Contacts of the helix formed by residues 115 - 142 (chain A) in PDB entry 1P27
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 115 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLU* 5.0 3.6 - - - +
73A ASP 3.9 6.8 + - - +
76A LEU* 4.4 19.2 - - + +
77A TRP* 2.9 28.4 + - + +
113A SER* 3.8 0.7 - - - -
114A LYS* 1.3 76.5 - - - +
116A PRO* 1.3 73.7 - - - +
117A GLU* 3.2 5.9 + - - +
118A GLY* 3.1 21.8 + - - -
119A LEU* 3.1 18.0 + - - +
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Residues in contact with PRO 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A VAL* 3.7 22.9 - - + +
111A ASN* 4.1 26.5 - - + +
113A SER* 3.4 17.0 - - - +
114A LYS* 3.6 0.4 - - - -
115A ASP* 1.3 90.2 - - - +
117A GLU* 1.3 72.1 + - + +
120A ARG* 3.0 30.9 + - - +
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Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLU* 4.6 6.1 - - - +
115A ASP* 3.2 6.0 - - - +
116A PRO* 1.3 86.6 - - + +
118A GLY* 1.3 61.9 + - - +
120A ARG* 2.7 40.9 + - - +
121A VAL* 3.3 18.7 + - - +
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Residues in contact with GLY 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE* 5.3 0.3 - - - +
72A GLU* 3.6 31.4 - - - +
77A TRP* 3.4 14.1 - - - -
115A ASP* 3.1 17.2 + - - -
117A GLU* 1.3 78.0 - - - +
119A LEU* 1.3 66.1 + - - +
121A VAL* 3.2 13.2 + - - +
122A PHE 3.3 8.7 + - - -
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TRP* 3.8 40.0 - - + +
78A PRO* 4.0 17.7 - - + -
101A THR* 4.5 4.5 - - - +
104A ILE* 3.7 30.5 - - + -
109A ASP 5.4 0.4 - - - +
110A VAL* 4.1 24.9 - - + -
113A SER* 3.4 28.3 - - - +
115A ASP 3.1 17.3 + - - +
118A GLY* 1.3 76.4 - - - +
120A ARG* 1.3 55.3 + - - +
122A PHE* 3.2 9.4 + - + +
123A TYR* 2.9 25.8 + - - +
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Residues in contact with ARG 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 3.3 25.8 - - + -
110A VAL* 3.7 8.4 - - + +
111A ASN* 2.4 40.2 + - - +
116A PRO* 3.0 21.9 + - - +
117A GLU* 2.7 46.1 + - - +
119A LEU* 1.3 74.5 - - - +
121A VAL* 1.3 64.9 + - + +
123A TYR* 3.3 4.4 + - + +
124A TYR* 3.0 53.3 + - + -
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A SER* 3.0 36.6 - - - +
68A GLU 4.3 2.0 - - - +
69A ILE* 4.1 21.1 - - + +
72A GLU* 4.2 18.2 - - - +
117A GLU 3.5 14.1 - - - +
118A GLY* 3.2 8.0 + - - +
120A ARG* 1.3 76.6 - - + +
122A PHE* 1.3 58.8 + - - +
124A TYR* 3.5 3.7 + - - +
125A LEU* 3.0 28.8 + - - +
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Residues in contact with PHE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 4.9 0.9 - + - -
69A ILE* 4.3 16.1 - - + +
77A TRP* 3.7 30.3 - + + -
86A GLN* 3.6 34.3 - - + -
88A LEU* 3.8 31.4 - - + -
99A PHE* 3.8 15.5 - + + -
101A THR* 3.6 26.0 - - + -
104A ILE* 4.0 13.5 - - + -
118A GLY 3.3 2.0 + - - +
119A LEU* 3.2 13.7 + - + +
121A VAL* 1.3 76.8 - - - +
123A TYR* 1.3 67.6 + - - +
125A LEU* 3.7 2.4 - - + +
126A VAL* 2.9 42.6 + - + +
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Residues in contact with TYR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ILE* 4.0 32.5 - - + -
105A GLY 4.1 3.7 + - - -
106A SER* 3.5 24.8 - - - -
107A LEU* 3.6 40.0 + - + +
110A VAL* 4.0 17.5 - - + -
119A LEU 2.9 13.4 + - - +
120A ARG* 3.3 11.9 + - - +
122A PHE* 1.3 84.6 - - - +
124A TYR* 1.3 74.1 + + - +
126A VAL* 4.1 3.9 - - - +
127A GLN* 3.1 51.9 + - + +
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Residues in contact with TYR 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 3.0 40.4 - - + +
120A ARG* 3.0 47.3 + - + +
121A VAL* 4.2 3.8 - - - +
123A TYR* 1.3 85.4 - + - +
125A LEU* 1.3 64.7 - - - +
127A GLN* 3.4 10.4 + - - +
128A ASP* 3.0 34.6 + - - +
108B ARG* 3.6 21.9 - - + +
109B ARG* 3.7 51.5 + - + +
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Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 4.3 14.6 - - + -
64A ILE* 4.9 6.1 - - + -
67A SER* 3.9 18.2 - - - +
69A ILE* 3.7 42.6 - - + -
88A LEU* 4.1 18.2 - - + -
90A ILE* 4.8 3.4 - - + -
121A VAL 3.0 19.2 + - - +
122A PHE* 3.7 4.7 - - + +
124A TYR* 1.3 73.6 - - - +
126A VAL* 1.3 60.7 + - + +
128A ASP* 3.2 7.5 + - - +
129A LEU* 2.8 54.7 + - + +
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 3.2 53.8 - - + +
24A PHE* 5.5 0.2 - - - -
86A GLN* 3.7 7.0 - - - +
88A LEU* 4.7 7.2 - - + -
122A PHE* 2.9 44.7 + - + +
123A TYR* 4.1 4.7 - - - +
125A LEU* 1.3 77.2 - - + +
127A GLN* 1.3 58.7 + - + +
129A LEU* 3.4 8.4 + - + +
130A LYS* 2.9 40.4 + - - +
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Residues in contact with GLN 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TYR* 3.1 52.5 + - + +
124A TYR* 3.7 15.8 - - - +
125A LEU 3.2 0.8 - - - -
126A VAL* 1.3 79.2 - - + +
128A ASP* 1.3 56.9 + - - +
130A LYS* 3.4 19.4 + - - +
131A CYS* 3.0 35.1 + - - -
108B ARG* 4.0 35.6 - - + +
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Residues in contact with ASP 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 4.4 16.3 - - + +
124A TYR* 3.0 24.5 + - - +
125A LEU* 3.5 9.1 - - - +
127A GLN* 1.3 73.2 - - - +
129A LEU* 1.3 65.5 + - - +
131A CYS* 3.3 8.1 + - - +
132A LEU* 3.2 21.5 + - - +
106B LEU 4.1 2.6 - - - +
107B ASP* 3.9 8.7 - - - +
108B ARG* 3.3 28.1 + - - +
109B ARG 5.6 0.2 + - - -
114B LYS* 3.0 38.7 + - + +
116B TYR* 4.4 2.9 + - - -
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 4.1 26.5 - - + -
9A TYR* 5.4 1.3 - - + -
24A PHE* 4.0 16.2 - - + -
26A PHE* 5.9 0.2 - - + -
60A LEU* 3.3 34.3 - - + -
63A ILE* 4.4 11.2 - - + -
64A ILE* 4.7 4.9 - - + -
88A LEU* 4.1 15.5 - - + -
125A LEU* 2.8 48.3 + - + +
126A VAL* 3.7 9.4 - - + +
128A ASP* 1.3 72.3 - - - +
130A LYS* 1.3 63.8 + - - +
132A LEU* 3.4 6.8 + - + +
133A VAL* 3.1 27.6 + - + +
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Residues in contact with LYS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 4.1 21.8 + - + +
11A VAL* 5.4 2.9 - - + +
22A LEU* 4.1 13.9 - - + -
24A PHE* 4.1 22.7 - - + -
126A VAL* 2.9 33.9 + - - +
127A GLN* 3.7 19.5 - - - +
128A ASP 3.3 0.2 - - - -
129A LEU* 1.3 73.9 - - - +
131A CYS* 1.3 60.2 + - - +
133A VAL* 3.4 0.8 + - - +
134A PHE* 2.8 58.9 + - + -
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Residues in contact with CYS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLN* 3.0 20.9 + - - +
128A ASP* 3.6 7.9 - - - +
129A LEU 3.3 0.2 - - - -
130A LYS* 1.3 75.8 - - - +
132A LEU* 1.3 62.4 + - - +
134A PHE* 3.9 7.7 - - - +
135A SER* 3.0 28.8 + - - -
105B ASN* 3.3 21.6 + - + +
106B LEU 4.9 3.4 - - - +
108B ARG* 3.0 48.7 - - - -
116B TYR* 4.3 2.7 - - - +
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 4.3 23.1 - - + -
56A VAL* 4.8 7.4 - - + +
59A GLU* 5.7 1.1 - - + -
60A LEU* 4.3 25.8 - - + +
63A ILE* 4.8 9.2 - - + -
128A ASP 3.2 9.3 + - - +
129A LEU* 3.6 9.2 - - - +
131A CYS* 1.3 80.0 - - - +
133A VAL* 1.3 56.6 + - - +
135A SER* 3.3 2.6 + - - -
136A LEU* 3.0 43.9 + - + +
76B PHE* 4.3 18.2 - - + -
105B ASN* 4.3 0.7 - - - +
116B TYR* 3.3 37.4 + - + +
118B LEU* 5.1 1.6 - - + -
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Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.6 32.3 - - + -
26A PHE* 3.6 35.7 - - + -
32A LEU* 4.5 5.8 - - + -
34A TYR* 3.8 30.3 - - + -
129A LEU 3.1 16.3 + - - +
130A LYS* 4.0 2.5 - - - +
132A LEU* 1.3 73.8 - - + +
134A PHE* 1.3 63.0 + - + +
136A LEU* 3.3 6.4 + - - -
137A ILE* 2.9 36.4 + - + +
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Residues in contact with PHE 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.7 31.6 - - + -
24A PHE* 5.8 0.7 - + - -
34A TYR* 4.0 17.7 - + - -
36A ASN* 5.3 0.7 - - - -
130A LYS* 2.8 50.4 + - + +
131A CYS* 3.9 6.5 - - - +
133A VAL* 1.3 74.8 - - + +
135A SER* 1.3 57.3 + - - +
137A ILE* 5.0 0.4 - - - -
138A GLY* 3.0 28.4 + - - -
145A PRO* 3.4 43.9 - - + +
103B HIS* 5.2 0.7 + - - -
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Residues in contact with SER 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A CYS 3.0 13.8 + - - -
132A LEU* 3.5 4.3 - - - -
133A VAL 3.2 0.2 - - - -
134A PHE* 1.3 77.2 - - - +
136A LEU* 1.3 62.3 + - - +
139A LEU* 3.0 30.3 + - - +
103B HIS* 2.8 38.4 + - - -
105B ASN* 3.0 24.7 + - - -
118B LEU* 4.2 16.8 - - - +
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 4.2 12.8 - - + -
32A LEU* 3.9 27.4 - - + -
52A VAL* 4.5 2.5 - - + -
56A VAL* 4.1 21.5 - - + -
132A LEU* 3.0 41.4 + - + +
133A VAL* 3.7 4.7 - - - +
135A SER* 1.3 76.8 - - - +
137A ILE* 1.3 58.9 + - - +
139A LEU* 4.3 0.3 - - - +
140A HIS* 3.0 31.5 + - - +
76B PHE* 4.9 1.6 - - + -
118B LEU* 4.0 10.5 - - + -
149B CYS* 3.6 31.2 - - - -
150B PHE* 3.4 17.6 - - + -
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Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.0 22.4 - - + +
34A TYR* 3.9 43.1 - - + -
48A LYS* 4.5 7.0 - - + +
49A GLU 5.6 0.2 - - - +
50A ALA* 5.8 2.9 - - + -
133A VAL* 2.9 36.4 + - + +
134A PHE* 4.5 1.8 - - - +
136A LEU* 1.3 71.8 - - - +
138A GLY* 1.3 66.5 + - - +
141A PHE* 3.0 51.7 + - + +
143A ILE* 3.9 23.5 - - + +
145A PRO* 5.2 3.8 - - + -
150B PHE* 6.3 1.1 - - + -
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Residues in contact with GLY 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE 3.0 20.2 + - - -
135A SER* 4.0 0.4 - - - -
137A ILE* 1.3 78.5 - - - +
139A LEU* 1.3 59.2 + - - +
142A LYS* 2.9 31.5 + - - +
143A ILE 3.3 22.5 + - - +
145A PRO* 4.3 6.9 - - - +
103B HIS* 5.8 1.6 - - - -
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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 SER 3.0 17.7 + - - +
136A LEU 4.3 1.1 - - - +
138A GLY* 1.3 76.7 - - - +
140A HIS* 1.3 66.2 + - - +
142A LYS* 3.4 39.7 + - - +
69B SER* 4.0 1.4 - - - -
74B ILE* 3.7 26.4 - - + +
101B ASN* 3.8 18.6 - - + +
103B HIS* 3.0 50.0 + - + +
118B LEU* 3.9 25.6 - - + +
120B GLU* 3.9 9.7 - - + +
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Residues in contact with HIS 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ALA* 3.6 28.0 - - + +
136A LEU 3.0 21.0 + - - +
137A ILE* 6.0 0.2 - - + -
139A LEU* 1.3 77.5 - - - +
141A PHE* 1.3 80.4 + + + +
67B GLN* 3.0 32.6 + - - -
68B ARG 3.6 10.9 + - - -
69B SER* 2.8 38.8 - - - -
70B VAL* 3.0 28.8 + - - +
74B ILE* 4.1 1.0 - - - +
150B PHE* 3.6 28.1 - + + +
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Residues in contact with PHE 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LYS* 3.6 49.4 - - + +
49A GLU 3.5 25.4 - - - -
50A ALA* 4.6 2.9 - - + -
137A ILE* 3.0 38.1 + - + +
140A HIS* 1.3 101.2 - + + +
142A LYS* 1.3 72.3 + - - +
143A ILE* 3.3 23.0 + - + +
70B VAL* 3.6 18.3 - - + +
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Residues in contact with LYS 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLY 2.9 15.2 + - - -
139A LEU* 3.4 30.7 + - - +
140A HIS 3.5 2.6 - - - -
141A PHE* 1.3 80.5 - - - +
143A ILE* 1.3 59.5 + - - +
70B VAL* 3.8 16.2 - - + -
71B GLU* 3.5 46.9 - - + +
100B LYS* 5.5 0.7 - - - -
101B ASN* 2.9 31.7 - - - +
120B GLU* 3.1 11.7 + - - +
----------------------------------------------------------
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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