Contacts of the helix formed by residues 105 - 127 (chain B) 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 GLN 105 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LYS* 3.6 37.4 + - + +
103B ALA 3.7 1.4 + - - +
104B ASP* 1.3 70.6 - - - +
106B GLY* 1.3 59.9 - - - +
108B ILE* 3.9 18.1 - - + +
109B LEU* 3.3 23.7 + - - +
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Residues in contact with GLY 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PRO 5.0 1.4 + - - -
40A LYS* 4.4 9.6 - - - -
41A LYS* 4.1 32.5 - - - +
44A ALA* 3.4 7.8 - - - +
104B ASP* 2.9 4.4 + - - +
105B GLN* 1.3 80.7 - - - +
107B THR* 1.3 56.4 + - - +
109B LEU* 3.7 0.8 - - - +
110B ALA 3.1 22.5 + - - -
1000B ARC 3.2 12.2 + - - -
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Residues in contact with THR 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS* 3.3 37.0 - - + +
103B ALA* 3.5 19.3 - - + +
104B ASP* 3.0 13.2 + - + +
106B GLY* 1.3 71.8 - - - +
108B ILE* 1.3 62.6 + - - +
110B ALA* 3.7 0.9 - - - +
111B LEU* 2.8 36.1 + - - +
151B VAL* 5.8 4.0 - - - -
156B PHE* 3.9 15.7 - - + -
1000B ARC 3.1 20.0 - - - +
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Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.8 27.6 - - + -
98B ALA* 3.9 26.0 - - + -
99B LEU* 5.2 10.5 - - + -
103B ALA* 3.5 24.5 - - + +
104B ASP 3.1 12.5 + - - +
105B GLN* 3.9 18.6 - - + +
107B THR* 1.3 76.0 + - - +
109B LEU* 1.3 59.6 + - - +
111B LEU* 3.2 8.4 + - - +
112B VAL* 2.9 36.3 + - + +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LYS* 5.0 2.0 - - + +
44A ALA* 4.8 2.5 - - + -
45A ILE* 3.4 43.1 - - + +
48A LEU* 4.0 9.3 - - + +
92A LEU* 4.9 7.9 - - + -
95A LEU* 4.8 10.8 - - + -
105B GLN 3.3 15.4 + - - +
106B GLY* 3.7 3.8 - - - +
107B THR 3.3 0.4 - - - -
108B ILE* 1.3 77.0 - - - +
110B ALA* 1.3 57.9 + - - +
111B LEU 2.8 5.8 + - - -
112B VAL* 3.0 6.0 + - + +
113B GLY* 2.8 31.4 + - - +
1003B ARC 4.2 24.2 - - + -
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA* 3.7 8.7 - - + +
48A LEU* 4.5 6.7 - - - -
106B GLY 3.1 5.3 + - - +
107B THR 3.8 2.0 - - - +
109B LEU* 1.3 78.7 - - - +
111B LEU* 1.3 58.4 + - + +
114B ALA* 3.2 25.8 + - - +
147B TYR* 3.8 5.4 - - - +
1000B ARC 3.4 65.9 - - + +
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU* 4.1 27.8 - - + +
98B ALA* 5.6 2.2 - - + -
107B THR 2.8 19.7 + - - +
108B ILE* 3.3 7.9 - - - +
109B LEU 2.8 1.2 + - - -
110B ALA* 1.3 78.9 - - + +
112B VAL* 1.3 61.2 + - + +
113B GLY 3.4 0.4 - - - -
114B ALA* 3.4 3.5 + - - +
115B ASP* 2.9 27.6 + - - +
147B TYR* 4.4 5.6 - - + +
148B ILE* 4.1 18.8 - - + +
151B VAL* 3.2 36.1 - - + -
152B LEU* 4.6 6.3 - - + -
156B PHE* 3.5 35.2 - - + -
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B PRO* 4.1 37.0 - - + +
94B LEU* 5.2 4.7 - - + -
95B LEU* 4.9 7.6 - - + +
108B ILE* 2.9 34.0 + - + +
109B LEU* 3.9 6.3 - - + +
111B LEU* 1.3 69.7 - - + +
113B GLY* 1.3 61.6 + - - +
115B ASP* 3.1 9.4 + - - +
116B GLY* 2.8 25.8 + - - -
1003B ARC 4.3 20.8 - - + +
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Residues in contact with GLY 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.6 28.4 - - - +
109B LEU 2.8 14.8 + - - -
112B VAL* 1.3 74.1 - - - +
114B ALA* 1.3 60.2 + - - +
116B GLY* 3.1 10.6 + - - -
117B ILE* 3.1 17.0 + - - +
1003B ARC 3.5 25.1 - - - +
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 3.9 1.6 - - - +
110B ALA 3.2 21.9 + - - +
111B LEU 3.4 5.3 + - - +
112B VAL 3.3 0.2 - - - -
113B GLY* 1.3 75.2 - - - +
115B ASP* 1.3 64.7 + - - +
117B ILE* 3.1 11.8 + - - +
118B MET* 2.9 21.5 + - - +
144B ALA* 4.1 9.0 - - + +
147B TYR* 3.9 15.9 - - + -
148B ILE* 4.1 9.0 - - + -
1000B ARC 3.3 23.8 - - + -
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Residues in contact with ASP 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B TRP 4.4 0.2 - - - +
87B LEU 4.6 0.9 - - - +
90B THR* 2.6 37.2 + - - -
91B PRO* 3.2 17.4 - - + +
94B LEU* 3.3 23.1 - - + +
111B LEU 2.9 14.4 + - - +
112B VAL* 3.2 12.1 - - - +
114B ALA* 1.3 77.9 - - - +
116B GLY* 1.3 62.6 + - - +
118B MET* 3.2 8.2 + - - +
119B ILE* 3.1 24.1 + - - +
148B ILE* 3.7 15.2 - - + +
182B TRP* 3.6 7.8 - - - -
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Residues in contact with GLY 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 4.6 10.8 - - - +
91B PRO* 5.4 1.1 - - - +
112B VAL 2.8 13.1 + - - -
113B GLY 3.1 3.3 + - - -
115B ASP* 1.3 77.8 + - - +
117B ILE* 1.3 56.2 + - - +
119B ILE* 3.4 1.4 + - - +
120B GLY* 2.8 29.6 + - - -
1003B ARC 3.3 35.3 - - - +
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 4.0 22.9 - - + -
51A ALA* 4.1 27.4 - - + +
52A ILE* 4.6 8.7 - - + -
55A THR* 3.6 24.9 - - + +
113B GLY 3.3 12.1 - - - +
114B ALA* 3.1 10.7 + - - +
116B GLY* 1.3 75.9 - - - +
118B MET* 1.3 56.0 + - - +
121B THR* 2.7 47.6 + - - +
140B ILE* 5.1 6.3 - - + -
144B ALA* 4.7 9.6 - - + -
1000B ARC 5.1 15.9 - - + -
1003B ARC 4.4 14.8 - - + -
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Residues in contact with MET 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B THR* 4.5 3.1 - - + -
114B ALA 2.9 10.0 + - - +
115B ASP* 3.2 26.2 + - - +
117B ILE* 1.3 75.2 - - - +
119B ILE* 1.3 78.8 + - + +
122B GLY* 3.1 11.6 + - - -
141B SER* 2.8 40.8 + - - +
144B ALA* 3.7 19.4 - - + +
145B MET* 3.5 30.5 - - - -
148B ILE* 4.4 7.0 - - + -
182B TRP* 4.2 5.8 - - + -
999B RET 3.4 43.2 - - + +
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Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TYR* 3.5 38.9 - - + +
86B TRP* 3.6 37.5 - - + +
87B LEU* 3.8 19.5 - - + +
90B THR* 3.9 8.7 - - - +
115B ASP* 3.1 12.7 + - - +
116B GLY 4.1 1.1 - - - +
118B MET* 1.3 89.8 - - + +
120B GLY* 1.3 56.9 + - - +
122B GLY* 2.9 2.9 + - - -
123B LEU* 2.8 32.9 + - + +
999B RET 3.7 26.7 - - + -
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Residues in contact with GLY 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 4.9 4.4 - - - +
116B GLY 2.8 15.9 + - - -
119B ILE* 1.3 77.7 - - - +
121B THR* 1.3 61.1 + - - +
123B LEU* 3.0 18.6 + - - +
124B VAL* 3.1 16.5 + - - +
1003B ARC 3.4 32.4 - - - +
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Residues in contact with THR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A THR* 3.7 17.7 + - - +
117B ILE* 2.7 38.9 + - - +
118B MET 4.1 1.8 - - - -
120B GLY* 1.3 71.1 - - - -
122B GLY* 1.3 62.6 + - - +
124B VAL* 3.2 11.1 + - - +
125B GLY 3.0 18.5 + - - -
137B TRP* 3.0 47.5 - - + +
140B ILE* 3.9 7.8 - - + +
141B SER* 3.6 14.6 - - - +
1003B ARC 4.7 1.4 - - - +
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Residues in contact with GLY 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B TYR* 3.3 9.6 + - - -
118B MET 3.1 12.3 + - - -
119B ILE 2.9 7.4 + - - -
121B THR* 1.3 77.3 - - - +
123B LEU* 1.3 56.9 + - - +
125B GLY* 3.1 3.0 + - - -
126B ALA* 2.8 30.1 + - - +
137B TRP* 5.6 1.3 - - - -
138B TRP* 6.3 0.4 - - - -
141B SER* 4.2 3.1 + - - -
189B TRP* 4.6 3.8 + - - -
999B RET 3.9 23.6 - - - -
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B TRP* 4.3 15.7 - - + +
83B TYR* 3.3 42.6 - - + +
119B ILE* 2.8 14.5 + - + +
120B GLY* 3.0 11.9 + - - +
122B GLY* 1.3 70.9 - - - +
124B VAL* 1.3 63.4 + - + +
126B ALA* 3.3 2.9 + - + +
127B LEU* 3.1 43.9 + - + +
1002B ARC 3.8 39.0 - - + -
1003B ARC 3.9 21.8 - - + -
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A THR* 5.6 0.4 - - + -
56A MET* 4.9 9.9 - - + -
59A SER* 5.2 0.9 - - - -
64A TYR* 4.0 34.9 - - + -
120B GLY 3.1 16.0 + - - +
121B THR* 3.3 10.3 - - - +
123B LEU* 1.3 74.3 - - - +
125B GLY* 1.3 52.0 + - - +
127B LEU* 3.0 5.2 + - - +
128B THR* 2.7 39.2 + - - +
137B TRP* 3.3 44.0 - - + +
1003B ARC 4.1 20.0 - - + -
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Residues in contact with GLY 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B THR 3.0 7.9 + - - -
122B GLY 3.6 2.5 - - - -
124B VAL* 1.3 80.2 - - - +
126B ALA* 1.3 61.0 + - - +
127B LEU 3.3 0.3 + - - -
128B THR* 3.3 3.6 + - - -
134B ARG* 3.1 36.0 + - - +
137B TRP* 3.6 28.9 - - - +
138B TRP 5.5 0.2 - - - -
189B TRP* 4.0 9.4 - - - -
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B VAL* 4.2 0.3 - - - +
78B ILE* 3.7 26.9 - - + +
83B TYR* 3.2 37.2 - - + +
122B GLY 2.8 16.1 + - - +
123B LEU* 3.6 6.1 - - + +
124B VAL 3.2 0.2 - - - -
125B GLY* 1.3 72.7 - - - +
127B LEU* 1.3 60.2 + - + +
134B ARG* 3.0 27.2 + - - +
189B TRP* 3.9 5.2 - - - +
194B GLU* 4.2 5.8 - - - +
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 3.7 13.1 - - + +
1003A GOL 3.6 23.3 - - + -
67B THR* 4.3 5.2 - - + -
69B VAL* 3.6 30.7 - - + +
78B ILE* 4.3 13.0 - - + -
80B TRP* 4.7 7.0 - - + -
123B LEU* 3.4 29.2 - - + +
124B VAL 3.0 4.8 + - - +
126B ALA* 1.3 79.1 - - + +
128B THR* 1.3 66.5 + - - +
129B LYS* 3.3 11.3 + - - +
1002B ARC 4.4 5.2 - - + -
1D GLC 3.4 43.9 - - - +
2D MAN 5.4 0.5 - - - +
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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