Contacts of the helix formed by residues 101 - 128 (chain A) in PDB entry 2QKW
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 LEU 101 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A MET* 1.3 74.6 - - - +
102A PRO* 1.3 72.6 - - + +
103A HIS* 3.2 26.5 - - + +
104A GLU* 2.8 33.1 + - - +
105A ASN* 2.8 19.4 + - - -
49B HIS* 3.6 42.8 - - + +
50B GLY* 3.9 18.6 - - - -
51B VAL* 3.9 11.7 - - + -
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Residues in contact with PRO 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 4.1 16.6 - - + +
36A LEU* 3.8 11.6 - - + +
86A GLN* 3.8 9.6 - - - +
90A MET* 3.7 39.3 - - + -
101A LEU* 1.3 97.1 - - + +
103A HIS* 1.3 60.8 + - - +
105A ASN* 3.2 18.8 + - - +
106A VAL* 3.3 18.2 + - - +
49B HIS* 5.1 5.4 - - - +
51B VAL* 4.0 16.2 - - + +
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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
----------------------------------------------------------
29A ASP* 3.4 40.1 + - - +
31A VAL* 3.6 14.1 - - + +
101A LEU* 3.5 35.6 - - + +
102A PRO* 1.3 78.8 - - - +
104A GLU* 1.3 71.6 + - + +
105A ASN 3.3 0.2 - - - -
106A VAL* 3.2 14.2 - - + +
107A ASP* 3.1 41.8 + - - +
49B HIS* 4.7 9.8 + + - -
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Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A MET* 3.4 21.6 - - + +
101A LEU* 2.8 47.2 + - - +
103A HIS* 1.3 99.6 - - + +
105A ASN* 1.3 56.5 + - - +
107A ASP* 3.9 5.0 - - - +
108A ASP* 3.1 35.3 + - - +
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Residues in contact with ASN 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 4.4 10.1 - - + -
79A THR* 4.9 1.3 - - + +
82A MET* 3.4 31.9 - - - +
83A ALA* 3.6 6.7 + - + +
86A GLN* 3.1 26.3 - - - +
100A MET* 3.4 18.7 - - - +
101A LEU 2.8 27.1 + - - -
102A PRO* 3.2 6.3 + - - +
104A GLU* 1.3 75.6 - - - +
106A VAL* 1.3 60.0 + - - +
108A ASP* 3.2 8.4 + - - +
109A MET* 2.8 41.3 + - + +
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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
----------------------------------------------------------
31A VAL* 3.8 27.8 - - + -
36A LEU* 4.2 20.6 - - + -
39A VAL* 4.4 16.6 - - + -
102A PRO 3.3 11.2 + - - +
103A HIS* 3.2 21.8 - - + +
105A ASN* 1.3 75.0 - - - +
107A ASP* 1.3 69.2 + - - +
109A MET* 3.9 11.9 - - + -
110A ARG* 2.8 50.2 + - + +
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Residues in contact with ASP 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A HIS* 3.1 30.2 + - - +
104A GLU* 4.0 7.0 - - - +
106A VAL* 1.3 89.4 - - - +
108A ASP* 1.3 58.9 + - - +
110A ARG* 4.7 8.2 + - - +
111A SER* 3.3 23.9 + - - -
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Residues in contact with ASP 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A HIS* 5.0 7.9 - - + -
79A THR* 4.2 16.7 + - + +
100A MET* 5.6 3.6 - - - +
104A GLU* 3.1 25.3 + - - +
105A ASN* 3.5 8.0 - - - +
106A VAL 3.1 0.6 - - - -
107A ASP* 1.3 80.2 - - - +
109A MET* 1.3 58.5 + - - +
111A SER* 3.3 6.7 - - - -
112A ALA* 3.1 22.0 + - - +
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Residues in contact with MET 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.6 32.8 - - + +
39A VAL* 3.8 14.4 - - + +
40A ARG* 3.6 37.9 - - - +
43A LEU* 3.5 25.7 - - + +
79A THR* 3.6 8.3 - - + -
80A LEU* 5.4 0.2 - - - -
83A ALA* 3.8 17.9 - - + -
105A ASN 2.8 29.8 + - - +
106A VAL* 3.8 5.4 - - - +
108A ASP* 1.3 75.4 - - - +
110A ARG* 1.3 64.7 + - - +
111A SER 3.1 1.6 - - - -
112A ALA* 3.2 7.6 + - - +
113A ILE* 3.1 30.8 + - - +
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Residues in contact with ARG 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 3.8 35.8 - - + +
42A GLN* 4.9 9.3 + - - +
106A VAL* 2.8 38.0 + - - +
107A ASP* 4.7 8.1 + - - +
109A MET* 1.3 75.4 - - - +
111A SER* 1.3 60.7 + - - +
113A ILE* 3.6 22.3 + - + +
114A THR* 3.3 13.3 + - - -
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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
----------------------------------------------------------
107A ASP 3.3 20.9 + - - -
108A ASP* 3.3 8.3 - - - -
109A MET 3.1 0.2 - - - -
110A ARG* 1.3 80.0 - - - +
112A ALA* 1.3 61.6 + - - +
114A THR* 3.3 19.5 + - - -
115A ASP* 3.0 21.5 + - - +
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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
----------------------------------------------------------
43A LEU* 3.7 21.8 - - + -
72A LEU* 4.4 1.3 - - + +
75A HIS* 4.9 8.5 - - + +
76A THR* 5.1 7.2 - - + +
79A THR* 4.8 9.4 - - - +
108A ASP 3.1 15.9 + - - +
109A MET* 3.2 12.3 + - - +
111A SER* 1.3 76.2 - - - +
113A ILE* 1.3 61.6 + - - +
115A ASP* 3.3 15.9 + - - +
116A TRP* 3.2 27.2 + - - -
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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
----------------------------------------------------------
39A VAL* 4.7 5.8 - - + +
42A GLN* 4.1 26.9 - - + +
43A LEU* 3.9 26.0 - - + +
46A SER* 3.8 27.8 - - - +
109A MET 3.1 17.5 + - - +
110A ARG* 3.8 20.4 - - + +
111A SER 3.2 0.4 - - - -
112A ALA* 1.3 74.5 - - - +
114A THR* 1.3 65.0 + - - +
116A TRP* 3.2 6.8 + - - +
117A SER* 3.1 24.7 + - - +
120A ARG* 4.6 1.6 + - - +
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Residues in contact with THR 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ARG 3.3 11.1 + - - -
111A SER* 3.3 14.0 + - - -
113A ILE* 1.3 76.6 - - - +
115A ASP* 1.3 59.4 + - - +
117A SER* 3.1 11.6 + - - +
118A ASP* 2.9 48.8 + - - +
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Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG* 4.8 2.3 + - - -
72A LEU* 3.6 23.4 - - + +
75A HIS* 5.4 5.0 - - - -
111A SER* 3.0 24.0 + - - +
112A ALA* 3.3 17.8 - - - +
113A ILE 3.2 0.4 - - - -
114A THR* 1.3 77.4 - - - +
116A TRP* 1.3 57.3 + - - +
118A ASP* 3.7 8.5 - - - +
119A MET* 3.1 30.7 + - - +
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Residues in contact with TRP 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 4.2 9.2 - - + -
46A SER* 3.8 7.4 - - - +
47A ALA* 3.6 34.6 - - + +
48A GLY 3.9 8.5 - - - -
49A LEU* 3.8 25.1 - - + -
69A TYR* 3.5 37.9 - + - -
72A LEU* 3.6 21.2 - - + +
73A TYR* 3.9 24.0 - + - -
76A THR* 3.1 28.7 + - - +
112A ALA 3.2 21.0 + - - -
113A ILE* 3.2 9.9 + - - +
114A THR 3.2 0.4 - - - -
115A ASP* 1.3 74.4 - - - +
117A SER* 1.3 56.8 + - - +
118A ASP 3.0 4.5 - - - -
119A MET* 3.0 9.9 + - + +
120A ARG* 2.9 47.0 + - - +
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 3.1 16.5 + - - +
114A THR* 3.1 19.1 + - - +
116A TRP* 1.3 75.2 - - - +
118A ASP* 1.3 62.1 + - - +
120A ARG* 3.5 29.1 - - - +
121A GLU* 3.6 19.1 + - - +
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Residues in contact with ASP 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG* 4.4 10.8 - - - +
114A THR* 2.9 34.7 + - - +
115A ASP* 3.7 8.8 + - - +
117A SER* 1.3 81.6 + - - +
119A MET* 1.3 54.1 + - - +
120A ARG 3.2 0.9 - - - -
121A GLU* 3.0 16.7 + - - +
122A ALA* 2.5 39.0 + - - +
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Residues in contact with MET 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 5.9 0.4 - - + -
66A ARG* 5.2 4.5 - - + +
68A ARG* 3.2 54.2 - - + +
69A TYR* 3.6 32.1 - - + +
72A LEU* 3.6 19.7 - - + -
115A ASP 3.1 17.6 + - - +
116A TRP* 3.0 18.5 + - + +
118A ASP* 1.3 74.9 - - - +
120A ARG* 1.3 55.7 + - + +
122A ALA* 3.1 3.6 + - - -
123A LEU* 2.7 75.7 + - + +
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Residues in contact with ARG 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER* 3.4 31.2 + - - +
48A GLY 4.1 10.2 + - - -
49A LEU* 3.7 17.9 - - + +
50A PRO* 3.5 21.5 - - + -
53A GLN* 2.7 45.0 + - - +
113A ILE* 4.6 2.2 + - - +
116A TRP* 2.9 18.4 + - + +
117A SER* 3.5 42.5 - - - +
119A MET* 1.3 76.6 - - + +
121A GLU* 1.3 60.4 + - - +
124A GLN* 3.4 7.6 + - - +
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Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER 3.6 12.4 + - - +
118A ASP* 3.0 23.9 + - - +
120A ARG* 1.3 76.9 - - - +
122A ALA* 1.3 60.4 + - - +
123A LEU 3.2 0.2 - - - -
124A GLN* 3.4 5.3 + - - +
125A HIS* 2.9 34.2 + - + +
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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
----------------------------------------------------------
66A ARG* 4.8 12.0 + - + +
68A ARG* 3.7 28.0 - - - +
118A ASP 2.5 20.4 + - - +
119A MET* 3.6 3.4 - - - +
121A GLU* 1.3 72.7 - - - +
123A LEU* 1.3 60.1 + - + +
125A HIS* 3.6 5.4 - - - +
126A ALA* 2.9 31.0 + - - +
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 3.5 32.3 - - + -
53A GLN* 3.6 22.2 - - + +
56A PHE 5.8 0.2 - - - +
57A VAL* 3.9 23.1 - - + -
62A PRO* 4.6 19.7 - - + -
66A ARG* 4.7 9.4 - - + +
69A TYR* 5.4 0.4 - - + -
119A MET* 2.7 52.0 + - + +
120A ARG 4.6 0.2 - - - +
122A ALA* 1.3 70.1 - - + +
124A GLN* 1.3 65.1 + - - +
125A HIS 3.1 1.1 - - - -
126A ALA* 4.5 2.7 - - - +
127A MET* 2.8 37.7 + - + +
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Residues in contact with GLN 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PRO* 5.7 0.3 - - - +
52A ASP* 4.7 6.5 + - - +
53A GLN* 2.8 26.9 + - - +
120A ARG 3.4 17.9 + - - +
121A GLU* 3.7 5.2 - - + +
123A LEU* 1.3 77.5 - - - +
125A HIS* 1.3 62.0 + - - +
127A MET* 3.8 12.0 - - - +
128A GLY* 3.2 19.6 + - - -
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Residues in contact with HIS 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG* 5.8 2.2 + - - -
121A GLU* 2.9 20.7 + - + +
122A ALA* 3.6 7.0 - - - +
124A GLN* 1.3 74.6 - - - +
126A ALA* 1.3 67.8 + - - +
128A GLY* 3.2 21.1 + - - +
129A ILE* 4.9 3.0 - - + +
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Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PRO* 4.0 22.2 - - + +
66A ARG* 3.6 31.0 - - + +
122A ALA 2.9 21.9 + - - +
123A LEU* 4.2 1.8 - - - +
125A HIS* 1.3 78.1 + - - +
127A MET* 1.3 57.7 + - - +
129A ILE* 3.1 32.6 - - - +
----------------------------------------------------------
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Residues in contact with MET 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP* 3.5 20.2 - - - +
53A GLN* 3.7 28.3 - - + +
56A PHE* 3.5 41.3 - - + +
57A VAL* 5.9 0.2 - - + -
60A GLN* 6.1 0.9 - - + +
62A PRO* 5.5 2.0 - - + +
123A LEU* 2.8 30.8 + - + +
124A GLN* 3.8 12.6 - - - +
126A ALA* 1.3 74.2 - - - +
128A GLY* 1.3 60.4 + - - +
129A ILE* 2.9 19.3 + - - +
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Residues in contact with GLY 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLN 3.2 13.0 + - - -
125A HIS 3.2 15.4 + - - +
127A MET* 1.3 74.2 - - - +
129A ILE* 1.3 59.0 + - - +
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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