Contacts of the helix formed by residues 102 - 129 (chain A) in PDB entry 4DOH
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 102 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A THR* 3.2 14.1 - - - +
101A PRO* 1.3 80.1 - - + +
103A HIS* 1.3 63.9 + - - +
104A TYR* 2.8 25.7 + - - +
105A THR* 3.0 32.1 + - - +
106A LEU* 3.1 16.1 + - - +
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Residues in contact with HIS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PRO 3.3 13.2 + - - -
102A ASP* 1.3 69.9 + - - +
104A TYR* 1.3 66.6 + - - +
106A LEU* 3.4 18.5 + - + +
107A ARG* 3.0 45.8 + - - +
85B PRO* 4.1 27.6 - - + +
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Residues in contact with TYR 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLU* 3.8 31.7 + - + -
49A ILE* 4.8 2.5 - - + -
102A ASP* 2.8 19.4 + - - +
103A HIS* 1.3 75.7 - - - +
105A THR* 1.3 73.6 + - - +
107A ARG* 3.3 28.0 + - - +
108A LYS* 3.1 54.8 + - + +
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Residues in contact with THR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 4.6 20.4 - - + +
52A SER* 4.8 11.3 + - - +
53A VAL* 5.2 3.4 - - + -
98A TYR* 4.3 7.6 - - + +
100A THR* 3.5 23.2 + - + -
102A ASP* 3.0 30.0 + - - +
104A TYR* 1.3 83.6 - - - +
106A LEU* 1.3 62.6 + - - +
108A LYS* 2.9 19.1 + - - +
109A ILE* 3.0 28.1 + - + +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TYR 4.3 11.2 - - - +
100A THR* 3.0 52.5 - - + +
101A PRO 4.6 0.4 - - - -
102A ASP 3.1 19.9 + - - +
103A HIS* 3.6 22.7 - - + +
105A THR* 1.3 77.1 - - - +
107A ARG* 1.3 61.6 + - + +
109A ILE* 3.2 12.8 + - + +
110A SER* 3.1 21.1 + - - -
84B ILE* 5.1 10.4 - - + +
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Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A HIS* 3.0 42.1 + - - +
104A TYR* 3.5 42.0 - - - +
105A THR 3.2 0.2 + - - -
106A LEU* 1.3 73.7 - - - +
108A LYS* 1.3 64.3 + - + +
110A SER* 3.0 16.4 + - - -
111A SER* 3.0 14.4 + - - -
70B TYR* 3.3 21.3 + - - +
84B ILE* 3.5 13.5 - - + -
85B PRO* 3.6 19.0 + - - +
86B SER 4.3 1.2 + - - -
87B SER* 3.7 28.4 + - - +
101B ASP 6.1 0.2 - - - +
102B ASP* 3.8 20.9 - - - +
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Residues in contact with LYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASN 5.2 0.2 + - - -
45A GLY* 3.7 27.8 - - - +
48A GLU* 3.8 18.4 + - - +
49A ILE* 3.9 28.7 - - + -
104A TYR* 3.1 46.0 + - + +
105A THR 2.9 8.4 + - - +
107A ARG* 1.3 76.7 - - + +
109A ILE* 1.3 59.2 + - - +
111A SER* 2.9 27.7 + - - +
112A LEU* 2.9 17.0 + - + +
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Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 4.0 16.8 - - + -
95A PHE* 3.5 41.6 - - + +
98A TYR* 3.4 35.9 - - + +
105A THR* 3.0 30.4 + - + +
106A LEU* 3.7 15.3 - - + +
107A ARG 3.2 0.2 - - - -
108A LYS* 1.3 75.0 - - - +
110A SER* 1.3 58.1 + - - +
112A LEU* 3.3 9.0 + - + +
113A ALA* 2.9 27.2 + - - +
162A LEU* 3.7 15.5 - - + -
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Residues in contact with SER 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU 3.1 10.6 + - - -
107A ARG* 3.0 12.0 + - - -
109A ILE* 1.3 74.2 - - - +
111A SER* 1.3 64.4 + - - +
113A ALA* 3.4 2.8 + - - -
114A ASN* 2.7 36.3 + - - -
70B TYR* 4.3 15.6 - - - -
74B TYR* 5.7 0.2 - - - -
75B GLU* 2.5 35.5 + - - -
84B ILE* 4.4 13.4 - - - +
109B TYR* 5.5 1.1 + - - -
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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
----------------------------------------------------------
45A GLY* 5.9 4.7 - - - -
107A ARG 3.0 11.2 + - - -
108A LYS* 2.9 19.9 + - - +
110A SER* 1.3 77.9 - - - +
112A LEU* 1.3 65.6 + - - +
114A ASN* 3.2 2.8 + - - +
115A SER* 2.9 29.1 + - - -
101B ASP 5.4 0.2 + - - -
102B ASP 5.0 1.4 + - - -
104B THR* 2.6 38.4 + - - +
105B ALA* 4.5 0.7 - - - +
109B TYR* 5.3 0.9 - - - -
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 3.5 42.6 - - + +
45A GLY* 4.4 6.5 - - - -
46A PHE* 4.1 26.5 - - + +
49A ILE* 4.1 17.7 - - + -
95A PHE* 4.0 16.4 - - + -
108A LYS 2.9 15.4 + - - +
109A ILE* 3.7 9.6 - - - +
111A SER* 1.3 78.1 - - - +
113A ALA* 1.3 56.2 + - - +
115A SER* 3.3 4.3 + - - -
116A PHE* 2.8 37.4 + - + -
162A LEU* 4.6 4.3 - - + -
165A LEU* 3.7 21.3 - - + -
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 3.6 4.7 - - - +
95A PHE* 3.6 35.1 - - + -
109A ILE 2.9 16.5 + - - +
110A SER* 4.0 3.6 - - - +
111A SER 3.2 0.2 - - - -
112A LEU* 1.3 76.0 - - - +
114A ASN* 1.3 58.6 + - - +
116A PHE* 3.2 3.3 + - - +
117A LEU* 2.9 26.3 + - - +
74B TYR* 3.5 32.9 - - + +
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Residues in contact with ASN 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A SER* 2.7 35.0 + - - +
111A SER 4.0 0.4 - - - +
113A ALA* 1.3 72.6 - - - +
115A SER* 1.3 66.5 + - - +
117A LEU* 3.1 16.6 + - - +
118A THR* 3.2 17.8 + - - +
72B GLY* 3.5 7.1 - - - -
73B GLU* 3.3 10.9 + - - +
74B TYR* 2.9 31.1 + - - +
75B GLU* 3.1 23.2 + - - -
105B ALA* 3.5 21.3 - - + -
107B VAL* 3.6 11.0 - - + +
109B TYR* 4.2 7.5 + - - +
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Residues in contact with SER 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLU* 3.4 24.2 + - - +
42A ILE* 3.6 30.1 - - - +
111A SER* 2.9 20.9 + - - -
112A LEU 3.5 4.5 - - - -
114A ASN* 1.3 77.1 - - - +
116A PHE* 1.3 60.2 + - - +
118A THR* 2.8 26.2 + - - -
119A ILE* 3.6 9.0 + - - +
104B THR 3.8 8.7 + - - -
105B ALA* 3.7 5.0 - - - +
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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
----------------------------------------------------------
42A ILE* 4.1 14.1 - - + -
87A LEU* 3.3 42.6 - - + +
90A TYR* 5.7 1.6 - + + -
91A LEU* 4.1 17.0 - - + +
95A PHE* 3.3 29.8 - + + -
112A LEU 2.8 30.7 + - - +
113A ALA 3.6 4.9 - - - +
115A SER* 1.3 72.5 - - - +
117A LEU* 1.3 57.6 + - - +
119A ILE* 3.2 16.3 + - + +
120A LYS* 3.0 24.3 + - - +
165A LEU* 3.8 20.2 - - + -
168A LEU* 3.9 18.2 - - + -
169A LEU* 4.2 15.5 - - + -
172A MET* 3.8 17.0 - - + -
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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
----------------------------------------------------------
91A LEU* 4.2 20.2 - - + +
113A ALA 2.9 13.1 + - - +
114A ASN* 3.1 13.2 + - - +
116A PHE* 1.3 74.2 - - - +
118A THR* 1.3 65.7 + - - +
119A ILE 3.1 1.8 - - - -
120A LYS* 3.3 9.8 + - + -
121A LYS* 2.9 33.7 + - + +
73B GLU* 3.5 39.7 - - + +
74B TYR* 3.6 21.1 - - + +
77B LEU* 4.8 5.4 - - + -
78B TYR* 4.3 19.7 - - + +
107B VAL* 4.6 4.0 - - + -
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Residues in contact with THR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASN 3.2 8.8 + - - +
115A SER* 2.8 19.5 + - - +
117A LEU* 1.3 76.7 - - - +
119A ILE* 1.3 65.9 + - - +
121A LYS* 3.3 20.6 + - - +
122A ASP* 3.3 18.0 + - - +
106B THR* 3.7 25.4 - - - +
107B VAL* 3.5 27.8 - - + -
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 5.5 0.2 - - + -
35A ILE* 4.0 21.5 - - + -
37A THR* 4.4 26.2 - - + -
38A ASN 5.7 2.0 - - - +
39A LEU* 5.1 0.7 - - + -
42A ILE* 4.0 26.7 - - + -
83A LEU* 5.0 6.3 - - + -
87A LEU* 3.5 16.2 - - + -
115A SER 3.6 10.3 - - - +
116A PHE* 3.2 21.3 + - + +
117A LEU 3.1 0.6 - - - -
118A THR* 1.3 77.4 - - - +
120A LYS* 1.3 66.3 + - - +
121A LYS 3.0 1.3 - - - -
122A ASP* 3.0 9.1 + - - +
123A LEU* 3.0 25.9 + - + +
172A MET* 4.9 11.2 - - + -
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Residues in contact with LYS 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 2.7 53.5 - - + +
87A LEU* 3.8 12.2 - - + +
88A ARG* 4.1 25.6 - - + +
91A LEU* 3.8 31.4 - - + -
116A PHE 3.0 8.1 + - - +
117A LEU* 3.7 15.0 - - + +
119A ILE* 1.3 75.1 - - - +
121A LYS* 1.3 59.0 + - + +
123A LEU* 3.3 6.5 + - - +
124A ARG* 2.7 60.2 + - - +
78B TYR* 5.2 7.0 - - - +
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Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 2.9 30.3 + - + +
118A THR* 3.4 12.9 - - - +
119A ILE 3.0 0.2 - - - -
120A LYS* 1.3 79.8 - - + +
122A ASP* 1.3 63.2 + - - +
124A ARG* 3.4 16.9 + - - +
125A LEU 3.3 15.2 + - - -
73B GLU* 2.7 31.5 + - - +
106B THR 4.9 3.8 + - - -
107B VAL* 4.2 12.3 - - + +
108B PRO* 4.6 6.5 - - - +
206D GLN* 5.9 4.0 - - - +
215D TYR* 3.7 42.3 + - + +
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Residues in contact with ASP 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 3.6 29.8 - - + +
36A ALA 4.1 16.6 + - - +
118A THR 3.3 11.2 + - - +
119A ILE* 3.0 9.2 + - - +
121A LYS* 1.3 76.2 - - - +
123A LEU* 1.3 67.2 + - - +
125A LEU* 3.1 13.2 + - - +
126A CYS* 3.0 23.6 + - - -
215D TYR* 4.3 9.9 + - - -
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.5 32.3 - - + -
33A CYS* 4.3 2.5 - - - -
35A ILE* 4.2 10.3 - - + -
80A CYS* 4.0 15.5 - - - +
83A LEU* 4.0 11.2 - - + -
84A ARG* 3.7 44.0 - - + +
87A LEU* 4.0 21.5 - - + -
119A ILE* 3.0 21.5 + - + +
120A LYS* 3.7 8.1 - - - +
122A ASP* 1.3 76.0 - - - +
124A ARG* 1.3 57.5 + - - +
126A CYS* 3.2 6.9 + - - +
127A HIS* 2.9 26.9 + - - +
132A CYS* 4.2 1.9 - - - -
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Residues in contact with ARG 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 3.5 16.9 - - - +
120A LYS* 2.7 51.2 + - - +
121A LYS* 3.6 15.9 - - - +
123A LEU* 1.3 75.7 - - - +
125A LEU* 1.3 59.8 + - - +
127A HIS* 3.2 4.0 + - - +
128A ALA* 2.8 26.7 + - - +
166D LEU* 3.7 24.7 - - + -
168D ALA* 5.5 1.0 - - - +
178D GLU* 2.8 31.6 + - - -
180D VAL* 3.8 28.9 - - + +
206D GLN* 4.5 9.6 + - - -
215D TYR* 6.0 0.7 - - - -
218D PHE* 4.9 12.3 - - - -
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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
----------------------------------------------------------
121A LYS 3.3 9.2 + - - +
122A ASP* 3.1 15.4 + - - +
124A ARG* 1.3 78.3 - - - +
126A CYS* 1.3 65.8 + - - +
128A ALA* 2.9 5.4 + - + +
129A HIS* 2.9 45.9 + - + +
166D LEU* 4.4 13.7 - - + -
182D MET* 3.8 28.5 - - + -
208D PHE* 3.6 31.4 - - + -
215D TYR* 3.6 19.5 - - - +
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Residues in contact with CYS 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A CYS* 2.0 55.0 - - + -
34A VAL 4.4 2.0 - - - -
35A ILE* 4.1 9.4 - - - -
80A CYS* 4.1 5.8 - - - -
122A ASP 3.0 14.9 + - - -
123A LEU 3.3 8.7 - - - +
125A LEU* 1.3 75.2 - - - +
127A HIS* 1.3 62.4 + - - +
129A HIS* 3.3 9.9 + - - +
131A THR* 2.8 39.6 + - - +
132A CYS* 4.1 0.9 - - - -
----------------------------------------------------------
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Residues in contact with HIS 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 3.2 38.0 + - - +
123A LEU 2.9 13.1 + - - +
124A ARG 3.3 9.9 - - - +
126A CYS* 1.3 76.7 - - - +
128A ALA* 1.3 57.5 + - - +
130A MET* 2.9 24.8 + - - +
132A CYS* 3.5 30.9 + - + +
134A CYS* 6.1 3.3 - - - -
178D GLU 6.0 0.2 + - - -
179D HIS* 5.9 0.6 - - - -
180D VAL* 4.0 32.6 + - + +
----------------------------------------------------------
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG 2.8 14.4 + - - +
125A LEU* 2.9 8.5 + - + +
127A HIS* 1.3 77.4 - - - +
129A HIS* 1.3 59.5 + - - +
130A MET* 3.1 16.9 + - - +
166D LEU* 3.8 15.0 - - + -
180D VAL* 4.6 15.5 - - + +
181D LYS 4.7 2.0 - - - -
182D MET* 3.4 43.9 + - + +
----------------------------------------------------------
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Residues in contact with HIS 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 2.9 38.3 + - + +
126A CYS* 3.8 7.7 - - - +
127A HIS 3.1 0.2 - - - -
128A ALA* 1.3 78.1 - - - +
130A MET* 1.3 73.8 + - - +
131A THR* 3.3 15.7 + - + +
24C ALA* 4.0 28.1 - - - -
25C LEU 5.1 1.6 - - - -
164D GLU* 4.1 7.3 + - - -
182D MET* 3.9 31.5 - - + +
208D PHE* 5.6 2.2 - + - -
----------------------------------------------------------
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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
------------------------------------------------------------
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