Contacts of the helix formed by residues 87 - 111 (chain B) in PDB entry 3PJA
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 PHE 87 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLU* 4.5 7.6 - - + -
20B ILE* 4.0 23.6 - - + -
21B ARG* 3.6 59.0 - - + -
24B ILE* 3.5 27.8 - - + +
83B GLN* 4.5 4.1 + - - -
86B ARG* 1.3 110.6 - - + +
88B HIS* 1.3 63.8 + - - +
89B GLU 3.2 2.9 - - - -
90B HIS* 2.9 35.8 + + + +
91B TRP* 3.0 20.0 - - + +
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Residues in contact with HIS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B TYR* 3.9 15.2 + - - +
86B ARG 3.2 5.5 + - - +
87B PHE* 1.3 75.5 - - - +
89B GLU* 1.3 59.7 + - - +
90B HIS 2.7 12.3 + - - -
91B TRP* 3.4 29.9 + + + +
92B ARG* 2.9 60.1 + - + +
136B ASP* 3.5 16.7 + - + +
139B ASP* 2.9 27.9 + - - -
86D ARG* 5.9 6.7 - - + -
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Residues in contact with GLU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PHE 3.0 2.0 + - - -
88B HIS* 1.3 82.3 - - - +
90B HIS* 1.3 69.6 + - + +
92B ARG* 3.4 29.8 + - - -
93B PHE* 3.3 33.8 - - + -
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Residues in contact with HIS 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ARG* 6.1 2.0 - - - -
24B ILE* 5.4 7.2 - - + -
25B ARG* 6.0 4.5 - - - -
28B VAL* 4.4 9.4 - - + +
32B GLU* 5.4 0.3 - - - +
87B PHE* 2.9 32.5 + + + +
88B HIS 2.7 7.5 + - - -
89B GLU* 1.3 87.1 - - + +
91B TRP* 1.3 61.8 + - + +
92B ARG* 3.1 4.3 + - - -
93B PHE* 4.3 9.9 + - - -
94B VAL* 4.3 9.0 - - - +
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Residues in contact with TRP 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 4.7 11.9 - - + +
28B VAL* 3.6 24.6 - - + +
31B LEU* 6.6 0.2 - - + -
84B TYR 3.3 28.9 - - - -
85B TYR* 4.4 7.6 - + - -
87B PHE* 3.0 44.3 + - + +
88B HIS* 3.7 29.6 - + - -
90B HIS* 1.3 74.7 - - + +
92B ARG* 1.3 66.1 + - - +
93B PHE 3.2 1.8 - - - -
94B VAL* 3.5 6.2 + - + +
95B LEU* 3.0 58.3 + - + +
133B PHE* 4.2 32.4 - + + -
134B HIS* 3.7 17.7 - - + -
139B ASP* 4.9 0.2 - - - -
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Residues in contact with ARG 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B HIS* 2.9 57.2 + - + +
89B GLU* 3.4 31.3 + - - -
90B HIS 3.1 1.0 - - - -
91B TRP* 1.3 78.8 - - - +
93B PHE* 1.3 77.9 + - + +
95B LEU* 3.6 4.7 - - - +
96B GLN* 2.9 49.2 + - - +
136B ASP* 4.2 6.3 + - - -
138B GLU* 3.8 15.2 - - - +
139B ASP* 3.2 27.3 + - - +
142B SER* 5.0 2.4 + - - -
188B ASN* 3.7 24.6 - - - +
190B SER* 4.5 9.7 + - - -
191B LEU* 5.8 2.0 - - - +
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Residues in contact with PHE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLU* 3.3 46.0 - - + -
90B HIS 4.3 8.0 + - - -
91B TRP 3.2 0.4 - - - -
92B ARG* 1.3 95.4 - - + +
94B VAL* 1.3 66.4 + - + +
95B LEU 3.1 0.7 - - - -
96B GLN* 3.9 19.0 - - - +
97B ARG* 3.0 25.5 + - - +
194B ARG* 6.1 0.2 - - - -
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 3.6 20.4 - - + -
31B LEU* 3.6 23.8 - - + +
32B GLU* 3.5 60.8 - - + +
35B ALA* 5.0 3.4 - - + -
90B HIS 4.3 6.7 - - - +
91B TRP* 4.1 9.2 - - + +
93B PHE* 1.3 76.1 - - + +
95B LEU* 1.3 57.5 + - - +
97B ARG* 3.5 6.1 + - + +
98B LEU* 3.0 38.5 + - + +
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 6.1 4.3 - - + -
72B LEU* 5.7 3.4 - - + -
91B TRP* 3.0 50.9 + - + +
92B ARG 3.6 4.9 - - - +
94B VAL* 1.3 75.7 - - - +
96B GLN* 1.3 66.1 + - - +
98B LEU* 3.2 8.3 + - + +
99B VAL* 3.0 26.9 + - - +
123B LEU* 4.6 9.2 - - + -
125B ILE* 3.4 27.8 - - + -
134B HIS 3.8 8.3 - - - +
135B LEU* 3.7 22.9 - - + -
139B ASP* 3.7 18.8 - - + +
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Residues in contact with GLN 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ARG* 2.9 44.7 + - - +
93B PHE* 3.5 18.1 + - - +
95B LEU* 1.3 75.4 - - - +
97B ARG* 1.3 58.2 + - - +
99B VAL* 3.2 10.0 + - - +
100B PHE* 2.9 23.7 + - - +
139B ASP* 3.1 38.5 + - - +
142B SER* 3.4 24.6 + - - -
143B GLY* 3.6 9.6 - - - +
146B ILE* 4.7 7.2 - - + -
194B ARG* 3.1 25.1 + - - +
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Residues in contact with ARG 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLU 5.4 1.8 + - - -
35B ALA* 3.9 24.7 - - + +
36B ARG* 4.9 7.3 - - - +
39B LEU* 4.1 29.5 - - - +
93B PHE 3.0 18.8 + - - +
94B VAL* 3.9 7.0 - - - +
96B GLN* 1.3 78.7 - - - +
98B LEU* 1.3 55.8 + - - +
100B PHE* 3.4 14.1 + - + +
101B LEU* 3.0 40.3 + - + +
146B ILE* 4.9 5.6 - - + +
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.9 39.9 - - + +
35B ALA* 3.9 30.7 - - + +
38B ILE* 4.7 2.0 - - + -
65B PHE* 4.2 21.9 - - + -
68B VAL* 4.4 20.0 - - + -
94B VAL* 3.0 24.4 + - + +
95B LEU* 3.2 8.3 + - + +
97B ARG* 1.3 73.9 - - - +
99B VAL* 1.3 65.6 + - - +
101B LEU* 3.6 6.5 + - + +
102B ALA* 3.0 25.1 + - - +
123B LEU* 4.1 18.6 - - + +
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.0 22.1 + - + +
96B GLN* 3.2 9.8 + - - +
98B LEU* 1.3 74.7 - - - +
100B PHE* 1.3 66.1 + - - +
102B ALA* 3.3 2.5 + - - +
103B ALA* 2.9 23.6 + - + +
119B VAL* 4.2 19.6 - - + +
123B LEU* 4.6 4.9 - - + -
135B LEU* 3.8 34.8 - - + -
140B TYR* 3.9 41.5 - - + +
143B GLY* 4.1 7.6 - - - -
144B VAL* 4.9 2.0 - - + +
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Residues in contact with PHE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.6 10.8 - - + -
96B GLN 2.9 13.3 + - - +
97B ARG* 3.4 20.4 - - + +
98B LEU 3.3 0.2 - - - -
99B VAL* 1.3 75.6 - - - +
101B LEU* 1.3 86.9 + - + +
103B ALA* 3.0 6.2 + - - +
104B PHE* 2.9 37.0 + + + -
143B GLY* 3.5 19.0 - - - +
146B ILE* 3.4 24.7 - - + -
147B LEU* 3.5 25.8 - - + -
150B GLU* 3.6 44.4 - - + -
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ALA* 3.9 37.5 - - + +
38B ILE* 4.0 17.3 - - + -
39B LEU* 3.8 26.2 - - + +
42B LEU* 4.6 13.8 - - + +
65B PHE* 3.9 11.4 - - + -
97B ARG* 3.0 26.4 + - + +
98B LEU* 3.9 10.3 - - + +
100B PHE* 1.3 99.6 - - + +
102B ALA* 1.3 58.1 + - - +
104B PHE* 3.2 7.9 + - + +
105B VAL* 3.0 32.1 + - - +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 3.5 24.6 - - + -
98B LEU 3.0 20.2 + - - +
99B VAL* 3.8 5.6 - - - +
101B LEU* 1.3 76.3 - - - +
103B ALA* 1.3 57.6 + - - +
105B VAL* 3.2 3.0 + - - +
106B VAL* 3.0 34.4 + - - +
114B VAL* 4.7 0.4 - - - -
119B VAL* 4.7 15.3 - - + -
122B ILE* 4.7 17.9 - - + -
123B LEU* 4.8 2.7 - - + -
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 2.9 21.9 + - + +
100B PHE* 3.0 6.5 + - - +
102B ALA* 1.3 76.1 - - - +
104B PHE* 1.3 57.0 + - - +
106B VAL* 3.5 3.3 + - - +
107B TYR* 3.0 27.5 + - - +
112B THR 4.6 2.4 - - - +
113B LEU* 5.0 4.9 - - + -
114B VAL* 3.5 26.6 + - + +
140B TYR* 6.3 0.2 - - + -
143B GLY 5.3 1.3 - - - +
144B VAL* 5.4 5.2 - - + -
147B LEU* 3.7 25.8 - - + +
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Residues in contact with PHE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.7 36.8 - - + -
45B VAL* 5.1 8.7 - - + -
46B HIS* 5.3 3.8 - + - -
100B PHE* 2.9 29.4 + + + +
101B LEU* 3.3 10.5 - - + +
103B ALA* 1.3 75.5 - - - +
105B VAL* 1.3 58.8 + - - +
107B TYR* 3.2 2.5 + - + +
108B LEU* 3.0 56.6 + - + +
147B LEU* 3.7 22.4 - - + +
150B GLU* 3.9 27.1 - - + -
151B LEU* 4.0 20.2 - - + -
154B LEU* 4.4 9.0 - - + -
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 5.2 0.9 - - + -
42B LEU* 4.7 15.3 - - + -
58B CYS* 3.8 21.3 - - + +
61B ALA* 3.7 27.4 - - + -
62B ARG* 4.1 16.2 - - + +
65B PHE* 4.3 9.6 - - + -
101B LEU 3.0 15.6 + - - +
102B ALA* 3.2 9.8 + - - +
104B PHE* 1.3 76.6 - - - +
106B VAL* 1.3 63.7 + - + +
108B LEU* 3.2 5.5 + - + +
109B GLU* 3.0 50.8 + - - +
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 4.0 21.3 - - - +
102B ALA 3.0 17.7 + - - +
103B ALA 3.8 4.7 - - - +
105B VAL* 1.3 76.9 - - + +
107B TYR* 1.3 57.6 + - - +
109B GLU* 3.7 9.0 - - - +
110B THR* 2.9 47.3 + - + +
112B THR* 3.8 13.7 - - - +
114B VAL* 3.8 36.8 - - + +
122B ILE* 4.4 7.2 - - + -
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Residues in contact with TYR 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ALA 3.0 18.0 + - - +
104B PHE* 3.6 8.5 - - + +
105B VAL 3.1 0.4 - - - -
106B VAL* 1.3 73.5 - - - +
108B LEU* 1.3 69.2 + - + +
109B GLU 3.0 4.5 - - - -
111B GLU* 2.7 69.5 + - + +
112B THR 3.8 6.7 - - - +
147B LEU* 5.0 4.0 - - + -
151B LEU* 3.9 34.8 - - + -
154B LEU* 5.7 0.2 - - + -
166B ARG* 5.6 7.4 - - + +
169B HIS* 3.7 12.8 + - - +
170B ILE* 3.5 37.4 + - + +
173B PHE* 3.5 39.4 - + + +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 5.0 10.3 - - + -
45B VAL* 4.8 11.2 - - + -
54B ILE* 3.9 45.8 - - + +
57B ARG* 6.2 1.1 - - + -
58B CYS* 3.9 13.0 - - - -
104B PHE* 3.0 57.8 + - + +
105B VAL* 3.2 6.7 + - - +
107B TYR* 1.3 80.8 - - + +
109B GLU* 1.3 59.5 + - - +
111B GLU* 5.9 0.6 - - - +
154B LEU* 4.4 14.8 - - + -
166B ARG* 5.1 11.7 + - - +
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PRO* 6.3 0.7 - - + -
58B CYS* 3.4 25.2 - - + +
59B LEU* 6.0 0.9 - - - +
62B ARG* 3.0 41.9 + - - -
105B VAL* 3.0 34.9 + - - +
106B VAL* 3.7 9.9 - - - +
107B TYR 3.0 0.8 - - - -
108B LEU* 1.3 81.4 - - - +
110B THR* 1.3 70.9 + - + +
111B GLU* 3.9 0.7 - - - -
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Residues in contact with THR 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B VAL* 2.9 19.4 + - + +
109B GLU* 1.3 92.7 - - + +
111B GLU* 1.3 72.8 + - - +
112B THR* 2.6 39.5 + - - +
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B TYR* 2.7 59.2 + - + +
108B LEU 5.9 0.4 - - - +
109B GLU 5.8 0.4 - - - -
110B THR* 1.3 73.6 - - - +
112B THR* 1.3 61.9 + - - +
166B ARG* 5.4 7.8 + - - +
169B HIS* 3.3 45.4 + - + +
173B PHE* 4.5 5.5 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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