Contacts of the helix formed by residues 82 - 111 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F TRP* 4.3 5.2 - - - -
81F GLU* 1.3 78.9 - - - +
83F VAL* 1.3 66.3 + - - +
84F GLU* 3.6 9.3 + - - +
85F GLU* 3.0 40.1 + - - +
86F MET* 2.8 26.8 + - - +
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Residues in contact with VAL 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F PHE* 4.0 15.9 - - + -
35F TRP* 4.4 6.5 - - + -
37F LEU* 3.9 17.9 - - + -
40F LEU* 4.1 4.3 - - + -
82F ASP* 1.3 72.0 - - - +
84F GLU* 1.3 54.0 + - - +
86F MET* 3.0 11.5 + - - +
87F LEU* 2.7 55.5 + - + +
141F ILE* 4.3 2.9 - - + -
146F LEU* 5.0 7.6 - - + -
149F TYR* 4.0 20.9 - - + -
150F LEU* 3.9 23.6 - - + -
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Residues in contact with GLU 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F ASP* 3.4 7.5 + - - +
83F VAL* 1.3 77.8 - - - +
85F GLU* 1.3 59.0 + - - +
87F LEU* 3.1 2.3 + - - +
88F ARG* 2.6 70.2 + - - +
138F LEU* 3.9 22.2 - - + +
141F ILE* 4.3 20.3 - - + +
142F GLN* 3.9 20.9 + - - +
146F LEU* 5.7 3.7 - - + +
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Residues in contact with GLU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ILE 4.8 0.2 - - - +
80F GLY* 4.0 12.1 - - - -
81F GLU* 3.7 31.3 + - - +
82F ASP* 3.0 37.2 + - - +
84F GLU* 1.3 75.1 - - - +
86F MET* 1.3 58.6 + - - +
88F ARG* 3.4 8.6 + - - +
89F SER* 3.0 28.9 + - - -
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Residues in contact with MET 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F HIS* 3.2 58.3 - - + +
31F MET* 3.7 44.2 - - + -
32F PHE* 3.4 30.3 - - + -
35F TRP* 3.7 17.5 - - + -
79F ILE 3.3 11.0 - - - +
80F GLY* 4.6 1.8 - - - +
82F ASP 2.8 27.3 + - - +
83F VAL* 3.3 11.4 - - - +
85F GLU* 1.3 74.0 - - - +
87F LEU* 1.3 65.9 + - - +
89F SER* 3.2 1.3 + - - -
90F ASP* 3.1 19.0 + - - +
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Residues in contact with LEU 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F PHE* 3.9 24.0 - - + -
40F LEU* 5.2 3.1 - - + -
44F GLU* 3.8 22.4 - - - +
83F VAL* 2.7 36.1 + - + +
86F MET* 1.3 73.8 - - - +
88F ARG* 1.3 64.0 + - - +
90F ASP* 3.2 8.3 + - - +
91F LEU* 3.0 22.2 + - - +
133F TRP* 4.7 6.5 - - + -
134F LEU* 4.1 16.2 - - + +
137F GLU* 4.1 15.7 - - + -
138F LEU* 3.7 19.7 - - + -
141F ILE* 4.2 10.8 - - + -
149F TYR* 3.9 17.9 - - - +
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Residues in contact with ARG 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F GLU* 2.6 53.3 + - - +
85F GLU* 3.7 7.9 - - - +
87F LEU* 1.3 77.2 - - - +
89F SER* 1.3 58.2 + - - +
91F LEU* 3.3 9.3 + - + +
92F ALA* 2.9 29.1 + - - +
138F LEU* 4.0 37.7 + - + +
142F GLN* 5.0 9.1 - - - +
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Residues in contact with SER 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F GLN* 3.1 10.6 + - - -
28F HIS* 4.7 0.2 - - - -
78F ASN* 2.6 53.5 + - - +
79F ILE 4.7 1.3 - - - -
80F GLY* 5.9 0.4 - - - -
85F GLU 3.0 18.4 + - - -
86F MET* 3.6 6.7 - - - -
87F LEU 3.1 0.4 - - - -
88F ARG* 1.3 75.6 - - - +
90F ASP* 1.3 64.7 + - - +
92F ALA* 3.4 7.3 + - - +
93F LEU* 3.1 18.2 + - - +
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Residues in contact with ASP 90 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F GLN* 2.9 32.0 + - - +
25F TYR* 3.5 31.2 - - + +
28F HIS* 2.7 29.5 + - - -
44F GLU* 2.9 21.3 - - - +
86F MET 3.1 7.5 + - - +
87F LEU* 3.6 8.4 - - - +
89F SER* 1.3 75.6 - - - +
91F LEU* 1.3 62.0 + - - +
93F LEU* 3.2 7.1 + - - +
94F GLU* 3.0 26.7 + - - +
134F LEU* 4.2 9.4 - - + -
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Residues in contact with LEU 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F LEU 3.0 13.3 + - - +
88F ARG* 3.5 13.9 - - + +
89F SER 3.3 0.2 - - - -
90F ASP* 1.3 73.6 - - - +
92F ALA* 1.3 66.8 + - - +
93F LEU 3.2 0.2 + - - -
94F GLU* 3.2 2.2 + - - +
95F LEU* 3.0 43.1 + - + +
131F ILE* 4.0 27.4 - - + -
134F LEU* 4.1 21.2 - - + +
135F GLU* 4.1 23.3 - - + +
138F LEU* 3.7 24.5 - - + -
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Residues in contact with ALA 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F ARG 2.9 16.9 + - - +
89F SER* 3.4 7.6 + - - +
91F LEU* 1.3 74.6 - - - +
93F LEU* 1.3 57.4 + - - +
95F LEU* 3.4 10.9 + - - +
96F ASP* 3.0 35.8 + - - +
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Residues in contact with LEU 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F ASN* 5.2 7.7 - - + +
20F VAL* 3.7 34.3 - - + -
21F ALA* 3.8 27.4 - - + +
24F GLN* 4.0 21.1 - - + +
25F TYR* 6.1 2.0 - - + -
76F LYS 5.0 5.6 - - - +
89F SER 3.1 12.7 + - - +
90F ASP* 3.4 11.0 - - - +
91F LEU 3.1 0.4 - - - -
92F ALA* 1.3 74.7 - - - +
94F GLU* 1.3 65.7 + - + +
96F ASP* 3.3 10.4 + - + +
97F GLY* 3.0 19.6 + - - -
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Residues in contact with GLU 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F ALA* 6.0 1.6 - - - -
25F TYR* 2.4 36.1 + - + +
51F GLU* 3.6 4.0 - - - +
90F ASP 3.0 20.7 + - - +
91F LEU* 3.2 4.7 + - - +
93F LEU* 1.3 71.5 - - + +
95F LEU* 1.3 60.9 + - - +
97F GLY* 3.2 2.1 + - - -
98F ALA* 2.8 30.8 + - - +
127F GLU* 2.6 39.0 - - - +
130F HIS* 3.1 24.9 + - - -
131F ILE* 3.6 21.3 - - + +
134F LEU* 4.1 9.9 - - + -
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Residues in contact with LEU 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F LEU* 3.0 36.9 + - + +
92F ALA* 3.5 9.0 - - - +
94F GLU* 1.3 77.3 - - - +
96F ASP* 1.3 63.5 + - - +
98F ALA* 3.4 5.5 + - + +
99F LYS* 3.2 31.1 + - - +
131F ILE* 3.6 35.2 - - + -
135F GLU* 5.3 3.6 - - - +
1K MET* 4.5 13.7 - - + -
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Residues in contact with ASP 96 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F ASN* 5.5 0.4 - - - +
92F ALA* 3.0 22.1 + - - +
93F LEU* 3.9 10.4 - - + +
95F LEU* 1.3 75.7 - - - +
97F GLY* 1.3 62.1 + - - +
99F LYS* 3.4 26.4 + - - +
100F ASN* 3.2 30.1 + - - +
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Residues in contact with GLY 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F LEU* 4.6 0.2 - - - +
17F ASN* 3.6 28.2 + - - -
93F LEU 3.0 14.5 + - - -
94F GLU* 3.7 2.7 - - - -
96F ASP* 1.3 74.0 - - - +
98F ALA* 1.3 60.9 + - - +
100F ASN* 3.3 2.6 + - - +
101F LEU* 2.9 36.1 + - - +
127F GLU* 6.1 0.7 - - - -
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Residues in contact with ALA 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F GLU 2.8 17.8 + - - +
95F LEU* 3.7 7.4 - - + +
96F ASP 3.3 0.2 - - - -
97F GLY* 1.3 75.3 - - - +
99F LYS* 1.3 56.8 + - - +
101F LEU* 3.2 4.4 + - - +
102F ARG* 2.8 57.9 + - - +
124F LEU* 3.9 17.2 - - + +
127F GLU* 5.4 3.5 - - + +
128F GLU* 5.2 0.2 - - - +
131F ILE* 4.3 15.9 - - + -
1K MET* 5.8 0.2 - - - -
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Residues in contact with LYS 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F LEU* 3.2 18.1 + - - +
96F ASP* 3.4 32.9 + - - +
98F ALA* 1.3 77.7 - - - +
100F ASN* 1.3 66.5 + - - +
102F ARG* 3.2 11.9 + - - +
103F GLU* 3.1 22.4 + - - +
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Residues in contact with ASN 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F TYR* 4.8 4.1 - - + -
13F LYS* 3.5 34.0 + - - +
14F LEU* 3.7 18.4 - - + +
17F ASN* 2.9 25.1 + - - +
96F ASP* 3.2 15.0 + - - +
97F GLY 3.3 6.5 + - - +
99F LYS* 1.3 80.7 - - - +
101F LEU* 1.3 55.8 + - - +
103F GLU* 3.3 13.4 + - - +
104F ALA* 2.9 30.1 + - - +
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Residues in contact with LEU 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F LEU* 3.8 20.4 - - + -
18F GLU* 5.2 2.0 - - - +
58F TYR* 3.5 20.9 - - - +
97F GLY* 2.9 22.1 + - - +
98F ALA 3.5 4.7 - - - +
100F ASN* 1.3 72.9 - - - +
102F ARG* 1.3 60.9 + - - +
104F ALA* 3.3 2.5 + - - +
105F ILE* 2.9 39.0 + - + +
120F MET* 3.7 31.6 - - + +
123F ILE* 4.1 7.2 - - + -
124F LEU* 3.9 32.5 - - + -
127F GLU* 3.9 20.0 - - + +
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Residues in contact with ARG 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F ALA* 2.8 47.3 + - - +
99F LYS* 3.2 9.8 + - - +
101F LEU* 1.3 74.6 - - - +
103F GLU* 1.3 63.7 + - - +
105F ILE* 4.6 0.4 - - - -
106F GLY 3.3 17.2 + - - -
124F LEU* 4.1 17.2 - - + +
128F GLU* 2.7 36.7 + - - -
1K MET* 3.8 18.2 - - - +
111K VAL 5.4 0.7 - - - -
112K HIS* 3.1 49.4 + - + +
113K ASP* 4.7 9.3 + - - +
114K TYR* 3.5 17.5 - - - -
115K VAL* 4.7 0.6 - - - +
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Residues in contact with GLU 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F LYS* 5.2 1.6 + - - -
10F TYR* 2.6 34.4 + - + +
13F LYS* 6.4 1.3 - - - -
99F LYS* 3.1 13.4 + - - +
100F ASN* 3.7 16.7 + - - +
102F ARG* 1.3 79.3 - - - +
104F ALA* 1.3 61.1 + - - +
106F GLY* 3.3 1.7 + - - -
107F TYR* 3.2 20.1 + - - +
112K HIS* 5.3 3.6 - - - -
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Residues in contact with ALA 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F TYR* 3.7 35.6 - - + -
14F LEU* 3.9 11.2 - - + -
100F ASN 2.9 17.0 + - - +
101F LEU 3.8 2.5 - - - +
103F GLU* 1.3 75.7 - - - +
105F ILE* 1.3 57.4 + - - +
107F TYR* 3.2 3.1 + - - +
108F ALA* 2.9 31.2 + - - +
120F MET* 3.6 23.6 - - + +
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Residues in contact with ILE 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F LEU* 2.9 24.9 + - + +
104F ALA* 1.3 76.0 - - - +
106F GLY* 1.3 61.9 + - - +
108F ALA* 3.4 0.9 + - - +
109F ASP 3.2 17.0 + - - -
117F ARG* 3.3 35.1 + - + +
120F MET* 3.6 40.4 - - + +
121F ILE* 4.0 17.0 - - + -
124F LEU* 3.9 27.6 - - + -
114K TYR* 3.5 32.5 - - + -
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Residues in contact with GLY 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F ARG 3.3 9.5 + - - -
103F GLU 3.3 2.9 + - - -
104F ALA 3.3 0.2 - - - -
105F ILE* 1.3 79.5 - - - +
107F TYR* 1.3 61.5 + - - +
109F ASP* 3.5 4.7 - - - +
110F SER* 3.2 20.4 + - - -
117F ARG* 4.3 4.3 - - - -
112K HIS* 4.8 5.8 - - - -
114K TYR* 3.4 18.1 + - - -
----------------------------------------------------------
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Residues in contact with TYR 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F ASP* 2.9 36.9 + - - -
6F LYS* 3.4 29.9 - - + +
7F VAL* 3.7 15.5 - - + -
10F TYR* 3.8 36.6 - + + +
103F GLU 3.2 7.9 + - - +
104F ALA 3.2 5.0 + - - +
106F GLY* 1.3 75.5 - - - +
108F ALA* 1.3 61.7 + - - +
110F SER* 2.8 32.7 + - - -
111F VAL* 3.1 27.7 + - + +
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Residues in contact with ALA 108 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F VAL* 4.4 7.4 - - + -
104F ALA 2.9 15.9 + - - +
105F ILE 3.8 3.6 - - - +
106F GLY 3.4 0.2 - - - -
107F TYR* 1.3 80.6 - - - +
109F ASP* 1.3 59.8 + - - +
111F VAL* 3.5 9.5 + - - +
112F HIS 3.0 3.6 + - - -
113F ASP* 2.8 50.7 + - + +
116F SER* 4.7 1.8 - - - -
117F ARG* 4.0 4.5 - - + +
120F MET* 3.6 21.5 - - + -
----------------------------------------------------------
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Residues in contact with ASP 109 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F ILE 3.2 5.5 + - - -
106F GLY 3.5 9.0 - - - +
108F ALA* 1.3 76.4 - - - +
110F SER* 1.3 64.4 + - - +
112F HIS* 3.2 14.0 + - - -
114F TYR* 3.3 20.7 + - - -
117F ARG* 3.2 35.0 + - - +
109I ASP* 5.5 3.4 - - - +
117I ARG* 2.7 35.0 + - - -
109K ASP* 5.4 3.7 - - - +
----------------------------------------------------------
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Residues in contact with SER 110 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F GLY 3.2 6.8 + - - -
107F TYR* 2.8 32.2 + - - -
109F ASP* 1.3 81.0 - - - +
111F VAL* 1.3 59.8 + - - +
112F HIS* 3.3 14.9 + - - -
----------------------------------------------------------
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Residues in contact with VAL 111 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F ASP* 3.7 17.9 - - + +
7F VAL* 3.7 27.4 - - + -
107F TYR* 3.1 45.8 + - + +
108F ALA 3.6 7.0 - - - +
110F SER* 1.3 77.3 - - - +
112F HIS* 1.3 72.6 + - - +
113F ASP* 3.3 5.6 + - + +
102I ARG* 5.5 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
------------------------------------------------------------
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