Contacts of the helix formed by residues 91 - 116 (chain J) in PDB entry 2IVB
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 91 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C PRO 3.4 1.6 - - - +
80C LEU* 3.8 18.8 - - + +
81C ARG* 2.8 38.3 + - - +
109I LYS* 3.0 35.7 + - - +
89J PRO* 3.5 0.8 - - - +
90J THR* 1.3 79.8 + - - +
92J PRO* 1.3 59.7 - - - +
93J THR* 3.3 24.6 + - - -
94J MET* 3.1 13.4 + - + +
95J TYR* 2.7 34.8 + - - +
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Residues in contact with PRO 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ARG* 3.6 28.3 - - + +
124C ILE* 4.3 9.4 - - + -
99H GLU* 3.3 39.9 - - + +
103H VAL* 3.9 17.0 - - + -
120I ILE* 3.9 13.9 - - + -
90J THR 3.4 6.0 - - - +
91J ASP* 1.3 87.4 - - - +
93J THR* 1.3 63.2 + - - +
95J TYR* 4.0 1.1 - - + -
96J ARG* 3.0 34.5 + - - +
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Residues in contact with THR 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ARG* 5.1 4.2 + - - -
109I LYS* 4.0 24.9 + - - +
112I VAL* 4.0 25.8 - - + -
113I HIS* 3.4 14.6 + - + -
119I GLY 2.8 26.2 + - - +
120I ILE* 3.8 13.9 - - - +
121I ILE 5.0 2.3 + - - +
91J ASP* 3.2 13.4 + - - -
92J PRO* 1.3 79.2 - - - +
94J MET* 1.3 62.6 + - - +
96J ARG* 3.7 6.1 + - - +
97J PHE* 3.4 23.3 - - + -
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Residues in contact with MET 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU* 3.7 29.8 - - - -
101I LEU* 3.8 9.5 - - + +
105I GLY* 3.5 36.6 - - - +
106I THR* 3.9 20.0 - - + -
109I LYS* 3.8 15.7 - - + +
83J CYS* 4.2 11.9 - - - +
84J ILE* 4.4 16.4 - - + -
89J PRO* 3.8 19.7 - - + +
91J ASP* 3.1 12.5 + - + +
93J THR* 1.3 75.1 - - - +
95J TYR* 1.3 66.5 + - - +
97J PHE* 3.2 21.5 + - - +
98J TYR 3.6 6.2 + - - -
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Residues in contact with TYR 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H ILE* 5.7 0.4 - - + +
89H PRO 4.2 6.2 + - - -
90H THR* 4.6 7.8 + - - -
95H TYR* 3.4 61.6 - + - +
99H GLU* 4.4 1.3 - - - +
88J ILE* 4.0 9.9 - - + -
89J PRO* 3.4 26.8 - - - +
90J THR 5.0 0.4 - - - -
91J ASP 2.7 22.1 + - - +
92J PRO* 3.3 11.2 + - + +
94J MET* 1.3 74.2 - - - +
96J ARG* 1.3 72.1 + - - +
98J TYR* 3.0 41.1 + + + +
99J GLU* 2.8 49.3 + - + +
102J GLN* 5.1 1.4 - - - +
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Residues in contact with ARG 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ILE* 4.3 3.6 - - - +
1158C AZI 3.0 40.6 + - - -
96H ARG* 3.4 25.5 - - - +
99H GLU* 2.8 43.8 + - - -
120I ILE* 3.5 18.3 - - + +
121I ILE 3.3 26.5 - - - +
123I ALA* 3.8 20.2 - - + +
92J PRO* 3.0 29.8 + - - +
93J THR 4.0 7.6 - - - +
94J MET 3.3 0.6 - - - -
95J TYR* 1.3 87.0 - - - +
97J PHE* 1.3 60.7 + - + +
99J GLU* 3.4 7.4 + - - +
100J MET* 3.0 26.9 + - - +
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Residues in contact with PHE 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101I LEU* 4.0 17.0 - - + -
108I LEU* 4.0 45.5 - - + -
109I LYS 5.6 0.2 - - - -
112I VAL* 4.9 9.0 - - + -
121I ILE* 4.7 17.9 - - + -
126I PHE* 6.5 0.9 - + - -
146I LEU* 4.5 21.3 - - + -
93J THR* 3.4 24.5 - - + -
94J MET* 3.2 11.6 + - - +
96J ARG* 1.3 77.1 - - + +
98J TYR* 1.3 65.5 + - - +
100J MET* 3.4 15.2 + - + +
101J LEU* 3.3 25.1 + - - +
144J ILE* 4.2 28.7 - - + -
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Residues in contact with TYR 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I ILE* 4.6 4.9 - - + -
87I ARG* 2.7 37.0 + - - +
98I TYR* 4.4 11.2 - + - -
101I LEU* 3.8 28.6 - - + +
88J ILE* 3.4 33.9 - - + +
89J PRO* 4.0 15.0 - - + -
94J MET 3.6 3.0 + - - -
95J TYR* 3.0 38.5 + + + +
97J PHE* 1.3 78.2 - - - +
99J GLU* 1.3 61.2 + - - +
101J LEU* 3.0 24.8 + - + +
102J GLN* 3.1 41.7 + - + +
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Residues in contact with GLU 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H THR 4.9 1.9 - - - +
92H PRO* 3.3 33.2 - - + +
95H TYR* 4.3 1.7 - - - +
96H ARG* 2.7 47.0 + - - -
123I ALA* 3.4 17.6 - - + +
124I ILE* 4.2 3.5 - - - +
95J TYR* 2.8 38.3 + - + +
96J ARG* 3.6 9.8 - - - +
98J TYR* 1.3 71.4 - - - +
100J MET* 1.3 60.6 + - - +
102J GLN* 3.0 10.4 + - + -
103J VAL* 2.8 34.0 + - + +
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Residues in contact with MET 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I PHE* 5.2 2.2 - - + -
123I ALA* 4.7 6.7 - - + +
126I PHE* 3.7 33.7 - - + -
128I LEU* 4.2 4.5 - - - -
144I ILE* 5.9 0.2 - - + -
146I LEU* 3.8 34.1 - - + -
96J ARG 3.0 13.5 + - - +
97J PHE* 3.5 17.7 - - + +
98J TYR 3.2 0.4 - - - -
99J GLU* 1.3 76.7 - - - +
101J LEU* 1.3 71.8 + - + +
103J VAL* 4.5 3.1 - - - +
104J TYR* 2.8 35.6 + - + +
108J LEU* 3.8 26.0 - - + -
146J LEU* 4.7 8.3 - - + -
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Residues in contact with LEU 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I CYS* 3.3 5.5 - - - -
84I ILE* 4.2 16.5 - - + +
89I PRO* 5.6 2.5 - - + -
94I MET 5.3 0.9 - - - +
97I PHE* 3.3 37.9 - - + +
98I TYR* 3.6 41.1 - - + +
101I LEU* 4.7 6.1 - - + -
97J PHE 3.4 14.6 - - - +
98J TYR* 3.0 20.7 + - + +
100J MET* 1.3 93.9 - - + +
102J GLN* 1.3 57.7 + - - +
105J GLY* 2.8 33.7 + - - +
108J LEU* 5.3 1.3 - - + -
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Residues in contact with GLN 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H THR* 3.7 36.1 - - - +
50I GLN* 3.9 0.2 - - - +
82I GLY* 3.3 16.3 + - - -
83I CYS* 2.8 36.7 + - - +
84I ILE* 3.1 45.8 + - + +
87I ARG* 4.4 5.2 + - - +
95J TYR* 5.1 1.8 - - - +
98J TYR* 3.1 45.3 + - + +
99J GLU* 3.0 12.4 + - - +
101J LEU* 1.3 76.6 - - - +
103J VAL* 1.3 64.4 + - + +
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Residues in contact with VAL 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H PRO* 3.9 28.5 - - + -
50I GLN* 3.1 48.9 - - + +
51I GLN* 3.9 14.8 - - - +
81I ARG* 4.2 13.9 - - + +
83I CYS* 4.6 1.1 - - - -
123I ALA 5.6 5.4 - - - +
124I ILE* 6.0 1.6 - - + -
99J GLU* 2.8 25.1 + - + +
100J MET* 4.9 0.9 - - - -
102J GLN* 1.3 80.2 - - + +
104J TYR* 1.3 86.8 + - + +
105J GLY 3.7 0.8 + - - -
106J THR* 5.0 0.5 + - - -
107J THR* 4.9 1.6 + - - -
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Residues in contact with TYR 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C PHE* 3.3 33.6 - + - -
41I ALA* 4.2 10.1 - - + -
42I PHE* 5.3 0.2 - - - -
45I ALA* 3.9 27.1 - - + -
51I GLN* 3.1 21.4 + - - +
123I ALA 5.2 5.6 - - - -
126I PHE* 3.8 34.0 + + - -
128I LEU* 3.9 26.0 - - + -
100J MET* 2.8 24.2 + - + +
103J VAL* 1.3 91.2 - - + +
105J GLY* 1.3 57.9 + - - +
106J THR 3.4 2.2 - - - -
107J THR* 3.1 16.1 + - + -
108J LEU* 2.9 31.1 + - + +
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Residues in contact with GLY 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I CYS* 3.7 2.4 - - - -
94I MET* 3.6 24.5 - - - +
97I PHE* 5.8 1.7 - - - -
100J MET 3.8 0.2 + - - -
101J LEU* 2.8 32.4 + - - -
103J VAL 3.7 1.0 - - - -
104J TYR* 1.3 71.6 - - - +
106J THR* 1.3 57.3 + - - +
108J LEU* 3.4 12.1 + - - +
109J LYS 3.0 22.9 + - - -
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Residues in contact with THR 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 3.8 43.8 - - + +
48I LEU* 3.6 20.7 + - - +
50I GLN* 4.5 5.5 - - - +
83I CYS* 3.4 38.0 - - + +
94I MET* 3.9 18.2 - - + -
103J VAL 5.0 0.5 + - - -
105J GLY* 1.3 75.9 - - - +
107J THR* 1.3 59.0 + - - +
109J LYS* 3.5 7.9 + - - +
110J ALA* 3.0 27.9 + - - +
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Residues in contact with THR 107 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I ALA* 3.6 26.7 - - + +
44I THR* 4.0 9.6 - - + -
45I ALA* 3.2 27.7 + - - +
48I LEU* 3.9 11.9 - - - +
50I GLN* 5.6 0.5 - - - +
128I LEU* 5.3 3.1 - - + -
103J VAL 4.9 1.6 + - - -
104J TYR* 3.1 21.9 + - + -
106J THR* 1.3 75.7 + - - +
108J LEU* 1.3 61.3 + - - +
110J ALA* 3.3 2.3 + - - +
111J LEU* 2.8 50.7 + - + +
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Residues in contact with LEU 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I PHE* 4.1 39.7 - - + -
128I LEU* 4.0 20.9 - - + -
130I VAL* 3.8 26.5 - - + -
144I ILE* 4.2 18.8 - - + -
100J MET* 3.8 28.7 - - + -
101J LEU* 5.3 0.7 - - + -
104J TYR* 2.9 18.6 + - + +
105J GLY* 3.6 10.8 - - - +
107J THR* 1.3 76.3 - - - +
109J LYS* 1.3 57.1 + - - +
111J LEU* 4.3 2.4 - - - +
112J VAL* 2.8 38.5 + - + +
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Residues in contact with LYS 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 4.8 1.3 - - - +
5A GLN 3.3 25.4 - - - +
6A ILE* 5.0 4.5 - - + -
78A ILE* 4.3 3.0 - - - +
79A PRO 3.0 22.3 + - - -
80A LEU* 3.8 15.0 - - + -
81A ARG* 4.8 1.2 - - - +
91I ASP* 2.9 38.8 + - - +
93I THR* 3.9 15.7 + - + +
94I MET* 4.0 11.4 - - + +
97I PHE* 5.4 1.0 - - - -
105J GLY 3.0 13.9 + - - +
106J THR* 3.5 9.4 - - - +
108J LEU* 1.3 76.7 - - - +
110J ALA* 1.3 63.3 + - - +
112J VAL* 3.8 1.2 - - - +
113J HIS* 2.8 67.9 + - + +
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Residues in contact with ALA 110 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 3.8 16.1 + - - +
6A ILE* 5.3 4.0 - - + -
29I PHE* 3.6 30.3 - - + -
44I THR* 4.1 12.3 - - + -
48I LEU* 4.2 5.8 - - + -
106J THR 3.0 20.2 + - - +
107J THR 3.3 4.2 + - - +
109J LYS* 1.3 72.5 - - - +
111J LEU* 1.3 59.6 + - - +
113J HIS* 3.4 2.9 + - - +
114J GLU* 3.0 28.6 + - - +
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Residues in contact with LEU 111 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I PHE* 4.0 17.0 - - + -
40I GLU* 4.0 18.4 - - + +
41I ALA* 3.9 22.9 - - + +
44I THR* 3.7 23.1 - - + +
128I LEU* 5.3 0.7 - - + -
130I VAL* 4.5 15.7 - - + -
1160I CL 4.0 16.8 - - + -
107J THR* 2.8 40.2 + - + +
108J LEU 4.3 1.6 - - - +
110J ALA* 1.3 71.9 - - - +
112J VAL* 1.3 57.3 + - - +
114J GLU* 3.3 5.5 + - + +
115J LYS* 2.8 51.7 + - + +
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Residues in contact with VAL 112 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I THR* 4.1 20.2 - - + -
97I PHE* 4.8 11.2 - - + -
130I VAL* 4.5 16.8 - - + -
144I ILE* 5.4 0.7 - - + -
108J LEU* 2.8 24.1 + - + +
109J LYS 3.8 3.6 - - - +
111J LEU* 1.3 76.3 - - - +
113J HIS* 1.3 61.6 + - - +
116J PHE* 2.8 41.2 + - + +
117J GLY 3.3 4.4 + - - +
119J GLY 4.7 4.7 - - - +
120J ILE 4.9 1.3 - - - -
121J ILE* 3.8 40.4 - - + +
150J TYR* 5.0 1.1 - - + -
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Residues in contact with HIS 113 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ILE* 3.3 23.8 - - + +
4A SER* 3.7 27.8 - - - -
78A ILE* 3.5 19.5 - - + +
81A ARG* 5.1 0.2 - - - -
93I THR* 3.4 24.9 - - + -
109J LYS* 2.8 56.4 + - + +
110J ALA 3.9 3.6 - - - +
112J VAL* 1.3 77.0 - - - +
114J GLU* 1.3 63.2 + - - +
117J GLY* 3.1 37.3 + - - +
118J ASP* 3.9 3.1 - - - -
119J GLY 3.5 16.8 + - - -
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Residues in contact with GLU 114 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.8 23.0 - - + +
2A ILE* 3.6 11.0 - - + +
22I LYS* 4.4 2.6 + - - -
28I SER* 3.4 17.5 - - - -
29I PHE* 2.9 36.3 + - + +
30I ALA* 3.1 30.7 + - - +
40I GLU* 3.8 8.0 - - - +
110J ALA 3.0 17.6 + - - +
111J LEU* 3.8 7.9 - - + +
113J HIS* 1.3 79.6 - - - +
115J LYS* 1.3 65.0 + - + +
116J PHE 5.1 0.3 - - - -
117J GLY 5.0 0.2 + - - -
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Residues in contact with LYS 115 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I GLU* 3.3 34.2 + - - +
130I VAL* 3.4 42.3 + - + +
131I LYS* 5.6 0.6 - - - +
132I LYS* 3.1 35.1 + - + +
1160I CL 4.1 4.9 - - - -
111J LEU* 2.8 28.7 + - + +
114J GLU* 1.3 78.0 - - + +
116J PHE* 1.3 74.2 + - + +
----------------------------------------------------------
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Residues in contact with PHE 116 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130I VAL* 4.3 13.5 - - + -
132I LYS* 3.5 39.5 - - + +
140I GLU* 3.6 18.8 - - + +
141I ARG 3.5 21.5 - - - -
142I ALA* 3.4 31.6 - - + -
112J VAL* 2.8 27.1 + - + +
113J HIS 4.0 0.2 - - - -
114J GLU 3.5 0.9 - - - -
115J LYS* 1.3 89.7 - - + +
117J GLY* 1.3 56.9 + - - +
121J ILE* 4.3 4.9 - - + -
150J TYR* 3.5 49.8 + + + -
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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