Contacts of the helix formed by residues 78 - 107 (chain F) in PDB entry 4NFI
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 78 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F ARG 4.8 6.1 + - - +
76F LYS* 3.4 10.1 + - - +
77F GLN* 1.3 80.0 - - - +
79F ALA* 1.3 65.0 + - - +
80F ASP* 3.3 11.8 + - - +
81F SER* 2.8 41.2 + - - -
82F LEU* 3.0 23.0 + - - +
84F ARG* 4.4 1.0 + - - -
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Residues in contact with ALA 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F ASP* 1.3 74.7 - - - +
80F ASP* 1.3 65.0 + - - +
82F LEU* 3.5 6.4 + - - +
83F GLN* 3.0 33.4 + - + +
86F TRP* 5.3 0.5 - - - -
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Residues in contact with ASP 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F ASP* 3.3 7.9 + - - +
79F ALA* 1.3 79.3 - - - +
81F SER* 1.3 67.7 + - - +
83F GLN* 3.3 10.8 + - - +
84F ARG* 3.1 45.8 + - - +
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Residues in contact with SER 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F PHE* 3.9 19.5 - - - -
76F LYS 3.3 25.4 + - - -
77F GLN* 4.4 0.2 - - - -
78F ASP* 2.8 25.8 + - - -
80F ASP* 1.3 74.3 - - - +
82F LEU* 1.3 58.5 + - - +
84F ARG* 3.1 28.5 + - - +
85F ALA* 3.0 26.9 + - - +
216F MET* 4.7 0.2 - - - +
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Residues in contact with LEU 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F VAL* 5.2 2.2 - - + -
68F PHE* 4.0 24.2 - - + -
69F ARG* 3.5 50.3 - - + +
77F GLN* 3.9 18.8 - - + +
78F ASP 3.0 15.3 + - - +
79F ALA* 3.9 6.3 - - - +
81F SER* 1.3 74.3 - - - +
83F GLN* 1.3 65.6 + - - +
85F ALA* 3.1 6.0 + - + +
86F TRP* 2.9 53.6 + - + +
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Residues in contact with GLN 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F HIS* 3.3 24.6 + - - -
23F GLN* 4.3 9.6 + - - +
79F ALA* 3.0 23.0 + - - +
80F ASP* 3.3 12.8 + - - +
82F LEU* 1.3 74.6 - - - +
84F ARG* 1.3 58.8 + - + +
86F TRP* 3.5 18.5 + - + -
87F THR* 2.9 32.9 + - - -
146F TYR* 3.9 22.0 + - + -
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Residues in contact with ARG 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F ASP* 4.4 1.4 + - - -
80F ASP* 3.1 33.2 + - - +
81F SER* 3.1 37.2 + - - +
83F GLN* 1.3 77.8 - - - +
85F ALA* 1.3 58.0 + - - +
87F THR* 3.2 6.2 + - - -
88F VAL* 2.9 33.1 + - - +
146F TYR* 3.4 36.0 + - + +
147F CYS* 4.3 6.5 - - - -
150F GLN* 3.5 32.3 + - - +
152F TYR* 3.2 21.2 + - - +
216F MET* 3.6 12.8 - - + +
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Residues in contact with ALA 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F VAL* 3.9 8.1 - - + +
65F VAL* 3.9 11.8 - - + +
68F PHE* 3.6 45.1 - - + -
81F SER 3.0 10.0 + - - +
82F LEU* 3.1 10.1 + - + +
84F ARG* 1.3 77.7 - - - +
86F TRP* 1.3 56.2 + - - +
88F VAL* 3.3 1.4 + - - -
89F GLY* 2.9 26.0 + - - -
216F MET* 3.5 12.3 - - + +
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Residues in contact with TRP 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F GLU* 5.0 3.0 + - - -
16F ASP* 3.6 42.5 - - + +
17F PHE* 3.6 15.9 - + + +
20F HIS* 3.6 41.3 - + + +
65F VAL* 3.5 39.2 - - + +
69F ARG* 4.7 4.7 - - - +
79F ALA 5.3 0.7 - - - -
82F LEU* 2.9 47.3 + - + +
83F GLN* 3.8 22.2 - - + +
85F ALA* 1.3 76.1 - - + +
87F THR* 1.3 62.2 + - - +
89F GLY 3.5 0.2 + - - -
90F TRP* 3.0 28.8 + - - -
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Residues in contact with THR 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F HIS* 3.0 19.1 - - - -
24F ILE* 4.0 8.6 - - + +
83F GLN 2.9 21.4 + - - -
84F ARG* 3.2 5.6 + - - +
86F TRP* 1.3 78.3 - - - +
88F VAL* 1.3 60.8 + - + +
90F TRP* 3.1 4.9 + - - +
91F CYS* 2.8 29.4 + - - -
142F LEU* 3.9 23.0 - - + +
143F LEU* 5.7 0.4 - - - -
146F TYR* 3.5 43.5 - - + -
147F CYS* 5.6 0.7 - - - -
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Residues in contact with VAL 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F VAL* 4.1 8.1 - - + -
84F ARG 2.9 19.4 + - - +
85F ALA 3.9 2.9 - - - +
87F THR* 1.3 75.0 - - + +
89F GLY* 1.3 65.2 + - - +
91F CYS* 3.1 8.6 + - - +
92F VAL* 3.1 21.5 + - - +
143F LEU* 4.1 7.4 - - + -
147F CYS* 4.0 13.5 - - - -
156F LEU* 3.9 18.6 - - + -
160F PHE* 4.3 15.5 - - + -
212F ALA* 3.9 28.3 - - + -
216F MET* 3.9 22.0 - - + -
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Residues in contact with GLY 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F PHE* 3.8 5.6 - - - -
61F GLY* 3.3 38.6 - - - -
64F VAL* 3.8 9.2 - - - +
85F ALA 2.9 17.2 + - - -
86F TRP 3.8 2.2 - - - -
88F VAL* 1.3 76.2 - - - +
90F TRP* 1.3 60.6 + - - +
92F VAL* 3.1 10.0 + - - +
93F GLU* 3.1 9.9 + - - +
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Residues in contact with TRP 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F PHE* 2.9 61.4 + + - -
18F VAL* 4.3 7.6 - - - -
20F HIS* 4.0 6.7 - - - -
21F PHE* 3.4 49.9 - + + +
24F ILE* 3.9 32.3 - - + -
53F ALA* 3.5 21.3 - - + -
54F ILE* 3.8 7.9 - - + -
58F TYR* 3.8 24.9 - + - -
86F TRP 3.0 16.5 + - - +
87F THR 3.6 6.7 - - - +
89F GLY* 1.3 74.7 - - - +
91F CYS* 1.3 55.8 + - - +
93F GLU* 3.1 21.0 + - + +
94F LEU* 2.8 38.3 + - + +
142F LEU* 5.2 0.9 - - + -
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Residues in contact with CYS 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F THR* 2.8 19.7 + - - -
88F VAL* 3.1 11.4 + - - +
90F TRP* 1.3 75.2 - - - +
92F VAL* 1.3 63.5 + - - +
94F LEU* 3.2 9.9 + - - +
95F LEU* 2.9 23.0 + - - +
139F ILE* 3.6 34.7 - - + +
142F LEU* 3.7 21.8 - - - -
143F LEU* 4.1 15.9 - - - -
160F PHE* 3.7 21.1 - - + -
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Residues in contact with VAL 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F ARG* 3.7 29.8 - - + +
61F GLY* 4.4 4.7 - - - -
64F VAL* 3.8 19.1 - - + -
88F VAL* 3.1 14.7 + - + +
89F GLY 3.1 6.9 + - - +
91F CYS* 1.3 75.1 - - - +
93F GLU* 1.3 57.8 + - - +
95F LEU* 3.2 5.8 + - + +
96F GLN* 3.0 26.0 + - - +
160F PHE* 3.7 20.6 - - + -
204F TYR* 4.4 9.1 - - + +
208F LEU* 4.2 25.4 - - + -
209F PRO* 4.6 5.4 - - + -
212F ALA* 5.5 0.7 - - + -
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Residues in contact with GLU 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F PHE* 4.2 13.0 - - + -
53F ALA* 4.4 7.0 - - - +
58F TYR* 3.4 37.7 + - + -
59F ASN 4.0 0.2 + - - -
60F ARG* 3.6 13.0 + - - +
61F GLY* 2.9 27.8 + - - +
89F GLY 3.1 14.2 + - - +
90F TRP* 3.1 30.8 + - + +
92F VAL* 1.3 77.2 - - - +
94F LEU* 1.3 58.6 + - - +
96F GLN* 3.3 8.6 + - - +
97F ALA* 2.9 27.8 + - - +
113F ARG* 4.2 17.8 + - - -
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Residues in contact with LEU 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F PHE* 5.6 0.4 - - + -
24F ILE* 4.9 5.8 - - + -
28F LEU* 4.9 3.6 - - + -
49F LEU* 3.3 31.9 - - + -
53F ALA* 4.2 12.6 - - + -
90F TRP* 2.8 22.9 + - + +
91F CYS* 3.2 10.1 + - - +
93F GLU* 1.3 72.5 - - - +
95F LEU* 1.3 66.6 + - - +
97F ALA* 3.2 4.1 + - - +
98F PHE* 2.9 24.6 + - - +
135F LEU* 3.9 22.6 - - + +
138F CYS* 4.0 20.9 - - + -
139F ILE* 3.9 11.9 - - + +
142F LEU* 3.7 30.3 - - + -
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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
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91F CYS 2.9 12.7 + - - +
92F VAL* 3.4 10.3 - - - +
94F LEU* 1.3 76.9 - - - +
96F GLN* 1.3 62.0 + - - +
98F PHE* 3.3 16.7 + - + +
99F PHE* 3.0 57.7 + - + -
136F GLU* 4.9 2.7 - - + -
139F ILE* 3.5 22.8 - - + +
140F TYR* 5.6 1.1 - - - +
160F PHE* 4.7 7.4 - - + -
163F SER* 5.1 3.6 - - - -
164F SER* 3.5 24.2 - - - +
204F TYR* 4.3 8.1 - - + -
208F LEU* 3.6 30.3 - - + -
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Residues in contact with GLN 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F ARG* 3.4 36.2 - - - +
92F VAL 3.0 12.9 + - - +
93F GLU* 3.5 15.3 - - - +
94F LEU 3.3 0.2 - - - -
95F LEU* 1.3 75.8 - - - +
97F ALA* 1.3 58.9 + - - +
99F PHE* 3.3 6.7 + - - +
100F LEU* 2.9 45.8 + - - +
112F ARG* 4.9 7.9 - - - +
113F ARG* 3.7 22.9 - - - +
204F TYR* 2.4 38.9 + - + -
401F JD5 5.6 2.2 + - - -
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Residues in contact with ALA 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F ASN* 3.6 21.3 - - + +
53F ALA* 4.1 12.6 - - + -
93F GLU 2.9 16.2 + - - +
94F LEU* 3.2 9.2 + - - +
96F GLN* 1.3 78.3 - - - +
98F PHE* 1.3 61.4 + - - +
100F LEU* 3.5 11.3 - - - +
101F VAL* 3.1 30.7 + - - +
113F ARG* 5.1 0.7 - - - +
135F LEU* 3.8 18.8 - - + -
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Residues in contact with PHE 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F LEU 2.9 12.4 + - - +
95F LEU* 3.4 14.1 - - + +
97F ALA* 1.3 75.1 - - - +
99F PHE* 1.3 93.5 + + - +
101F VAL 3.5 0.2 + - - -
102F ALA* 3.3 18.2 + - + +
132F ALA* 3.2 38.5 - - + +
133F ASN* 3.8 24.9 - - - -
135F LEU* 3.9 4.9 - - + +
136F GLU* 3.6 46.4 - - + +
164F SER* 5.3 0.7 - - - -
168F GLU* 3.9 10.1 - - - -
401F JD5 3.5 30.1 - + - -
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Residues in contact with PHE 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F LEU* 3.0 38.3 + - + -
96F GLN* 3.6 6.1 - - - +
98F PHE* 1.3 111.9 - + - +
100F LEU* 1.3 57.1 + - - +
102F ALA* 3.7 0.3 - - - +
103F ASP* 2.8 32.7 + - - +
164F SER* 4.3 8.5 - - - -
167F THR* 3.6 27.1 - - + -
168F GLU* 4.5 7.6 - - - -
204F TYR* 3.6 46.2 - + - +
401F JD5 3.3 43.0 - + + -
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Residues in contact with LEU 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F ASN* 3.9 13.2 - - - +
96F GLN* 2.9 29.6 + - - +
97F ALA* 3.5 12.8 - - - +
99F PHE* 1.3 72.9 - - - +
101F VAL* 1.4 78.7 + - + +
103F ASP* 4.2 6.1 - - - -
104F ASP* 2.9 38.3 + - - +
112F ARG* 3.8 44.2 - - + +
113F ARG* 3.4 44.6 - - - +
401F JD5 5.7 2.0 - - - -
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Residues in contact with VAL 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F VAL* 5.8 0.2 - - + -
52F ASN* 3.5 37.2 - - + +
97F ALA 3.1 18.7 + - - +
98F PHE 3.9 2.9 - - - +
100F LEU* 1.4 82.1 - - + +
102F ALA* 1.3 62.4 + - - +
104F ASP* 3.5 4.5 + - - +
105F ILE* 3.4 21.6 + - + +
118F TRP* 4.2 13.0 - - + -
119F TYR* 5.0 2.2 - - - +
128F ALA* 3.6 38.6 - - + +
131F ASP* 5.3 0.2 - - + -
132F ALA* 3.8 9.9 - - + +
135F LEU* 4.4 6.5 - - + -
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Residues in contact with ALA 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F PHE* 3.3 10.8 + - + +
99F PHE 3.8 0.4 - - - +
101F VAL* 1.3 76.8 - - - +
103F ASP* 1.3 66.0 + - - +
105F ILE* 3.2 15.0 + - - +
106F MET* 3.1 31.9 + - + +
129F ILE* 6.3 1.1 - - - -
132F ALA* 4.4 8.7 - - + +
401F JD5 3.5 34.8 - - + +
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Residues in contact with ASP 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F PHE 2.8 22.2 + - - +
100F LEU* 3.8 5.4 - - - +
102F ALA* 1.3 73.3 - - - +
104F ASP* 1.3 57.6 + - - +
106F MET* 3.2 4.1 + - - -
107F ASP* 2.8 32.5 + - - +
112F ARG* 3.7 5.2 + - - -
171F GLN* 3.7 4.0 + - - -
401F JD5 2.9 46.5 + - + -
402F MG 2.1 24.9 - - - -
404F MG 2.1 28.9 - - - -
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Residues in contact with ASP 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F LEU* 2.9 23.5 + - - +
101F VAL* 3.9 5.1 - - - +
103F ASP* 1.3 78.6 - - - +
105F ILE* 1.3 62.0 + - - +
108F SER 3.2 2.1 + - - -
109F SER* 3.0 43.4 + - - -
111F THR 4.9 0.7 - - - +
112F ARG* 2.8 46.6 + - - +
117F CYS* 3.5 34.4 - - + +
118F TRP 5.7 0.3 + - - -
119F TYR* 3.3 11.3 - - + -
401F JD5 4.5 0.3 + - - -
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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 VAL 3.4 17.5 + - - +
102F ALA* 3.4 13.0 - - - +
103F ASP 3.2 0.6 - - - -
104F ASP* 1.3 77.2 - - - +
106F MET* 1.3 65.8 + - + +
108F SER* 3.2 16.1 + - - -
119F TYR* 3.5 36.5 + - + -
126F LEU* 3.9 24.5 - - + -
128F ALA* 4.0 24.0 - - + -
129F ILE* 4.1 24.5 - - + +
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Residues in contact with MET 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F ALA* 3.1 28.4 + - + +
103F ASP* 3.8 3.8 - - - +
105F ILE* 1.3 83.6 - - + +
107F ASP* 1.3 65.9 + - - +
108F SER* 3.4 2.3 + - - -
171F GLN* 3.9 9.4 - - + +
175F LEU* 3.8 34.5 - - + +
264F ASP* 5.6 0.7 - - - -
401F JD5 3.5 41.1 - - + +
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Residues in contact with ASP 107 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F ASP* 2.8 20.9 + - - +
106F MET* 1.3 78.3 - - - +
108F SER* 1.3 70.8 + - - +
109F SER* 3.3 14.5 + - - +
175F LEU* 4.6 5.5 - - - +
260F THR* 3.6 9.5 + - - +
261F ASP* 5.7 0.7 - - - +
264F ASP* 2.6 31.4 - - - +
266F LYS* 3.1 24.4 + - - -
401F JD5 2.7 1.0 + - - -
402F MG 2.1 31.2 - - - -
404F MG 2.2 21.5 - - - -
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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