Contacts of the helix formed by residues 82 - 108 (chain A) in PDB entry 4NEF
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 SER 82 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLU* 2.7 30.6 + - - -
76A LEU* 3.8 1.3 - - - -
81A VAL* 1.4 77.3 - - - +
83A VAL* 1.4 59.4 + - - +
84A LEU* 3.7 5.8 + - - +
85A ARG* 3.1 16.1 + - - +
86A ALA* 2.9 25.5 + - - +
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 3.7 28.4 - - + +
82A SER* 1.4 72.7 - - - +
84A LEU* 1.3 59.9 + - + +
86A ALA* 3.7 1.1 - - + +
87A ALA* 3.1 29.6 + - + +
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLU* 4.1 12.3 - - + +
4A LEU* 4.1 25.1 - - + +
9A PHE* 3.7 24.0 - - + -
82A SER* 3.8 9.0 - - - +
83A VAL* 1.3 80.0 - - + +
85A ARG* 1.4 64.0 + - - +
87A ALA* 3.4 5.6 + - + +
88A PHE* 3.2 53.2 + - + -
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Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLU* 2.8 33.8 + - - +
8A ALA* 5.7 1.6 - - - +
9A PHE* 3.7 31.2 - - + +
12A ALA* 3.6 16.4 - - - +
63A SER* 5.4 0.4 - - - +
80A HIS 5.6 0.4 + - - -
81A VAL* 3.6 34.9 - - + +
82A SER* 3.1 15.8 + - - +
84A LEU* 1.4 75.8 - - - +
86A ALA* 1.4 54.6 + - - +
88A PHE* 3.3 1.9 + - - +
89A TYR* 2.8 77.0 + - + +
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A THR* 3.5 20.9 - - + +
73A VAL* 6.0 1.6 - - + -
76A LEU* 3.7 30.5 - - + -
81A VAL* 3.5 7.5 - - + +
82A SER 2.9 17.3 + - - +
83A VAL* 3.7 5.8 - - + +
85A ARG* 1.4 75.4 - - - +
87A ALA* 1.4 55.3 + - - +
90A VAL* 3.0 36.4 + - + +
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL* 3.1 18.6 + - + +
84A LEU* 3.6 7.4 - - + +
85A ARG 3.3 0.2 - - - -
86A ALA* 1.4 72.9 - - - +
88A PHE* 1.4 62.5 + - + +
90A VAL* 3.4 5.9 + - - +
91A ALA* 2.9 32.3 + - - +
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Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.5 29.6 - - + -
9A PHE* 3.5 30.3 - + + -
13A VAL* 3.6 22.9 - - + +
84A LEU* 3.2 45.4 + - + +
85A ARG 3.6 2.5 - - - +
87A ALA* 1.4 80.2 - - + +
89A TYR* 1.4 58.3 + - - +
91A ALA* 4.0 6.5 - - + +
92A ALA* 3.1 27.2 + - - +
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Residues in contact with TYR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA* 3.2 25.5 - - + +
13A VAL* 4.1 12.6 - - + -
16A GLU* 3.7 21.9 - - + +
63A SER* 2.9 29.7 + - - -
66A HIS* 3.3 30.3 - + - -
72A THR* 3.7 20.0 - - + -
81A VAL* 4.9 3.4 - - + -
85A ARG* 2.8 65.2 + - + +
87A ALA 3.3 0.2 - - - -
88A PHE* 1.4 75.5 - - - +
90A VAL* 1.4 53.6 + - - +
92A ALA* 3.1 6.9 + - - +
93A GLN* 2.8 44.7 + - - +
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PRO* 3.9 30.7 - - + +
72A THR* 3.9 15.5 - - + -
73A VAL* 4.8 9.2 - - + -
86A ALA* 3.0 23.0 + - + +
87A ALA* 3.9 5.4 - - - +
89A TYR* 1.4 73.2 - - - +
91A ALA* 1.3 57.8 + - - +
93A GLN* 3.3 9.3 + - - +
94A LEU* 3.0 51.7 + - + +
205A TRP* 6.0 2.9 - - + -
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA 2.9 18.4 + - - +
88A PHE* 4.0 7.4 - - + +
90A VAL* 1.3 78.4 - - - +
92A ALA* 1.4 54.5 + - - +
94A LEU* 3.6 9.3 + - - +
95A LEU* 3.1 40.5 + - + +
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A VAL* 3.5 33.2 - - + +
16A GLU* 4.3 3.6 - - + -
17A PHE* 3.4 25.5 - - + +
88A PHE 3.1 20.0 + - - +
89A TYR 3.1 6.1 + - - +
91A ALA* 1.4 71.9 - - - +
93A GLN* 1.3 55.9 + - - +
95A LEU* 4.6 6.1 - - - -
96A GLY 2.9 28.4 + - - -
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Residues in contact with GLN 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLU* 2.9 28.7 - - + +
20A THR* 3.4 31.3 - - + +
66A HIS* 3.6 3.1 - - - +
68A ASN 3.7 12.6 - - - +
69A PRO* 3.1 41.2 - - + +
72A THR* 2.7 22.3 + - - -
89A TYR* 2.8 19.5 + - - +
90A VAL* 3.3 14.0 + - - +
92A ALA* 1.3 73.3 - - - +
94A LEU* 1.4 59.1 + - - +
96A GLY 3.4 0.2 + - - -
97A ALA* 2.9 32.9 + - - +
186A ALA* 4.1 2.9 - - + -
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PRO* 4.3 7.2 - - + -
90A VAL* 3.0 38.8 + - + +
91A ALA* 4.0 7.6 - - - +
93A GLN* 1.4 74.4 - - - +
95A LEU* 1.3 60.8 + - + +
97A ALA* 3.9 1.7 - - - +
98A VAL* 3.2 30.8 + - - +
186A ALA* 4.1 22.9 - - + +
189A LEU* 3.8 22.9 - - + -
205A TRP* 3.7 29.8 - - + -
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 3.9 14.8 - - + -
91A ALA* 3.1 29.6 + - + +
92A ALA* 3.9 5.8 - - - +
94A LEU* 1.3 74.4 - - + +
96A GLY* 1.3 59.6 + - - +
98A VAL* 3.4 13.8 - - + +
99A ALA* 3.1 28.9 + - - +
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Residues in contact with GLY 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 3.4 36.7 - - - -
21A LEU* 3.1 19.5 - - - +
92A ALA 2.9 13.8 + - - -
93A GLN 3.8 1.1 - - - -
95A LEU* 1.3 73.4 - - - +
97A ALA* 1.3 56.3 + - - +
99A ALA* 3.3 1.6 + - - +
100A GLY 2.9 24.9 + - - -
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A THR* 3.9 6.1 - - + -
24A VAL* 3.3 27.6 - - + +
93A GLN 2.9 18.2 + - - +
94A LEU* 3.9 4.0 - - - +
96A GLY* 1.3 74.3 - - - +
98A VAL* 1.4 57.2 + - + +
100A GLY 3.0 2.3 + - - -
101A ALA 3.0 24.8 + - - -
186A ALA* 3.3 34.5 - - + +
190A ALA* 3.3 7.0 - - + +
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LEU 3.2 14.9 + - - +
95A LEU* 3.4 25.1 - - + +
97A ALA* 1.4 76.9 - - + +
99A ALA* 1.4 57.8 + - + +
101A ALA* 3.8 2.3 - - - +
102A ALA* 2.9 31.8 + - - +
189A LEU* 4.6 8.3 - - + -
190A ALA* 3.8 26.0 - - - +
193A VAL* 4.2 28.9 - - + -
194A VAL* 4.0 4.6 - - + +
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 4.5 7.6 - - + -
21A LEU* 3.8 20.0 - - + -
95A LEU 3.1 20.1 + - - +
96A GLY* 3.5 6.1 - - - +
98A VAL* 1.4 76.5 - - + +
100A GLY* 1.3 57.3 + - - +
102A ALA* 3.9 5.3 - - - +
103A LEU* 3.0 33.6 + - + +
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Residues in contact with GLY 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.5 30.9 - - - +
24A VAL* 4.1 5.8 - - - -
25A PHE* 3.7 12.9 - - - -
96A GLY 2.9 11.4 + - - -
97A ALA 3.0 4.6 + - - -
99A ALA* 1.3 76.6 - - - +
101A ALA* 1.4 55.4 + - - +
103A LEU* 3.7 2.6 + - - -
104A LEU* 3.1 27.5 + - - +
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 3.7 8.6 - - + +
28A LEU* 4.2 8.1 - - + -
97A ALA 3.0 14.1 + - - +
98A VAL 3.8 1.3 - - - +
100A GLY* 1.4 73.3 - - - +
102A ALA* 1.4 59.7 + - - +
104A LEU* 3.5 7.0 + - - +
105A HIS* 3.0 28.8 + - - +
116A LEU* 3.8 11.7 - - + +
190A ALA* 3.7 33.7 - - + +
191A PRO 4.1 2.2 - - - -
194A VAL* 3.8 8.1 - - + -
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A VAL 2.9 18.5 + - - +
99A ALA* 3.9 6.5 - - - +
101A ALA* 1.4 75.1 - - - +
103A LEU* 1.4 62.3 + - - +
105A HIS* 3.5 10.8 + - - +
106A GLU* 3.2 21.3 + - - +
194A VAL* 3.8 14.8 - - + +
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 4.1 20.9 - - + -
25A PHE* 3.7 18.4 - - + -
99A ALA* 3.0 18.4 + - + +
100A GLY* 3.7 6.1 - - - +
102A ALA* 1.4 73.9 - - - +
104A LEU* 1.4 62.1 + - - +
106A GLU* 3.4 18.2 - - - +
107A ILE* 3.2 25.6 + - + +
132C THR* 4.3 13.5 - - + -
136C PHE* 3.7 42.8 - - + -
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL 4.8 0.9 - - - +
25A PHE* 3.8 20.8 - - + +
28A LEU* 3.7 19.7 - - + -
29A GLY* 3.5 34.8 - - - +
32A LEU* 3.7 15.5 - - + -
100A GLY 3.1 16.5 + - - +
101A ALA* 3.7 3.1 - - - +
102A ALA 3.4 0.2 - - - -
103A LEU* 1.4 75.2 - - - +
105A HIS* 1.3 63.4 + - - +
107A ILE* 3.2 14.1 + - + +
108A THR* 2.7 48.9 + - - +
116A LEU* 4.1 10.5 - - + -
174C LEU* 4.6 2.5 - - + -
178C TYR* 3.5 14.4 - - - +
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Residues in contact with HIS 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ALA 3.0 17.0 + - - +
102A ALA* 3.5 8.8 + - - +
104A LEU* 1.3 77.3 - - - +
106A GLU* 1.3 68.2 + - - +
108A THR 3.2 2.9 - - - +
113A ARG* 2.8 68.3 + - + +
116A LEU* 4.3 14.1 - - + +
194A VAL* 4.1 22.1 - - + +
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ALA 3.2 9.5 + - - +
103A LEU* 3.4 20.9 - - - +
104A LEU 3.3 0.2 - - - -
105A HIS* 1.3 87.1 + - - +
107A ILE* 1.3 65.2 - - - +
113A ARG* 4.2 5.0 + - - +
129C GLN* 2.7 28.6 + - - +
132C THR* 4.6 9.7 + - - +
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Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PHE* 3.7 26.9 - - + -
103A LEU* 3.3 16.2 - - + +
104A LEU* 3.5 11.7 - - + +
106A GLU* 1.3 89.0 - - - +
108A THR* 1.3 57.8 + - - +
109A PRO* 3.9 1.7 - - - +
125C THR* 4.2 0.2 - - - +
129C GLN* 3.3 53.9 - - + +
132C THR* 3.7 23.3 - - + -
133C VAL* 3.7 19.1 - - + -
178C TYR* 3.5 37.8 - - + +
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Residues in contact with THR 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.8 25.8 - - + -
33A ASN* 4.3 5.8 - - - +
104A LEU* 2.7 31.5 + - - +
105A HIS* 3.4 0.4 + - - -
107A ILE* 1.3 77.1 - - - +
109A PRO* 1.4 76.3 - - + +
112A ILE* 4.4 4.3 - - + -
113A ARG* 2.7 53.0 + - + +
116A LEU* 5.7 0.4 - - - -
129C GLN* 4.2 1.8 - - - -
178C TYR* 2.9 23.4 + - - +
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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