
80C TRP* 2.8 20.2 + - - +
82C ARG* 1.3 81.0 - - + +
84C ALA* 1.3 60.7 - - - +
86C TRP* 4.2 26.9 - + - -
87C LEU* 2.9 30.7 + - - +
119C ILE* 3.4 14.3 - - + +
122C GLY* 3.6 8.7 - - - -
123C LEU* 3.5 52.5 - - + -
126C ALA* 3.5 13.9 - - + +
189C TRP* 2.8 19.5 + + - -
194C GLU* 2.4 33.3 + - - -
208C PHE* 6.0 0.3 - - - -
999C RET 4.5 4.9 - - + -
1002C ARC 5.7 1.8 - - - -
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Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002A ARC 4.2 9.2 - - + -
52C ILE* 5.7 0.2 - - - -
56C MET* 3.7 16.8 - - - -
80C TRP* 3.3 26.5 + - + -
81C ALA 3.4 10.1 - - - +
83C TYR* 1.3 79.9 - - - +
85C ASP* 1.3 64.9 + - - +
87C LEU* 3.5 7.1 - - - +
88C PHE* 3.4 24.1 - - - -
1002C ARC 4.1 22.4 - - + +
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Residues in contact with ASP 85 (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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52C ILE* 3.6 10.6 - - - +
53C ALA* 3.2 33.6 - - - +
56C MET* 3.4 25.1 - - + +
57C TYR* 4.6 8.5 - - - -
60C MET* 6.0 0.3 - - - +
81C ALA 3.1 4.8 + - - +
82C ARG* 3.1 12.0 - - - +
84C ALA* 1.3 76.8 - - - +
86C TRP* 1.3 65.0 + - + +
88C PHE* 3.1 6.4 + - - +
89C THR* 2.8 52.5 + - - +
212C ASP* 5.5 0.5 - - - +
216C LYS* 4.4 4.5 + - - -
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Residues in contact with TRP 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ARG* 2.7 52.6 + - + +
83C TYR* 4.1 22.4 - + - +
85C ASP* 1.3 82.4 + - - +
87C LEU* 1.3 64.3 + - - +
89C THR* 4.1 4.5 - - - -
90C THR* 2.6 36.6 + - + +
119C ILE* 3.3 33.9 - - + -
185C TYR* 3.5 34.5 - + - -
208C PHE* 4.1 17.7 - + - -
212C ASP* 3.4 25.9 + - - -
216C LYS* 4.2 0.9 - - - -
999C RET 3.6 48.6 - - + +
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Residues in contact with LEU 87 (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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1001B ARC 5.7 7.2 - - + -
1002B ARC 4.4 15.3 - - + -
83C TYR 2.9 21.4 + - - +
84C ALA* 3.5 6.1 - - - +
85C ASP 3.2 0.2 - - - -
86C TRP* 1.3 77.7 - - - +
88C PHE* 1.3 80.9 + - + +
90C THR* 4.5 0.2 + - - -
91C PRO* 3.3 16.1 - - - +
115C ASP* 4.5 1.6 - - - +
116C GLY* 4.7 15.7 - - - +
119C ILE* 3.6 24.6 - - + +
120C GLY* 4.6 9.2 - - - +
1002C ARC 3.3 34.8 - - + -
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Residues in contact with PHE 88 (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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1002A ARC 3.5 52.5 - - + +
1002B ARC 4.6 12.1 - - + -
52C ILE* 4.3 18.2 - - + -
84C ALA 3.4 24.5 - - - -
85C ASP 3.1 4.4 + - - +
87C LEU* 1.3 100.3 - - + +
89C THR* 1.3 64.8 + - - +
91C PRO* 3.2 15.7 - - - +
92C LEU* 3.4 20.6 - - + +
1002C ARC 3.6 44.9 - - + -
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Residues in contact with THR 89 (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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49C VAL* 3.5 28.3 + - + +
52C ILE* 3.8 8.0 - - - +
85C ASP* 2.8 31.8 + - - +
86C TRP* 4.6 1.6 - - - -
88C PHE* 1.3 76.0 - - - +
90C THR* 1.3 72.4 + - + +
92C LEU* 3.0 20.5 + - - +
93C LEU* 3.2 13.1 + - + +
216C LYS* 3.2 29.2 - - - +
999C RET 3.4 13.7 - - + -
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Residues in contact with THR 90 (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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86C TRP* 2.6 28.5 + - + +
89C THR* 1.3 78.5 - - + +
91C PRO* 1.4 61.3 - - - +
93C LEU* 3.0 18.5 + - - +
94C LEU* 3.1 11.3 + - - +
115C ASP* 2.5 33.9 + - - -
118C MET* 4.4 4.5 - - + -
119C ILE* 3.8 4.2 - - - +
182C TRP* 3.9 12.2 - - + -
999C RET 3.5 50.3 - - + -
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Residues in contact with PRO 91 (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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87C LEU 3.3 20.4 - - - +
88C PHE* 3.2 17.0 - - - +
89C THR 3.4 1.8 - - - -
90C THR* 1.4 90.8 - - - +
92C LEU* 1.3 50.3 + - + +
94C LEU* 3.0 11.0 + - + +
95C LEU* 2.7 36.1 + - - +
112C VAL* 4.1 31.8 - - + +
115C ASP* 3.0 25.6 - - + +
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Residues in contact with LEU 92 (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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109A LEU* 4.5 17.5 - - + -
1002A ARC 4.4 28.5 - - + -
45C ILE* 3.2 34.8 - - + +
48C LEU* 4.6 13.2 - - + -
49C VAL* 3.9 15.7 - - + -
52C ILE* 4.0 23.1 - - + -
88C PHE* 3.4 18.2 - - + +
89C THR* 3.0 8.5 + - - +
91C PRO* 1.3 75.8 - - + +
93C LEU* 1.3 61.5 + - - +
95C LEU* 3.2 13.4 + - + -
96C ASP* 3.0 23.6 + - - +
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Residues in contact with LEU 93 (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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46C THR* 6.1 1.6 - - + -
49C VAL* 3.5 32.3 - - + -
89C THR* 3.2 22.4 + - + +
90C THR* 3.0 9.8 + - - +
92C LEU* 1.3 78.3 - - - +
94C LEU* 1.3 64.1 + - - +
96C ASP* 3.5 8.7 + - - +
97C LEU* 3.3 26.5 + - + +
178C THR* 6.1 0.7 - - + -
182C TRP* 4.1 12.3 - - + +
215C ALA 4.0 16.6 - - - +
216C LYS* 5.1 2.0 - - + +
219C PHE* 3.9 29.3 - - + -
999C RET 3.6 33.9 - - + -
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Residues in contact with LEU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C THR 3.1 6.3 + - - +
91C PRO* 3.0 10.6 + - + +
93C LEU* 1.3 78.5 - - - +
95C LEU* 1.3 54.0 + - - +
97C LEU* 3.1 11.2 + - + +
98C ALA* 2.7 37.3 + - - +
111C LEU* 4.2 33.5 - - + +
112C VAL* 5.6 4.5 - - + +
115C ASP* 3.9 33.7 - - + +
148C ILE* 4.0 17.7 - - + -
152C LEU* 4.5 19.5 - - + -
156C PHE* 5.0 1.4 - - - -
182C TRP* 3.3 29.4 - - + -
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Residues in contact with LEU 95 (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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109A LEU* 4.8 9.0 - - + -
45C ILE* 3.8 22.0 - - + -
91C PRO 2.7 13.6 + - - +
92C LEU* 3.5 23.1 - - + +
94C LEU* 1.3 77.4 - - - +
96C ASP* 1.3 51.7 - - - +
98C ALA* 3.6 2.6 - - + +
99C LEU* 2.7 48.3 + - + +
108C ILE* 3.7 35.7 - - + -
112C VAL* 4.7 8.5 - - + -
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Residues in contact with ASP 96 (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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42C PHE* 3.5 25.9 - - - -
45C ILE* 3.4 31.0 - - - +
46C THR* 2.6 28.3 + - - -
92C LEU 3.0 8.4 + - - +
93C LEU* 3.6 12.1 - - - +
95C LEU* 1.3 75.9 - - - +
97C LEU* 1.3 59.9 + - - +
100C LEU* 3.0 28.6 + - - +
219C PHE* 3.7 16.2 - - + -
223C LEU* 3.2 22.0 - - + +
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Residues in contact with LEU 97 (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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93C LEU* 3.3 13.2 + - + +
94C LEU* 3.1 16.2 + - + +
96C ASP* 1.3 80.8 - - + +
98C ALA* 1.3 62.3 + - - +
100C LEU* 3.6 4.9 + - + +
101C VAL* 3.4 28.9 + - - +
152C LEU* 4.4 23.8 - - + -
156C PHE* 3.9 4.6 - - + -
171C PHE* 4.3 19.5 - - + -
174C LEU* 3.9 24.7 - - + -
175C ARG* 5.4 1.8 - - - +
178C THR* 4.1 18.4 - - + +
219C PHE* 3.4 35.4 - - + -
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Residues in contact with ALA 98 (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 2.7 19.9 + - - +
95C LEU* 3.7 8.7 - - + +
97C LEU* 1.3 71.3 - - - +
99C LEU* 1.3 62.1 + - + +
100C LEU 3.3 0.2 + - - -
101C VAL 3.4 1.2 + - - -
102C ASP 3.0 8.5 + - - -
103C ALA* 2.9 32.2 + - + -
108C ILE* 3.9 33.4 - - + -
111C LEU* 5.2 2.5 - - + -
156C PHE* 3.8 16.6 - - + -
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Residues in contact with LEU 99 (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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38C ASP* 5.5 1.7 - - - +
41C LYS* 3.9 39.7 - - + +
42C PHE* 3.7 23.8 - - + -
45C ILE* 3.8 28.5 - - + -
95C LEU* 2.7 28.8 + - + +
98C ALA* 1.3 75.3 - - - +
100C LEU* 1.3 61.1 + - - +
102C ASP* 3.4 13.6 + - - +
108C ILE* 4.9 14.6 - - + -
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C PHE* 3.8 14.1 - - + -
96C ASP 3.0 16.7 + - - +
97C LEU* 3.8 7.6 - - + +
98C ALA 3.2 0.6 - - - -
99C LEU* 1.3 79.1 - - - +
101C VAL* 1.3 59.0 + - - +
102C ASP 3.2 0.9 + - - -
163C MET* 3.8 8.1 - - - +
167C VAL* 3.6 30.6 - - + +
170C THR* 4.0 14.8 - - + -
171C PHE* 3.7 42.2 - - + +
174C LEU* 4.2 11.2 - - + -
223C LEU* 4.4 10.8 - - + -
228C ALA 3.1 27.4 - - - +
229C ILE* 5.6 0.2 - - + -
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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