Contacts of the helix formed by residues 104 - 140 (chain A) in PDB entry 4JRZ
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 ARG 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A TYR* 3.5 19.8 - - + -
97A TYR* 3.6 56.6 - - + +
100A SER 3.7 0.4 + - - -
101A ALA* 3.0 37.7 + - - +
102A GLN 3.1 1.0 - - - -
103A LEU* 1.3 80.5 - - - +
105A LEU* 1.3 84.1 + - + +
106A ALA 3.6 1.6 - - - -
107A PRO* 3.5 4.9 - - - +
108A LEU* 3.0 27.0 + - + +
211A GTX 2.7 40.0 + - - -
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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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102A GLN* 3.5 40.8 + - + +
104A ARG* 1.3 120.9 - - + +
106A ALA* 1.3 58.2 + - - +
108A LEU* 3.1 14.4 + - + +
109A TYR* 3.0 59.8 + - + +
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Residues in contact with ALA 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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92A ARG* 5.5 0.4 - - - -
102A GLN 4.9 1.6 + - - -
103A LEU 5.2 0.4 - - - -
105A LEU* 1.3 77.1 - - - +
107A PRO* 1.3 72.3 - - + +
109A TYR* 3.0 15.1 + - + +
110A ALA* 3.0 21.1 + - - +
113A ARG* 5.2 1.2 + - - -
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Residues in contact with PRO 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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89A ALA* 3.5 7.5 - - - +
92A ARG* 3.5 31.6 - - + +
93A TYR* 3.3 34.0 - - - +
103A LEU 3.9 12.8 - - - +
104A ARG 3.5 13.7 - - - +
106A ALA* 1.3 94.5 - - + +
108A LEU* 1.3 54.1 + - - -
110A ALA* 3.7 8.4 - - + +
111A SER* 3.0 29.5 + - - -
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Residues in contact with LEU 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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90A ARG* 4.0 11.2 - - - +
93A TYR* 3.7 20.8 - - + -
104A ARG 3.0 20.9 + - - +
105A LEU* 3.3 18.8 - - + +
106A ALA 3.1 0.6 - - - -
107A PRO* 1.3 76.7 - - - +
109A TYR* 1.3 69.3 + - + +
111A SER* 2.9 27.4 + - - +
112A ALA* 2.9 19.3 + - + +
211A GTX 3.3 57.0 - - + +
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Residues in contact with TYR 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* 3.0 53.3 + - + +
106A ALA* 3.0 11.0 + - + +
108A LEU* 1.3 86.4 - - + +
110A ALA* 1.3 66.6 + - - +
112A ALA* 3.6 5.3 + - + +
113A ARG* 3.2 45.2 + - - +
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 5.2 6.1 - - + +
89A ALA* 3.9 5.6 - - + -
92A ARG* 3.2 29.8 - - - +
106A ALA 3.0 10.8 + - - +
107A PRO 3.7 5.8 - - - +
109A TYR* 1.3 75.7 - - - +
111A SER* 1.3 62.6 + - - +
113A ARG* 3.1 34.5 + - - +
114A ALA* 3.1 14.3 + - - +
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Residues in contact with SER 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TYR* 3.3 20.7 - - - -
89A ALA* 3.5 16.9 - - - +
90A ARG* 3.8 31.8 + - - -
107A PRO 3.0 15.5 + - - -
108A LEU* 2.9 26.9 + - - +
110A ALA* 1.3 76.7 - - - +
112A ALA* 1.3 55.7 + - - +
114A ALA* 3.6 2.1 + - - +
115A LEU* 3.1 23.0 + - - +
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Residues in contact with ALA 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 LEU* 2.9 18.3 + - + +
109A TYR* 4.2 6.5 - - + +
110A ALA 3.2 0.2 - - - -
111A SER* 1.3 81.1 + - - +
113A ARG* 1.3 61.9 + - + +
115A LEU* 4.3 7.0 - - - -
116A PHE* 2.9 28.9 + - - +
211A GTX 3.6 30.0 - - + +
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Residues in contact with ARG 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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106A ALA 5.2 0.6 + - - -
109A TYR* 3.2 37.0 + - - +
110A ALA* 3.1 28.7 + - - +
112A ALA* 1.3 75.7 - - + +
114A ALA* 1.3 58.3 + - - +
116A PHE* 3.2 11.0 + - - +
117A LEU* 2.9 29.3 + - - +
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Residues in contact with ALA 114 (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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82A CYS* 4.0 18.3 - - - +
85A VAL* 3.9 25.8 - - + -
86A TYR* 4.0 10.3 - - - +
110A ALA 3.1 14.5 + - - +
111A SER 3.8 4.3 - - - +
113A ARG* 1.3 75.3 - - - +
115A LEU* 1.3 64.6 + - - +
117A LEU* 3.2 11.0 + - - +
118A LEU* 3.1 28.2 + - - +
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Residues in contact with LEU 115 (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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59A TYR* 3.8 34.3 - - + -
62A LEU* 4.4 12.1 - - + +
63A PHE* 4.1 20.2 - - + +
66A THR* 3.8 24.7 - - + +
86A TYR* 4.1 18.3 - - + +
111A SER 3.1 19.1 + - - +
112A ALA* 3.8 6.7 - - - +
114A ALA* 1.3 75.3 - - - +
116A PHE* 1.3 61.6 + - - +
118A LEU* 3.4 7.7 + - + +
119A VAL* 3.1 32.3 + - + +
211A GTX 4.3 17.3 - - + -
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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
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112A ALA 2.9 18.6 + - - +
113A ARG* 3.3 10.8 - - - +
114A ALA 3.2 0.2 - - - -
115A LEU* 1.3 76.2 - - - +
117A LEU* 1.3 73.7 + - + +
119A VAL* 3.4 8.4 + - + +
120A ALA* 3.0 32.1 + - + +
211A GTX 3.6 20.2 - - + +
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Residues in contact with LEU 117 (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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82A CYS* 4.1 23.8 - - - -
113A ARG 2.9 13.2 + - - +
114A ALA* 3.2 13.0 + - - +
116A PHE* 1.3 81.6 - - + +
118A LEU* 1.3 59.9 + - - +
120A ALA* 3.1 11.3 + - + +
121A LEU* 2.9 45.6 + - + +
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PHE* 4.0 30.1 - - + -
66A THR* 3.6 26.1 - - - +
67A LEU* 4.3 10.1 - - + -
70A ALA* 3.6 13.0 - - + +
79A ALA* 3.6 39.9 - - + +
82A CYS* 3.6 19.1 - - + +
83A GLY 4.4 3.8 - - - +
86A TYR* 5.2 1.1 - - + -
114A ALA 3.1 16.9 + - - +
115A LEU* 3.7 10.3 - - + +
116A PHE 3.4 0.2 - - - -
117A LEU* 1.3 76.6 - - - +
119A VAL* 1.3 56.3 + - - +
121A LEU* 4.4 3.4 - - + -
122A ALA* 2.9 30.1 + - - +
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Residues in contact with VAL 119 (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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66A THR* 4.1 22.9 - - + -
115A LEU* 3.1 24.2 + - + +
116A PHE* 3.7 13.7 - - + +
117A LEU 3.2 0.4 - - - -
118A LEU* 1.3 75.7 - - - +
120A ALA* 1.3 58.4 + - - +
122A ALA* 3.5 6.4 + - - +
123A ALA* 2.9 31.4 + - + +
211A GTX 5.3 6.3 - - + -
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Residues in contact with ALA 120 (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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116A PHE* 3.0 27.6 + - + +
117A LEU* 3.1 17.5 + - + +
119A VAL* 1.3 76.6 - - - +
121A LEU* 1.3 62.3 + - + +
123A ALA* 3.3 5.8 + - - +
124A LEU* 2.8 41.1 + - + +
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Residues in contact with LEU 121 (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* 4.1 7.9 - - + -
74A PHE* 3.6 58.1 - - + +
78A ALA* 4.3 19.3 - - + -
79A ALA* 4.8 5.4 - - + +
82A CYS* 4.4 18.6 - - - -
117A LEU* 2.9 31.4 + - + +
118A LEU* 3.7 6.7 - - + +
120A ALA* 1.3 78.0 - - + +
122A ALA* 1.3 56.8 + - - +
124A LEU* 3.3 7.8 + - + -
125A GLY* 2.8 28.4 + - - -
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Residues in contact with ALA 122 (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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66A THR* 4.4 5.6 - - - +
69A VAL* 3.8 26.2 - - + +
70A ALA* 3.8 18.3 - - + +
73A PHE* 4.8 0.3 - - - +
118A LEU 2.9 22.1 + - - +
119A VAL* 3.7 7.2 - - - +
121A LEU* 1.3 72.4 - - - +
123A ALA* 1.3 58.2 + - - +
125A GLY* 3.6 1.9 - - - -
126A LEU* 2.9 36.6 + - + +
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Residues in contact with ALA 123 (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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119A VAL* 2.9 21.9 + - + +
120A ALA* 3.7 5.6 - - - +
122A ALA* 1.3 73.1 - - - +
124A LEU* 1.3 62.3 + - + +
126A LEU* 3.3 4.8 + - - -
127A LEU* 2.9 37.9 + - + +
207A PLM 3.8 17.3 - - + +
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Residues in contact with LEU 124 (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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74A PHE* 4.4 21.1 - - + -
120A ALA* 2.8 29.5 + - + +
121A LEU* 3.6 8.7 - - + +
123A ALA* 1.3 72.4 - - + +
125A GLY* 1.3 63.2 + - - +
127A LEU* 3.1 15.3 + - + +
128A ALA* 3.0 25.5 + - - +
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Residues in contact with GLY 125 (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 PHE* 3.2 38.2 - - - +
74A PHE* 4.3 5.5 - - - -
121A LEU 2.8 16.7 + - - -
122A ALA 3.6 2.2 - - - -
124A LEU* 1.3 77.4 - - - +
126A LEU* 1.3 58.9 + - - +
128A ALA* 3.7 7.7 + - - +
129A HIS* 3.4 18.9 + - - +
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Residues in contact with LEU 126 (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 VAL* 4.0 18.4 - - + -
73A PHE* 4.0 36.3 - - + -
122A ALA* 2.9 21.5 + - + +
123A ALA* 3.8 5.8 - - - +
124A LEU 3.2 0.4 - - - -
125A GLY* 1.3 75.8 - - - +
127A LEU* 1.3 60.4 + - - +
129A HIS* 3.3 2.9 + - + +
130A PHE* 3.0 53.9 + - + +
207A PLM 4.3 22.7 - - + -
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Residues in contact with LEU 127 (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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123A ALA* 2.9 27.8 + - + +
124A LEU* 3.1 20.4 + - + +
126A LEU* 1.3 74.9 - - - +
128A ALA* 1.3 58.7 + - - +
130A PHE* 5.2 0.2 - - - -
131A LEU* 2.8 68.9 + - + +
207A PLM 3.4 24.2 - - + -
210A PLM 4.1 13.5 - - + -
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE 5.7 0.7 - - - +
124A LEU 3.0 15.7 + - - +
125A GLY* 3.7 8.3 - - - +
127A LEU* 1.3 75.7 - - - +
129A HIS* 1.3 59.8 + - - +
132A PRO* 3.3 22.9 - - - +
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Residues in contact with HIS 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 4.2 26.5 - + + -
125A GLY 3.4 10.6 + - - +
126A LEU* 3.3 11.3 + - - +
127A LEU 3.1 0.8 - - - -
128A ALA* 1.3 81.5 - - - +
130A PHE* 1.3 91.0 + + + +
132A PRO* 4.5 2.6 - - - +
133A ALA* 5.0 7.1 + - - +
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Residues in contact with PHE 130 (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 PHE* 6.1 0.2 - + - -
126A LEU* 3.0 43.5 + - + +
127A LEU* 5.2 0.2 - - - -
129A HIS* 1.3 102.9 - + - +
131A LEU* 1.3 66.7 + - - +
132A PRO 3.5 0.7 - - - -
133A ALA* 3.5 7.6 + - + +
134A ALA* 3.1 22.3 + - - +
207A PLM 3.6 68.2 - - + -
210A PLM 4.3 9.6 - - + -
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 2.8 42.7 + - + +
130A PHE* 1.3 73.4 - - - +
132A PRO* 1.4 61.2 - - + +
134A ALA* 2.9 7.2 + - + +
135A LEU* 2.8 60.7 + - + +
206A PLM 6.1 2.0 - - + -
210A PLM 3.6 23.1 - - + +
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Residues in contact with PRO 132 (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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127A LEU 3.8 0.7 - - - +
128A ALA* 3.3 26.0 - - - +
129A HIS 4.5 1.8 - - - +
130A PHE 3.8 2.0 - - - +
131A LEU* 1.4 93.9 - - + +
133A ALA* 1.3 61.9 + - - +
135A LEU* 3.5 3.6 + - + +
136A ARG* 3.0 26.2 + - - +
206A PLM 4.1 46.0 - - + +
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Residues in contact with ALA 133 (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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129A HIS 5.0 6.6 + - - +
130A PHE* 3.5 8.6 + - - +
131A LEU 3.3 0.6 - - - -
132A PRO* 1.3 79.7 - - - +
134A ALA* 1.3 60.6 + - - +
136A ARG* 3.8 17.6 + - - +
137A ALA* 3.2 23.9 + - - +
206A PLM 5.1 2.8 - - + +
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Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PHE 3.1 13.8 + - - +
131A LEU* 2.9 11.9 + - + +
133A ALA* 1.3 75.2 - - - +
135A LEU* 1.3 68.3 + - + +
137A ALA* 3.2 6.9 + - - +
138A ALA* 2.9 23.3 + - - +
210A PLM 4.1 34.8 - - + -
----------------------------------------------------------
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 2.8 52.5 + - + +
132A PRO* 3.9 3.4 - - + +
134A ALA* 1.3 74.5 - - + +
136A ARG* 1.3 51.9 + - - +
138A ALA* 3.2 9.4 + - + +
139A LEU* 2.8 41.2 + - + +
206A PLM 3.6 38.6 - - + -
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Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PRO 3.0 16.5 + - - +
133A ALA* 4.1 13.6 + - - +
135A LEU* 1.3 75.6 - - - +
137A ALA* 1.3 53.9 + - - +
139A LEU* 3.2 8.0 + - - +
140A LEU* 2.5 59.0 + - + +
206A PLM 3.4 51.9 - - + +
----------------------------------------------------------
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Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ALA 3.2 17.1 + - - +
134A ALA* 3.2 6.5 + - - +
136A ARG* 1.3 76.8 - - - +
138A ALA* 1.3 66.4 - - - +
140A LEU* 3.5 10.0 + - - +
141A GLY* 3.3 17.0 + - - -
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Residues in contact with ALA 138 (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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134A ALA 2.9 12.9 + - - +
135A LEU* 3.4 14.8 - - + +
137A ALA* 1.3 76.1 - - - +
139A LEU* 1.3 64.7 + - + +
141A GLY* 3.0 11.8 + - - -
142A ARG* 3.3 17.2 + - - +
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 2.8 23.5 + - + +
136A ARG* 3.5 8.3 - - + +
138A ALA* 1.3 70.5 - - + +
140A LEU* 1.3 57.7 + - + +
141A GLY 2.8 7.3 + - - -
142A ARG* 3.2 12.3 + - + +
143A LEU* 3.8 21.1 - - + +
144A ARG* 2.8 17.3 + - - -
206A PLM 5.6 9.9 - - + -
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ARG* 2.5 48.8 + - + +
137A ALA* 3.6 9.9 - - - +
138A ALA 3.3 0.2 - - - -
139A LEU* 1.3 68.6 - - + +
141A GLY* 1.3 54.0 + - - +
143A LEU* 5.0 8.3 - - + -
144A ARG* 2.7 36.0 + - - +
----------------------------------------------------------
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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