Contacts of the helix formed by residues 90 - 116 (chain A) in PDB entry 4LZ6
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 GLY 90 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLN* 3.0 14.8 - - - +
4A LYS* 3.2 30.7 - - - +
84A ARG 4.5 2.6 + - - -
85A LEU* 4.2 19.4 - - - +
88A ARG* 1.9 27.5 + - - -
89A ARG* 1.3 57.8 - - - +
91A GLU* 1.3 56.2 + - - -
92A GLU 3.8 0.2 - - - -
93A ALA* 4.0 5.7 - - - +
225A SER* 3.4 12.3 + - - -
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Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 3.3 17.0 - - + +
4A LYS* 3.3 32.8 - - - +
89A ARG 2.2 18.3 + - - +
90A GLY* 1.3 68.4 - - - -
92A GLU* 1.3 64.2 + - - +
93A ALA 3.1 1.3 - - - -
94A ASN* 3.4 23.0 + - + +
95A GLN* 3.0 21.5 + - - +
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Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 3.5 39.6 - - + +
89A ARG* 2.5 42.3 + - + +
91A GLU* 1.3 71.8 - - - +
93A ALA* 1.3 64.1 + - - +
95A GLN* 3.0 25.2 - - - +
96A VAL* 2.8 20.2 + - + +
237A VAL* 3.6 16.5 - - - +
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Residues in contact with ALA 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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80A VAL* 6.0 0.4 - - - +
81A ILE* 3.7 32.1 - - + +
84A ARG* 4.1 19.1 + - - +
85A LEU* 4.7 10.8 - - + -
89A ARG 3.9 0.8 + - - -
90A GLY 4.0 10.8 - - - +
92A GLU* 1.3 70.7 - - - +
94A ASN* 1.3 71.0 + - - +
95A GLN 2.5 3.8 + - - -
96A VAL* 2.6 17.7 + - - +
97A PHE* 3.5 5.9 + - - -
225A SER* 3.1 13.0 - - - +
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Residues in contact with ASN 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS* 5.2 4.1 - - - +
91A GLU* 3.4 35.0 + - + +
93A ALA* 1.3 68.8 - - - +
95A GLN* 1.3 60.5 + - - +
97A PHE* 3.8 9.2 - - - +
225A SER* 2.4 39.2 + - - +
226A LEU 2.6 29.4 + - - -
227A HIS* 3.0 39.7 + - - +
231A LEU* 2.9 30.6 - - + +
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Residues in contact with GLN 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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91A GLU 3.0 12.3 + - - +
92A GLU* 3.0 28.3 - - - +
93A ALA 2.5 7.9 + - - -
94A ASN* 1.3 72.5 - - - +
96A VAL* 1.3 69.0 + - + +
98A GLY* 3.4 1.6 + - - -
99A ASN* 3.1 29.5 + - - +
231A LEU* 3.3 31.8 + - + +
232A ARG* 4.0 7.3 - - - +
233A MET 4.6 3.0 - - - +
235A GLY* 4.7 10.5 - - - -
237A VAL* 5.2 3.3 - - + +
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLY* 4.4 7.9 - - - -
80A VAL* 3.6 28.5 - - + -
81A ILE* 3.6 18.4 - - + -
84A ARG* 4.4 0.9 - - - +
92A GLU* 2.8 18.7 + - - +
93A ALA* 2.6 11.5 + - - +
95A GLN* 1.3 66.5 - - - +
97A PHE* 1.3 61.7 + - - +
99A ASN* 2.4 36.5 + - - +
100A ILE* 2.9 26.5 + - + -
237A VAL* 3.2 33.9 - - + -
241A VAL* 4.8 0.7 - - + -
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Residues in contact with PHE 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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81A ILE* 3.8 10.6 - - + +
93A ALA 3.5 5.4 + - - +
94A ASN 3.8 12.3 - - - +
96A VAL* 1.3 84.9 - - - +
98A GLY* 1.3 63.5 + - - +
100A ILE* 3.0 16.3 + - - +
101A LEU* 3.0 45.2 - - + +
152A PHE* 5.5 4.5 - + - -
159A ILE* 3.7 25.1 - - + -
217A PHE* 2.8 66.2 - + + -
225A SER 4.1 6.5 - - - +
226A LEU* 3.9 18.2 - - + -
228A TRP* 5.8 7.4 - + - -
231A LEU* 5.7 1.6 - - + -
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Residues in contact with GLY 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ASN 3.9 2.4 + - - -
95A GLN 3.4 3.9 + - - -
96A VAL 2.8 4.0 + - - -
97A PHE* 1.3 80.5 - - - +
99A ASN* 1.3 54.6 + - - +
100A ILE 2.9 4.9 - - - -
101A LEU* 2.9 31.3 + - - +
102A THR* 3.1 10.2 + - - +
231A LEU* 4.5 8.8 - - - +
232A ARG* 3.1 23.9 - - - +
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Residues in contact with ASN 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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95A GLN* 3.1 22.3 + - - +
96A VAL* 2.4 49.0 + - - +
98A GLY* 1.3 68.6 - - - +
100A ILE* 1.3 55.4 + - - +
102A THR* 2.6 28.7 + - + -
103A VAL* 3.8 5.9 - - - +
232A ARG* 3.3 6.7 - - + +
233A MET 4.9 0.7 - - - +
234A LYS 4.9 0.4 - - - -
235A GLY* 3.8 20.8 - - - +
237A VAL* 3.5 9.1 - - - +
238A ILE* 3.6 34.0 - - - +
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Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 3.5 37.5 - - + +
74A GLY* 5.5 0.4 - - - -
77A GLY* 5.0 3.6 - - - -
96A VAL* 3.3 26.7 - - + +
97A PHE* 3.1 14.6 - - - +
98A GLY 2.9 0.2 - - - -
99A ASN* 1.3 89.9 - - - +
101A LEU* 1.3 58.0 + - + +
102A THR 2.6 15.4 + - - -
103A VAL* 2.7 20.5 + - + +
104A ILE* 3.0 28.8 + - + +
155A ALA* 5.8 0.9 - - + -
159A ILE* 6.5 0.9 - - + -
237A VAL* 5.0 0.4 - - + -
238A ILE* 5.9 0.4 - - - -
241A VAL* 3.6 33.2 - - + -
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Residues in contact with LEU 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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97A PHE* 3.0 51.8 - - + +
98A GLY* 2.9 15.2 + - - +
100A ILE* 1.3 77.5 - - + +
102A THR* 1.3 62.2 + - - +
104A ILE* 3.5 19.3 - - + +
105A LEU* 2.9 44.5 + - + +
152A PHE* 3.5 39.5 - - + -
155A ALA* 5.3 5.8 - - + -
159A ILE* 6.1 2.5 - - + -
228A TRP* 5.5 13.2 - - + +
232A ARG* 5.3 4.3 - - + -
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Residues in contact with THR 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 GLY 3.1 13.2 + - - +
99A ASN* 2.6 30.3 + - + -
100A ILE 2.6 3.8 + - - -
101A LEU* 1.3 74.8 - - - +
103A VAL* 1.3 79.4 + - - +
105A LEU* 3.5 3.0 - - - +
106A VAL* 2.7 30.4 + - - +
232A ARG* 3.7 20.0 - - - +
233A MET 3.0 28.7 - - - +
234A LYS* 4.7 3.1 - - - -
238A ILE* 4.3 6.6 - - - +
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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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73A LEU* 3.6 41.7 - - + -
99A ASN 3.8 8.5 - - - +
100A ILE* 2.7 12.4 + - + +
102A THR* 1.3 92.8 + - - +
104A ILE* 1.3 64.0 + - - +
106A VAL* 2.9 16.5 - - + +
107A LEU* 2.8 29.6 + - + +
238A ILE* 4.3 24.9 - - + -
242A CYS* 5.7 2.5 - - - -
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Residues in contact with ILE 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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70A ALA* 5.2 6.1 - - + +
73A LEU* 4.4 12.5 - - + +
100A ILE* 3.0 36.7 + - + +
101A LEU* 3.5 22.4 - - + +
102A THR 2.9 0.8 + - - -
103A VAL* 1.3 72.7 - - - +
105A LEU* 1.3 60.0 + - + +
106A VAL 2.7 0.3 + - - -
107A LEU* 2.5 32.9 + - - +
108A SER* 2.7 20.6 + - - +
151A PHE* 3.8 29.8 - - + -
152A PHE* 4.1 13.2 - - + +
155A ALA* 3.8 26.0 - - + -
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Residues in contact with LEU 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 LEU* 2.9 49.5 + - + +
102A THR* 3.8 2.5 - - - +
104A ILE* 1.3 83.1 - - + +
106A VAL* 1.3 61.7 + - - +
108A SER* 3.7 18.9 - - - +
109A VAL* 4.1 10.4 + - - +
148A ILE* 6.3 3.6 - - + -
152A PHE* 5.2 5.2 - - + -
228A TRP* 6.5 2.5 - - + -
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Residues in contact with VAL 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 THR* 2.7 24.3 + - - +
103A VAL* 2.9 25.4 - - + +
104A ILE 2.7 3.8 + - - -
105A LEU* 1.3 72.9 - - - +
107A LEU* 1.3 67.8 + - + +
109A VAL* 3.2 12.8 + - - +
110A ILE* 3.1 30.0 + - + +
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Residues in contact with LEU 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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69A MET* 3.9 32.1 - - + -
70A ALA* 5.6 1.1 - - + +
73A LEU* 4.1 15.5 - - + -
103A VAL* 2.8 20.3 + - + +
104A ILE* 2.5 14.4 + - - +
106A VAL* 1.3 73.9 - - + +
108A SER* 1.3 52.4 + - - +
109A VAL 2.3 20.5 + - - -
110A ILE* 2.4 46.6 + - + +
111A GLY* 3.0 9.5 + - - -
151A PHE* 4.4 17.5 - - + -
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Residues in contact with SER 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ILE* 2.7 25.0 + - - +
105A LEU* 3.7 17.1 - - - +
107A LEU* 1.3 68.8 - - - +
109A VAL* 1.3 57.3 + - - +
111A GLY 4.3 0.2 - - - -
112A PHE* 3.6 12.6 + - - +
147A SER* 3.6 16.9 - - - -
148A ILE* 3.0 45.2 + - - +
151A PHE* 3.5 22.5 - - - -
152A PHE* 6.0 0.2 - - - +
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Residues in contact with VAL 109 (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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105A LEU 4.1 9.0 - - - +
106A VAL 3.2 11.6 + - - +
107A LEU 2.3 14.1 + - - -
108A SER* 1.3 72.3 - - - +
110A ILE* 1.3 58.5 + - + +
111A GLY 2.9 4.9 - - - -
112A PHE* 2.7 13.6 + - + -
113A ILE* 2.6 56.0 + - + +
148A ILE* 6.2 0.9 - - + -
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Residues in contact with ILE 110 (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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106A VAL* 3.1 47.3 - - + +
107A LEU* 2.4 39.9 + - + +
109A VAL* 1.3 76.8 - - + +
111A GLY* 1.3 55.8 + - - +
113A ILE* 3.5 15.4 - - + +
114A SER* 2.8 28.2 + - - +
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Residues in contact with GLY 111 (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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107A LEU 3.0 8.0 + - - -
109A VAL 2.8 1.4 + - - -
110A ILE* 1.3 74.7 - - - +
112A PHE* 1.3 57.6 + - - +
113A ILE 3.2 1.1 - - - -
114A SER* 2.8 12.5 + - - -
115A ALA* 2.8 29.5 + - - +
144A LEU* 3.0 13.0 - - - +
147A SER* 3.7 17.5 - - - -
151A PHE* 5.7 3.8 - - - -
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Residues in contact with PHE 112 (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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108A SER 3.6 17.2 + - - +
109A VAL* 2.7 18.4 + - + +
111A GLY* 1.3 75.3 - - - +
113A ILE* 1.3 68.8 + - + +
115A ALA* 3.5 12.2 - - - +
116A PHE* 3.7 10.0 + - + +
144A LEU 4.0 7.4 - - - +
145A LEU* 2.8 42.3 - - + +
147A SER* 3.7 1.0 + - - -
148A ILE* 5.6 3.8 - - + -
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Residues in contact with ILE 113 (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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109A VAL* 2.6 42.6 + - + +
110A ILE* 3.5 17.0 - - + +
112A PHE* 1.3 76.1 - - + +
114A SER* 1.3 55.5 + - - +
115A ALA 2.8 12.9 + - - -
116A PHE* 2.9 15.7 + - - +
117A THR* 3.1 23.0 + - + +
118A LEU* 5.9 2.2 - - + -
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 2.8 17.9 + - - +
111A GLY* 2.8 30.3 + - - -
113A ILE* 1.3 70.4 - - - +
115A ALA* 1.3 60.6 + - - +
117A THR* 3.4 12.6 - - - -
118A LEU* 2.9 42.2 + - - -
119A LEU* 3.2 9.2 + - - -
144A LEU* 3.2 11.5 - - - +
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLY 2.8 21.2 + - - +
112A PHE* 3.5 9.0 - - - +
113A ILE 2.8 2.8 + - - -
114A SER* 1.3 69.7 - - - +
116A PHE* 1.3 55.3 + - - +
117A THR 2.7 13.7 + - - +
119A LEU* 3.2 30.4 - - + +
141A PHE* 4.1 12.4 - - + +
144A LEU* 3.6 24.7 - - + -
145A LEU* 4.2 19.7 - - + -
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Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 4.0 9.2 - - + +
113A ILE* 2.9 11.2 + - - +
115A ALA* 1.3 73.0 - - - +
117A THR* 1.3 62.0 + - - +
141A PHE* 4.3 18.9 - + + -
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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