Contacts of the helix formed by residues 102 - 128 (chain G) in PDB entry 2YW7
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 VAL 102 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G VAL* 4.1 12.3 - - + -
43G VAL 3.7 8.6 + - - +
44G GLY* 5.5 1.1 - - - -
46G ASN* 3.6 30.3 - - - +
47G PHE* 3.6 17.9 - - - +
50G VAL* 3.7 15.7 - - + -
101G THR* 1.3 72.3 - - - +
103G GLN* 1.3 70.3 + - - +
105G HIS 3.4 0.3 + - - -
106G LEU* 2.9 53.9 + - + +
155G HIS* 5.9 0.2 - - + -
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Residues in contact with GLN 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G THR* 3.2 26.9 - - - +
102G VAL* 1.3 82.2 + - - +
104G ALA* 1.3 65.4 + - - +
106G LEU* 4.2 4.4 - - - +
107G ALA* 3.1 25.6 + - - +
155G HIS* 4.9 15.9 + - + +
156G LEU 5.9 4.6 - - - -
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Residues in contact with ALA 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G VAL* 4.8 5.8 - - + +
100G ASP* 3.5 33.4 - - + +
101G THR* 3.3 17.9 + - - +
102G VAL 3.1 0.2 - - - -
103G GLN* 1.3 82.7 - - - +
105G HIS* 1.3 60.5 + - - +
107G ALA* 3.4 4.9 + - - +
108G ALA* 3.2 20.7 + - - +
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Residues in contact with HIS 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G VAL* 3.5 17.6 - - + +
41G ASN* 3.9 15.5 + - + -
42G VAL* 3.8 23.6 - - + -
95G TYR* 2.9 44.2 + + - +
97G VAL* 3.6 10.4 - - + +
98G GLU 2.7 29.4 + - - -
100G ASP* 3.4 22.0 + - + -
101G THR 3.1 23.0 + - - +
102G VAL 4.1 0.7 - - - +
104G ALA* 1.3 75.5 - - - +
106G LEU* 1.3 60.4 + - + +
108G ALA* 3.2 1.0 + - - -
109G LEU* 2.7 35.5 + - - +
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Residues in contact with LEU 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G VAL* 3.7 33.2 - - + -
53G MET* 4.9 14.6 - - - -
54G ILE* 5.6 0.4 - - + -
102G VAL* 2.9 35.9 + - + +
103G GLN 4.2 1.6 - - - +
105G HIS* 1.3 79.3 - - + +
107G ALA* 1.3 53.7 + - - +
109G LEU* 4.2 12.3 - - + -
110G ASP* 2.8 36.8 + - - +
152G VAL* 3.5 19.9 - - + +
154G ALA 5.1 1.8 - - - +
155G HIS* 3.6 39.0 - - + -
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Residues in contact with ALA 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G GLN 3.1 20.0 + - - +
104G ALA* 3.5 5.6 - - - +
106G LEU* 1.3 75.6 - - - +
108G ALA* 1.3 56.9 + - - +
110G ASP* 3.2 13.4 + - - +
111G LEU* 2.9 33.2 + - + +
155G HIS* 4.3 12.2 + - + +
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Residues in contact with ALA 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G TYR* 3.3 28.9 - - + +
97G VAL* 3.8 16.4 - - + -
104G ALA 3.2 10.8 + - - +
105G HIS 3.5 2.0 - - - +
107G ALA* 1.3 77.5 - - - +
109G LEU* 1.3 51.2 - - - +
111G LEU* 3.1 8.8 + - - +
112G VAL* 2.6 40.2 + - + +
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Residues in contact with LEU 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G THR* 5.0 3.1 - - + -
35G LEU* 3.8 21.5 - - + -
38G VAL* 3.8 44.9 - - + -
54G ILE* 3.9 17.7 - - + -
95G TYR* 3.9 9.6 - - + -
105G HIS 2.7 19.1 + - - +
106G LEU* 3.6 15.9 - - + +
108G ALA* 1.3 69.1 - - - +
110G ASP* 1.3 60.2 + - - +
112G VAL* 3.0 14.6 + - + +
113G TYR* 2.9 46.1 + - + -
148G PHE* 4.6 8.3 - - + -
152G VAL* 4.6 7.6 - - + -
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Residues in contact with ASP 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G LEU 2.8 22.4 + - - +
107G ALA* 3.4 7.4 - - - +
109G LEU* 1.3 73.1 - - - +
111G LEU* 1.3 78.7 + - - +
113G TYR* 4.9 1.3 - - - -
114G ASN* 3.5 8.7 + - - -
149G GLN* 2.9 28.0 - - - +
152G VAL* 3.9 17.2 - - + +
153G ARG* 2.7 46.1 + - + +
155G HIS* 5.4 4.0 - - - +
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Residues in contact with LEU 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G ALA* 2.9 17.0 + - + +
108G ALA* 3.1 11.6 + - - +
110G ASP* 1.3 95.8 + - - +
112G VAL* 1.3 64.2 + - - +
113G TYR 3.2 0.7 + - - -
114G ASN* 3.4 27.7 + - + +
115G GLY* 3.7 3.8 + - - -
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Residues in contact with VAL 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G ASP* 5.8 3.4 - - - +
31G LEU* 3.9 27.1 - - + -
34G THR* 5.1 6.3 - - + -
95G TYR* 3.7 31.4 - - + -
108G ALA* 2.6 26.5 + - + +
109G LEU* 3.3 14.4 - - + +
111G LEU* 1.3 75.5 - - + +
113G TYR* 1.3 62.9 + - + +
115G GLY* 3.5 3.6 + - - -
116G VAL* 3.4 23.6 + - + +
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Residues in contact with TYR 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G LEU* 3.4 31.5 - - + +
35G LEU* 3.5 7.1 - - + +
57G GLN* 3.0 27.5 + - - +
109G LEU* 2.9 35.1 + - + +
110G ASP* 4.7 0.7 - - - -
111G LEU 3.2 0.4 - - - -
112G VAL* 1.3 79.5 - - + +
114G ASN* 1.3 55.8 + - - +
116G VAL* 3.1 5.5 + - + +
117G ILE* 2.6 51.6 + - + +
145G LEU* 3.8 41.3 - - + -
148G PHE* 3.2 36.2 - + - -
149G GLN* 3.3 22.4 - - + +
152G VAL* 6.0 0.4 - - + -
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Residues in contact with ASN 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G ASP* 3.5 15.4 + - - -
111G LEU* 3.4 22.9 + - + +
112G VAL 3.4 0.2 - - - -
113G TYR* 1.3 74.0 - - - +
115G GLY* 1.3 55.8 + - - +
117G ILE* 4.7 3.4 - - - -
118G GLU* 2.5 48.0 + - + +
149G GLN* 3.3 13.4 + - - +
153G ARG* 3.4 29.7 + - - +
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Residues in contact with GLY 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G LEU 3.7 4.2 + - - -
112G VAL 3.5 6.8 + - - -
113G TYR 3.3 0.6 - - - -
114G ASN* 1.3 76.8 - - - +
116G VAL* 1.3 56.4 + - - +
118G GLU* 3.6 11.1 + - - +
119G ASP* 2.8 39.8 + - - +
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Residues in contact with VAL 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G THR* 3.5 35.1 - - + +
28G TYR* 4.8 7.0 - - + -
31G LEU* 4.3 27.8 - - + -
92G TRP* 6.0 3.1 - - + -
112G VAL* 3.4 20.3 + - + +
113G TYR* 3.1 11.5 + - + +
115G GLY* 1.3 72.1 - - - +
117G ILE* 1.3 61.6 + - + +
119G ASP* 3.9 2.6 - - - +
120G THR* 2.9 39.5 + - - +
145G LEU* 4.6 17.3 - - + -
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Residues in contact with ILE 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G TYR* 2.6 33.6 + - + +
114G ASN* 3.8 2.9 - - - +
116G VAL* 1.3 70.3 - - + +
118G GLU* 1.3 59.0 + - - +
120G THR* 3.4 5.8 + - - -
121G ARG* 2.8 62.6 + - + +
142G ALA* 4.5 7.6 - - - +
145G LEU* 3.5 44.6 - - + +
146G GLU* 3.7 20.0 - - + +
149G GLN* 3.8 26.2 - - + +
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Residues in contact with GLU 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G ASN* 2.5 31.8 + - + +
115G GLY* 3.6 9.9 + - - +
117G ILE* 1.3 73.1 - - - +
119G ASP* 1.3 63.8 + - - +
121G ARG* 3.4 16.8 + - - +
122G LYS* 3.2 53.0 + - - +
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Residues in contact with ASP 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G GLN* 5.2 5.6 - - - +
27G THR* 5.4 7.4 + - + +
91G THR* 4.6 10.9 + - - -
92G TRP* 4.6 14.9 - - - -
115G GLY 2.8 24.5 + - - +
116G VAL* 3.9 5.7 - - - +
118G GLU* 1.3 73.6 - - - +
120G THR* 1.3 66.0 + - - +
122G LYS* 3.0 27.1 + - - +
123G SER* 3.0 24.1 + - - -
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Residues in contact with THR 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G GLN* 2.5 27.0 + - - +
28G TYR* 4.6 3.5 + - - +
116G VAL* 2.9 27.1 + - - +
117G ILE* 3.6 6.7 - - - -
119G ASP* 1.3 73.6 - - - +
121G ARG* 1.3 66.5 + - - +
123G SER* 3.2 3.9 + - - +
124G ILE* 3.0 39.0 + - + +
138G LEU* 3.6 24.7 - - + +
142G ALA* 3.8 22.0 - - + +
145G LEU* 4.6 4.2 - - + +
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Residues in contact with ARG 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G ILE* 2.8 46.4 + - + +
118G GLU* 3.5 12.6 - - - +
120G THR* 1.3 76.0 - - - +
122G LYS* 1.3 58.2 + - + +
124G ILE* 3.4 13.2 + - + +
125G GLU* 3.1 39.2 + - - +
142G ALA* 5.3 5.8 - - + -
146G GLU* 3.6 28.7 + - - +
149G GLN* 5.3 6.5 - - - +
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Residues in contact with LYS 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118G GLU* 3.2 42.1 + - - +
119G ASP* 3.0 24.4 + - - +
121G ARG* 1.3 73.2 - - + +
123G SER* 1.3 58.6 + - - +
124G ILE 3.0 4.5 - - - -
125G GLU* 2.9 33.2 + - - +
126G LYS* 3.0 22.4 + - + +
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Residues in contact with SER 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G LEU* 4.2 28.3 + - - +
23G LYS* 6.0 1.2 - - - +
24G GLN* 4.3 10.3 + - - -
119G ASP 3.0 12.3 + - - -
120G THR* 3.2 8.0 + - - -
122G LYS* 1.3 73.4 - - - +
124G ILE* 1.3 56.4 + - - +
126G LYS* 3.7 11.7 - - - +
127G LEU* 2.9 38.3 + - - +
138G LEU* 4.3 17.3 - - - -
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Residues in contact with ILE 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G THR* 3.0 35.9 - - + +
121G ARG* 3.5 11.2 - - + +
122G LYS 3.0 0.6 - - - -
123G SER* 1.3 75.7 - - - +
125G GLU* 1.3 60.6 + - + +
126G LYS 3.0 5.4 + - - -
127G LEU* 5.2 0.2 - - - -
128G GLU* 3.6 6.8 + - - +
135G GLN* 3.2 46.8 + - - +
138G LEU* 3.8 34.5 - - + +
139G ILE* 3.7 20.6 - - + -
142G ALA* 4.0 7.9 - - + -
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Residues in contact with GLU 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G ARG* 3.1 22.0 + - - +
122G LYS* 2.9 18.7 + - - +
124G ILE* 1.3 74.4 - - + +
126G LYS* 1.3 62.4 + - + +
128G GLU* 4.3 12.1 - - - +
129G ASP* 4.8 5.9 - - - +
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Residues in contact with LYS 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G ASP* 5.8 1.8 + - - -
20G LEU* 3.5 39.3 - - + +
23G LYS* 5.4 3.2 - - - +
122G LYS* 3.2 18.6 - - + +
123G SER* 3.7 9.9 - - - +
124G ILE 3.0 0.6 - - - -
125G GLU* 1.3 80.5 - - + +
127G LEU* 1.3 54.0 + - - +
128G GLU 2.7 16.9 + - - -
129G ASP* 2.9 18.3 + - - +
130G LEU* 3.3 16.1 - - + +
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Residues in contact with LEU 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G VAL* 3.5 39.9 - - + -
20G LEU* 3.8 23.8 - - + -
21G LEU* 4.7 5.2 - - + -
123G SER* 2.9 30.3 + - - +
124G ILE 3.7 0.4 + - - -
126G LYS* 1.3 70.6 - - - +
128G GLU* 1.3 56.6 + - - +
129G ASP 3.2 0.9 - - - -
130G LEU* 3.1 7.1 + - + +
131G ASP 2.9 36.1 + - - +
132G LEU 3.6 1.2 + - - -
134G SER* 3.9 12.6 - - - +
135G GLN* 3.4 40.1 - - + +
138G LEU* 4.3 15.5 - - + -
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Residues in contact with GLU 128 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G ILE 3.6 9.7 + - - +
125G GLU* 4.3 10.5 - - - +
126G LYS 2.7 5.5 + - - +
127G LEU* 1.3 75.3 - - - +
129G ASP* 1.3 64.8 + - - +
130G LEU 3.8 0.2 + - - -
132G LEU* 5.0 17.9 - - + +
135G GLN* 3.7 27.0 + - - +
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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