Contacts of the helix formed by residues 82 - 108 (chain A) in PDB entry 3J41
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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9A PHE* 5.5 0.7 - - - -
76A LEU* 3.9 1.6 - - - -
81A MET* 1.3 78.1 - - - +
83A LEU* 1.3 63.7 + - - +
84A LEU* 3.1 12.2 + - - +
85A ARG* 3.1 27.0 + - - +
86A ALA* 3.1 23.9 + - - +
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Residues in contact with LEU 83 (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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76A LEU* 3.8 32.0 - - + +
81A MET 4.0 0.2 + - - -
82A SER* 1.3 73.4 - - - +
84A LEU* 1.3 58.8 + - - +
86A ALA* 3.9 0.6 - - - +
87A ILE* 3.0 55.1 + - + +
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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
----------------------------------------------------------
9A PHE* 4.5 17.0 - - + -
82A SER* 3.0 9.6 + - - +
83A LEU* 1.3 77.4 - - - +
85A ARG* 1.3 65.1 + - - +
87A ILE* 3.6 6.7 + - + +
88A CYS* 3.1 43.5 + - - -
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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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9A PHE* 3.5 55.4 - - + +
12A ALA* 4.5 8.9 - - - +
62A ILE 5.6 1.0 + - - -
81A MET* 3.8 20.6 - - + +
82A SER* 3.1 25.1 + - - +
84A LEU* 1.3 72.5 - - - +
86A ALA* 1.3 57.0 + - - +
88A CYS* 3.0 2.3 + - - +
89A TYR* 2.6 76.8 + - + +
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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 24.5 - - + -
73A PHE* 6.0 0.2 - - - -
76A LEU* 3.9 27.6 - - + -
81A MET* 3.5 8.6 - - + +
82A SER 3.1 14.3 + - - +
83A LEU 3.9 5.2 - - - +
85A ARG* 1.3 77.7 - - - +
87A ILE* 1.3 58.7 + - + +
89A TYR* 3.1 3.6 + - - +
90A MET* 2.8 38.1 + - - +
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Residues in contact with ILE 87 (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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83A LEU* 3.0 45.2 + - + +
84A LEU* 4.0 6.3 - - + +
85A ARG 3.3 0.4 - - - -
86A ALA* 1.3 75.3 - - + +
88A CYS* 1.3 59.9 + - - +
90A MET* 3.3 11.1 + - + +
91A VAL* 2.9 45.6 + - + +
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Residues in contact with CYS 88 (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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9A PHE* 3.9 19.1 - - + -
10A TRP* 5.5 5.2 - - - -
13A ILE* 3.8 28.1 - - + +
84A LEU* 3.1 37.5 + - - +
85A ARG 3.0 4.8 + - - +
87A ILE* 1.3 77.0 - - - +
89A TYR* 1.3 57.8 + - - +
91A VAL* 3.3 7.7 + - - +
92A ALA* 2.9 31.4 + - - +
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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
----------------------------------------------------------
9A PHE 5.3 0.2 - - - -
12A ALA* 3.6 16.3 - - + +
13A ILE* 4.6 11.0 - - + -
16A GLU* 3.7 28.9 - - + +
63A SER* 2.9 39.8 + - - -
66A HIS* 3.5 32.5 - + - -
72A THR* 3.7 6.1 - - + +
81A MET* 3.7 9.0 - - + -
85A ARG* 2.6 58.3 + - + +
86A ALA 3.2 9.9 - - - +
88A CYS* 1.3 74.5 - - - +
90A MET* 1.3 51.5 + - - +
92A ALA* 3.2 6.0 + - - +
93A GLN* 2.8 47.1 + - - +
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Residues in contact with MET 90 (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* 3.5 35.7 - - + +
72A THR* 4.0 10.1 - - + -
73A PHE* 5.2 8.3 - - + -
86A ALA* 2.8 25.8 + - - +
87A ILE* 3.8 8.7 - - + +
89A TYR* 1.3 73.4 - - - +
91A VAL* 1.3 61.9 + - + +
93A GLN* 3.3 17.7 - - - +
94A LEU* 2.8 42.9 + - + +
205A TRP* 4.4 17.5 - - + -
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Residues in contact with VAL 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 ILE* 2.9 38.8 + - + +
88A CYS* 3.5 9.0 - - - +
90A MET* 1.3 76.5 - - + +
92A ALA* 1.3 66.4 + - - +
94A LEU* 3.8 7.1 - - + +
95A LEU* 3.0 47.6 + - + +
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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 ILE* 3.5 35.2 - - + +
16A GLU* 4.2 4.7 - - + -
17A PHE* 3.5 24.6 - - + +
88A CYS 2.9 18.1 + - - +
89A TYR* 3.5 4.3 - - - +
91A VAL* 1.3 79.3 - - - +
93A GLN* 1.3 52.3 + - - +
95A LEU* 4.9 2.0 - - - -
96A GLY* 2.7 32.6 + - - -
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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* 3.1 26.8 - - + +
20A SER* 3.3 25.3 - - - +
66A HIS* 3.6 2.3 - - - +
67A VAL* 4.0 3.6 - - - -
68A ASN 3.6 9.2 - - - +
69A PRO* 3.0 45.7 - - + +
72A THR* 2.9 20.4 + - - -
89A TYR* 2.8 29.9 + - - +
90A MET* 3.3 13.4 - - - +
92A ALA* 1.3 72.6 - - - +
94A LEU* 1.3 59.9 + - - +
97A ALA* 2.8 30.8 + - - +
186A ALA* 3.8 5.1 - - + +
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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* 4.5 4.5 - - + -
90A MET* 2.8 32.7 + - + +
91A VAL* 3.8 7.0 - - + +
93A GLN* 1.3 74.3 - - - +
95A LEU* 1.3 71.3 + - + +
97A ALA* 3.5 2.1 + - - +
98A VAL* 3.0 31.6 + - - +
186A ALA* 3.9 24.0 - - + -
189A PHE* 3.8 30.6 - - + -
205A TRP* 3.9 29.6 - - + -
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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* 3.8 17.5 - - + -
91A VAL* 3.0 40.4 + - + +
92A ALA* 4.2 2.0 - - - +
94A LEU* 1.3 81.1 - - + +
96A GLY* 1.3 67.4 + - - +
98A VAL* 3.4 7.2 + - + +
99A ALA* 2.9 26.2 + - - +
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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* 3.5 29.5 - - - -
20A SER* 4.0 1.8 - - - -
21A LEU* 3.0 18.7 - - - +
92A ALA 2.7 21.2 + - - -
93A GLN 3.7 0.7 - - - -
95A LEU* 1.3 77.9 - - - +
97A ALA* 1.3 61.4 + - - +
99A ALA* 3.3 0.7 + - - +
100A GLY 3.0 18.2 + - - -
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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 SER* 3.8 3.0 - - - +
24A VAL* 3.4 28.8 - - + +
93A GLN 2.8 18.3 + - - +
94A LEU 3.8 4.0 - - - +
95A LEU 3.3 0.2 - - - -
96A GLY* 1.3 75.9 - - - +
98A VAL* 1.3 64.5 + - - +
100A GLY* 2.9 3.8 + - - -
101A ALA* 2.8 23.2 + - - +
186A ALA* 3.3 31.2 - - + +
190A ALA* 3.6 7.2 - - + +
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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 3.0 19.0 + - - +
95A LEU* 3.7 7.4 - - + +
97A ALA* 1.3 75.4 - - - +
99A ALA* 1.3 59.1 + - - +
101A ALA* 3.3 3.5 + - - +
102A ALA* 2.8 29.7 + - + +
189A PHE* 3.9 28.0 - - + -
190A ALA* 3.7 10.3 - - - +
193A ILE* 4.1 13.5 - - + -
194A LEU* 3.8 20.6 - - + +
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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* 4.4 10.8 - - + -
21A LEU* 4.0 17.5 - - + -
95A LEU 2.9 18.5 + - - +
96A GLY 3.6 4.5 - - - +
98A VAL* 1.3 78.1 - - - +
100A GLY* 1.3 52.6 + - - +
102A ALA* 2.9 8.3 + - - +
103A VAL* 2.7 42.9 + - + +
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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 37.8 - - - +
25A PHE* 3.4 14.3 - - - -
96A GLY 3.0 7.9 + - - -
97A ALA 2.9 6.0 + - - -
99A ALA* 1.3 77.5 - - - +
101A ALA* 1.3 57.5 + - - +
103A VAL* 4.5 0.9 - - - -
104A LEU* 2.9 30.2 + - - +
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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* 4.0 1.4 - - - +
28A LEU* 3.9 21.1 - - + -
97A ALA 2.8 15.7 + - - +
98A VAL 3.5 1.6 - - - +
100A GLY* 1.3 76.3 - - - +
102A ALA* 1.3 58.4 + - - +
104A LEU* 3.3 7.5 - - - +
105A TYR* 2.9 28.8 + - - +
116A LEU* 4.3 7.6 - - + +
190A ALA* 3.8 20.9 - - + +
191A PRO 4.7 0.2 - - - -
194A LEU* 3.5 21.1 - - + +
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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* 2.8 17.3 + - + +
99A ALA* 3.1 13.0 - - - +
101A ALA* 1.3 73.6 - - - +
103A VAL* 1.3 69.0 + - + +
105A TYR* 3.0 9.6 + - - +
106A SER* 2.9 21.7 + - - -
194A LEU* 3.6 13.2 - - + +
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Residues in contact with VAL 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* 4.9 6.1 - - + -
25A PHE* 3.9 13.2 - - + -
99A ALA* 2.7 29.7 + - + +
100A GLY* 4.0 5.4 - - - +
102A ALA* 1.3 73.6 - - + +
104A LEU* 1.3 60.4 + - - +
106A SER* 2.7 26.0 + - - +
107A VAL* 3.2 17.5 + - + +
132D ILE* 4.6 3.4 - - + -
136D PHE* 3.5 35.7 - - + -
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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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25A PHE* 3.5 27.1 - - + +
28A LEU* 4.0 23.6 - - + -
29A GLY* 3.8 15.3 - - - +
32A LEU* 4.1 11.2 - - + -
100A GLY 2.9 20.0 + - - +
101A ALA* 3.3 6.1 - - - +
102A ALA 3.0 0.2 - - - -
103A VAL* 1.3 74.8 - - - +
105A TYR* 1.3 56.9 + - - +
107A VAL* 3.2 3.3 + - + -
108A THR* 2.7 35.1 + - + +
116A LEU* 3.6 29.8 - - + -
174D PHE* 3.9 11.7 - - + -
178D TYR* 3.6 23.1 - - + +
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Residues in contact with TYR 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 2.9 13.8 + - - +
102A ALA* 3.3 11.4 - - - +
104A LEU* 1.3 77.1 - - - +
106A SER* 1.3 67.5 + - - +
108A THR* 3.2 21.6 + - - +
113A ARG* 3.1 61.1 + - + -
116A LEU* 4.2 24.2 - - + -
194A LEU* 5.5 5.2 - - + -
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Residues in contact with SER 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ALA 2.9 11.0 + - - -
103A VAL* 2.7 24.4 + - - +
105A TYR* 1.3 84.5 - - - +
107A VAL* 1.3 58.5 + - - +
113A ARG* 4.8 3.0 + - - +
129D GLN* 2.6 28.5 + - - +
132D ILE* 5.5 2.4 - - - +
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 5.2 5.2 - - + -
103A VAL* 3.3 17.9 - - + +
104A LEU* 3.2 5.5 + - + +
106A SER* 1.3 84.8 + - - +
108A THR* 1.3 60.6 + - - +
109A PRO* 4.0 2.3 - - - +
125D VAL* 4.6 1.7 - - - +
129D GLN* 2.8 53.0 + - + +
132D ILE* 3.6 33.9 - - + -
133D VAL* 3.1 22.4 - - + -
178D TYR* 3.7 12.8 - - + -
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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* 3.6 16.6 - - + +
104A LEU* 2.7 29.6 + - + +
105A TYR* 3.2 17.0 - - - +
107A VAL* 1.3 79.8 - - - +
109A PRO* 1.3 74.8 + - - +
112A VAL* 4.0 4.0 - - - +
113A ARG* 2.8 47.8 + - + +
116A LEU* 4.8 0.9 - - + -
129D GLN* 4.5 3.5 + - - -
178D TYR* 3.5 22.2 + - - -
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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
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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