Contacts of the helix formed by residues 82 - 111 (chain L) in PDB entry 3E1J
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 ASP 82 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L TRP* 4.3 4.9 - - - -
81L GLU* 1.3 79.1 - - - +
83L VAL* 1.3 66.2 + - - +
84L GLU* 3.5 9.3 + - - +
85L GLU* 3.0 39.1 + - - +
86L MET* 2.8 27.3 + - - +
146L LEU* 6.4 1.6 - - + -
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Residues in contact with VAL 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L PHE* 4.0 16.6 - - + -
35L TRP* 4.4 7.1 - - + -
37L LEU* 3.9 17.3 - - + -
40L LEU* 4.2 4.0 - - + -
82L ASP* 1.3 73.6 - - - +
84L GLU* 1.3 53.6 + - - +
86L MET* 3.0 11.5 + - - +
87L LEU* 2.8 56.0 + - + +
141L ILE* 4.3 4.0 - - + -
146L LEU* 5.0 7.9 - - + -
149L TYR* 4.0 20.6 - - + -
150L LEU* 3.9 24.7 - - + -
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Residues in contact with GLU 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82L ASP* 3.4 6.6 + - - +
83L VAL* 1.3 78.4 - - - +
85L GLU* 1.3 54.7 + - - +
87L LEU* 3.1 1.7 + - - +
88L ARG* 2.6 73.6 + - - +
138L LEU* 3.9 21.8 - - + +
141L ILE* 4.3 21.0 - - + +
142L GLN* 3.9 20.2 + - - +
146L LEU* 5.8 3.2 - - + +
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Residues in contact with GLU 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80L GLY* 4.0 12.5 - - - -
81L GLU* 3.7 31.4 + - - +
82L ASP* 3.0 38.0 + - - +
84L GLU* 1.3 76.3 - - - +
86L MET* 1.3 58.9 + - - +
88L ARG* 3.4 8.6 + - - +
89L SER* 3.0 28.8 + - - -
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Residues in contact with MET 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L HIS* 3.2 57.4 - - + +
31L MET* 3.7 45.3 - - + -
32L PHE* 3.4 30.7 - - + -
35L TRP* 3.7 17.3 - - + -
79L ILE 3.4 10.3 - - - +
80L GLY* 4.5 2.2 - - - +
82L ASP 2.8 27.2 + - - +
83L VAL* 3.4 11.9 - - - +
85L GLU* 1.3 74.3 - - - +
87L LEU* 1.3 65.4 + - - +
89L SER* 3.2 1.3 + - - -
90L ASP* 3.1 18.5 + - - +
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Residues in contact with LEU 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L PHE* 3.9 24.0 - - + -
40L LEU* 5.1 2.9 - - + -
44L GLU* 3.8 22.7 - - - +
83L VAL* 2.8 32.8 + - + +
86L MET* 1.3 78.8 - - - +
88L ARG* 1.3 61.4 + - - +
90L ASP* 3.2 7.4 + - - +
91L LEU* 3.0 22.2 + - - +
133L TRP* 4.7 6.7 - - + -
134L LEU* 4.1 16.2 - - + +
137L GLU* 4.1 16.2 - - + -
138L LEU* 3.7 19.3 - - + -
141L ILE* 4.2 11.4 - - + -
149L TYR* 3.9 17.9 - - - +
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Residues in contact with ARG 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84L GLU* 2.6 53.8 + - - +
85L GLU* 3.7 7.0 - - - +
87L LEU* 1.3 76.4 - - - +
89L SER* 1.3 58.5 + - - +
91L LEU* 3.3 9.6 + - + +
92L ALA* 2.9 28.9 + - - +
138L LEU* 4.0 35.1 + - + +
142L GLN* 5.1 8.9 - - - +
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Residues in contact with SER 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L GLN* 3.1 10.6 + - - -
78L ASN* 2.6 53.1 + - - +
79L ILE 4.7 1.1 - - - -
80L GLY* 5.9 0.4 - - - -
85L GLU 3.0 17.6 + - - -
86L MET* 3.6 8.1 - - - -
87L LEU 3.1 0.6 - - - -
88L ARG* 1.3 76.4 - - - +
90L ASP* 1.3 64.2 + - - +
92L ALA* 3.4 7.2 + - - +
93L LEU* 3.1 18.9 + - - +
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Residues in contact with ASP 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L GLN* 2.9 31.2 + - - +
25L TYR* 3.5 31.4 + - + +
28L HIS* 2.7 30.6 + - - -
44L GLU* 2.9 21.3 - - - +
86L MET 3.1 9.2 + - - +
87L LEU* 3.6 8.8 - - - +
89L SER* 1.3 75.0 - - - +
91L LEU* 1.3 56.7 + - - +
93L LEU* 3.2 6.4 + - - +
94L GLU* 3.0 32.1 + - - +
134L LEU* 4.3 9.6 - - + -
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Residues in contact with LEU 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87L LEU 3.0 12.0 + - - +
88L ARG* 3.5 15.0 - - + +
89L SER 3.3 0.2 - - - -
90L ASP* 1.3 74.2 - - - +
92L ALA* 1.3 66.9 + - - +
94L GLU* 3.2 2.0 + - - +
95L LEU* 3.0 42.1 + - + +
131L ILE* 4.0 27.6 - - + +
134L LEU* 4.0 20.8 - - + +
135L GLU* 4.1 22.7 - - + +
138L LEU* 3.7 24.5 - - + -
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Residues in contact with ALA 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88L ARG 2.9 18.9 + - - +
89L SER* 3.4 7.8 + - - +
91L LEU* 1.3 72.8 - - - +
93L LEU* 1.3 57.5 - - - +
95L LEU* 3.3 11.3 + - - +
96L ASP* 3.0 35.3 + - - +
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Residues in contact with LEU 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L ASN* 5.2 7.9 - - + +
20L VAL* 3.7 35.7 - - + -
21L ALA* 3.8 26.9 - - + +
24L GLN* 4.0 20.2 - - + +
25L TYR* 6.1 1.8 - - + -
76L LYS 5.0 5.2 - - - +
89L SER 3.1 12.7 + - - +
90L ASP* 3.4 11.4 - - - +
91L LEU 3.1 0.2 - - - -
92L ALA* 1.3 74.9 - - - +
94L GLU* 1.3 64.2 + - + +
96L ASP* 3.3 9.6 + - + +
97L GLY* 3.1 19.8 + - - -
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Residues in contact with GLU 94 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L ALA* 6.0 1.3 - - - -
25L TYR* 2.4 38.3 + - + +
51L GLU* 3.6 3.0 - - - +
90L ASP 3.0 19.1 + - - +
91L LEU* 3.7 5.8 - - - +
93L LEU* 1.3 71.5 - - + +
95L LEU* 1.3 60.6 + - - +
97L GLY* 3.2 2.2 + - - -
98L ALA* 2.8 30.7 + - - +
127L GLU* 2.6 38.8 - - - +
130L HIS* 3.0 24.9 + - - -
131L ILE* 3.6 21.9 - - + +
134L LEU* 4.1 10.3 - - + -
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Residues in contact with LEU 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91L LEU* 3.0 37.9 + - + +
92L ALA* 3.5 8.3 - - - +
94L GLU* 1.3 77.5 - - - +
96L ASP* 1.3 63.3 + - - +
98L ALA* 3.3 5.7 + - + +
99L LYS* 3.2 30.7 + - - +
131L ILE* 3.6 35.2 - - + -
135L GLU* 5.3 3.6 - - - +
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Residues in contact with ASP 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L ASN* 5.5 0.9 - - - +
92L ALA* 3.0 22.3 + - - +
93L LEU* 3.3 10.4 + - + +
95L LEU* 1.3 76.1 - - - +
97L GLY* 1.3 61.4 + - - +
99L LYS* 3.4 27.7 + - - +
100L ASN* 3.2 29.7 + - - +
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Residues in contact with GLY 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L ASN* 3.6 27.3 + - - -
93L LEU 3.1 14.3 + - - -
94L GLU* 3.2 3.5 + - - -
96L ASP* 1.3 74.5 - - - +
98L ALA* 1.3 60.1 + - - +
100L ASN* 3.3 2.8 + - - +
101L LEU* 2.9 37.1 + - - +
127L GLU* 6.1 0.7 - - - -
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Residues in contact with ALA 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94L GLU 2.8 17.8 + - - +
95L LEU* 3.7 7.2 - - + +
96L ASP 3.3 0.2 - - - -
97L GLY* 1.3 75.2 - - - +
99L LYS* 1.3 58.0 + - - +
101L LEU* 3.2 4.3 + - - +
102L ARG* 2.9 56.6 + - - +
124L LEU* 3.9 17.4 - - + +
127L GLU* 5.4 4.2 - - + +
131L ILE* 4.3 16.6 - - + -
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Residues in contact with LYS 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95L LEU* 3.2 17.7 + - - +
96L ASP* 3.4 33.2 + - - +
98L ALA* 1.3 77.5 - - - +
100L ASN* 1.3 66.6 + - - +
102L ARG* 3.2 12.0 + - - +
103L GLU* 3.1 22.4 + - - +
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Residues in contact with ASN 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L TYR* 4.8 3.8 - - + -
13L LYS* 3.5 33.7 + - + +
14L LEU* 3.6 17.6 - - + +
17L ASN* 2.9 25.4 + - - +
96L ASP* 3.2 15.4 + - - +
97L GLY 3.3 6.7 + - - +
99L LYS* 1.3 79.7 - - - +
101L LEU* 1.3 57.7 + - - +
103L GLU* 3.3 15.5 + - - +
104L ALA* 2.9 30.0 + - - +
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Residues in contact with LEU 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14L LEU* 3.8 21.3 - - + -
18L GLU* 5.2 1.8 - - - +
58L TYR* 3.5 21.5 - - - +
97L GLY 2.9 21.7 + - - +
98L ALA 3.5 5.2 - - - +
100L ASN* 1.3 73.3 - - - +
102L ARG* 1.3 59.9 + - - +
104L ALA* 3.3 2.3 + - - +
105L ILE* 2.9 39.8 + - + +
120L MET* 3.7 31.0 - - + +
123L ILE* 4.1 7.2 - - + -
124L LEU* 3.9 33.0 - - + -
127L GLU* 3.9 19.3 - - + +
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Residues in contact with ARG 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98L ALA* 2.9 46.3 + - - +
99L LYS* 3.2 10.2 + - - +
101L LEU* 1.3 76.1 - - - +
103L GLU* 1.3 63.4 + - - +
105L ILE* 3.5 7.9 + - - +
106L GLY* 3.3 17.3 + - - -
124L LEU* 4.1 18.8 - - + +
128L GLU* 2.7 36.7 + - - -
131L ILE* 5.9 0.6 - - - +
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Residues in contact with GLU 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L LYS* 5.2 1.4 + - - -
10L TYR* 2.7 39.0 + - + +
13L LYS* 5.8 3.6 - - - -
99L LYS 3.1 12.6 + - - +
100L ASN* 3.7 18.0 + - - +
101L LEU 3.3 0.2 - - - -
102L ARG* 1.3 78.4 - - - +
104L ALA* 1.3 61.2 + - - +
106L GLY* 3.3 1.6 + - - -
107L TYR* 3.2 19.6 + - - +
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Residues in contact with ALA 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L TYR* 3.7 34.3 - - + -
14L LEU* 3.9 11.2 - - + -
100L ASN 2.9 19.3 + - - +
101L LEU 3.8 2.2 - - - +
103L GLU* 1.3 73.0 - - - +
105L ILE* 1.3 57.5 + - - +
107L TYR* 3.2 3.6 + - - +
108L ALA* 2.9 30.3 + - - +
120L MET* 3.6 24.1 - - - +
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Residues in contact with ILE 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101L LEU* 2.9 24.6 + - + +
102L ARG* 3.8 5.8 - - - +
104L ALA* 1.3 74.8 - - - +
106L GLY* 1.3 62.9 + - - +
108L ALA* 3.5 1.2 + - - +
109L ASP 3.2 17.5 + - - -
117L ARG* 3.3 39.6 + - + +
120L MET* 3.6 39.9 - - + +
121L ILE* 4.0 22.4 - - + -
124L LEU* 3.9 27.8 - - + -
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Residues in contact with GLY 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102L ARG 3.3 10.8 + - - -
103L GLU 3.9 2.9 - - - -
105L ILE* 1.3 79.0 - - - +
107L TYR* 1.3 61.4 + - - +
109L ASP* 3.5 6.5 + - - +
110L SER* 3.3 20.3 + - - -
117L ARG* 4.3 7.9 - - - -
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Residues in contact with TYR 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4L ASP* 2.9 36.8 + - - -
6L LYS* 3.4 32.1 - - + +
7L VAL* 3.7 15.9 - - + -
10L TYR* 3.8 33.9 - + + +
103L GLU* 3.2 9.3 + - + +
104L ALA 3.2 6.8 + - - +
106L GLY* 1.3 75.2 - - - +
108L ALA* 1.3 66.9 + - - +
110L SER* 2.8 27.5 + - - -
111L VAL* 3.1 28.1 + - + +
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Residues in contact with ALA 108 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L VAL* 4.4 7.4 - - + -
104L ALA 2.9 17.8 + - - +
105L ILE 3.8 3.8 - - - +
107L TYR* 1.3 79.0 - - - +
109L ASP* 1.3 60.9 + - - +
111L VAL* 3.4 9.1 + - - +
112L HIS 3.0 3.6 + - - -
113L ASP* 2.8 50.7 + - + +
116L SER* 4.7 1.6 - - - -
117L ARG* 4.0 4.3 - - + +
120L MET* 3.6 21.3 - - + -
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Residues in contact with ASP 109 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G ASP* 5.4 3.6 - - - +
117G ARG* 2.8 34.0 + - - -
105L ILE 3.2 4.9 + - - -
106L GLY* 3.5 8.5 - - - +
107L TYR 3.2 0.2 - - - -
108L ALA* 1.3 76.0 - - - +
110L SER* 1.3 65.2 + - - +
112L HIS* 3.2 14.0 + - - -
114L TYR* 3.4 22.1 + - - -
117L ARG* 3.2 35.2 + - - +
----------------------------------------------------------
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Residues in contact with SER 110 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106L GLY 3.3 6.7 + - - -
107L TYR* 2.8 33.0 + - - -
109L ASP* 1.3 82.8 - - - +
111L VAL* 1.3 59.8 + - - +
112L HIS* 3.4 14.7 + - - -
----------------------------------------------------------
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Residues in contact with VAL 111 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G ARG* 5.5 0.5 - - - -
4L ASP* 3.8 18.8 - - + +
7L VAL* 3.7 28.3 - - + -
107L TYR* 3.1 44.6 + - + +
108L ALA 3.6 6.7 - - - +
110L SER* 1.3 76.4 - - - +
112L HIS* 1.3 71.5 + - - +
113L ASP* 3.3 5.8 + - + +
----------------------------------------------------------
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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