Contacts of the helix formed by residues 102 - 128 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C VAL* 3.6 15.4 - - + +
43C VAL 3.6 2.4 + - - +
45C PRO* 3.8 19.2 - - + +
46C ASN* 4.0 9.2 - - - +
47C PHE* 3.9 12.1 - - + +
50C VAL* 3.4 37.5 - - + -
101C THR* 1.3 73.0 - - - +
103C GLN* 1.3 71.2 + - - +
105C HIS* 4.3 5.2 - - - -
106C LEU* 2.8 52.9 + - + +
155C HIS* 5.0 3.6 - - - +
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Residues in contact with GLN 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PRO* 5.4 9.9 - - - +
45C PRO* 2.9 35.8 - - + +
46C ASN* 5.2 1.0 - - - +
101C THR* 3.2 10.5 - - + +
102C VAL* 1.3 87.5 - - - +
104C ALA* 1.3 58.7 + - - +
106C LEU* 6.0 0.2 - - - +
107C ALA* 3.5 16.1 - - - +
155C HIS 5.4 2.4 + - - -
156C LEU* 3.9 28.3 + - + +
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Residues in contact with ALA 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C VAL* 4.3 8.6 - - + +
100C ASP* 3.6 24.9 - - + +
101C THR* 2.9 19.0 + - - +
103C GLN* 1.3 77.4 - - - +
105C HIS* 1.3 61.2 + - - +
107C ALA* 3.5 6.4 - - - +
108C ALA* 3.0 24.4 + - - +
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Residues in contact with HIS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C VAL* 3.3 21.6 - - + +
41C ASN* 2.6 36.7 + - + -
42C VAL* 3.5 15.7 - - + -
50C VAL* 5.9 1.1 - - + -
95C TYR* 2.7 32.9 + + - -
97C VAL* 3.2 24.7 - - + +
98C GLU 3.0 15.9 + - - -
100C ASP 3.7 5.3 + - - -
101C THR 2.7 28.7 + - - +
102C VAL* 3.9 3.1 - - - +
104C ALA* 1.3 74.2 - - - +
106C LEU* 1.3 56.3 + - + +
107C ALA 3.1 1.1 - - - -
108C ALA* 2.8 7.4 + - - +
109C LEU* 2.8 36.1 + - - +
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Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C VAL* 4.2 13.9 - - + -
53C MET* 3.8 23.8 - - + -
102C VAL* 2.8 34.1 + - + +
105C HIS* 1.3 71.6 - - - +
107C ALA* 1.3 52.5 + - - +
109C LEU* 3.2 12.9 + - + -
110C ASP* 2.6 33.0 + - - +
152C VAL* 3.2 32.6 - - + +
155C HIS* 3.6 41.5 - - + +
156C LEU* 3.8 22.4 - - + -
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Residues in contact with ALA 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C GLN 3.5 17.4 + - - +
104C ALA* 3.5 12.1 - - - +
106C LEU* 1.3 78.6 - - - +
108C ALA* 1.3 63.0 + - - +
110C ASP* 3.2 22.0 + - - +
111C LEU* 3.3 15.5 + - + +
156C LEU* 4.0 12.0 - - + +
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Residues in contact with ALA 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C TYR* 3.2 30.1 - - + +
97C VAL* 3.5 21.3 - - + -
104C ALA 3.0 8.4 + - - +
105C HIS 2.8 14.0 + - - +
107C ALA* 1.3 71.4 - - - +
109C LEU* 1.3 61.2 + - - +
111C LEU* 3.2 12.2 + - - +
112C VAL* 3.1 25.4 + - - +
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Residues in contact with LEU 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 5.6 0.2 - - + -
34C THR* 4.8 5.6 - - + -
35C LEU* 3.8 24.9 - - + -
38C VAL* 3.9 38.8 - - + -
54C ILE* 4.1 26.0 - - + -
95C TYR* 4.7 0.7 - - + +
105C HIS 2.8 16.5 + - - +
106C LEU* 3.6 19.3 - - + +
108C ALA* 1.3 69.7 - - - +
110C ASP* 1.3 67.9 + - - +
112C VAL* 3.5 15.0 - - + +
113C TYR* 3.0 42.8 + - + -
148C PHE* 4.9 6.3 - - + -
152C VAL* 4.3 7.2 - - + -
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Residues in contact with ASP 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU 2.6 18.0 + - - +
107C ALA* 3.2 15.0 - - - +
109C LEU* 1.3 75.2 - - - +
111C LEU* 1.3 61.8 + - - +
113C TYR* 3.5 4.0 + - - +
114C ASN* 3.1 33.7 + - - -
149C GLN* 3.3 15.0 + - - +
152C VAL* 4.0 9.3 - - + +
153C ARG* 3.0 43.5 + - - +
156C LEU* 5.4 5.6 - - + -
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Residues in contact with LEU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ALA* 3.3 15.5 + - + +
108C ALA* 3.2 8.9 + - - +
109C LEU 3.2 0.4 - - - -
110C ASP* 1.3 81.1 - - - +
112C VAL* 1.3 66.7 + - - +
113C TYR 3.2 0.2 - - - -
114C ASN* 3.1 37.7 - - + +
115C GLY* 3.3 3.5 + - - -
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Residues in contact with VAL 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 4.8 13.9 - - + -
34C THR* 4.9 8.5 - - + +
92C TRP* 5.4 15.9 + - + +
95C TYR* 4.1 21.3 - - + -
108C ALA 3.1 19.3 + - - +
109C LEU* 3.5 20.0 - - + +
111C LEU* 1.3 73.5 - - - +
113C TYR* 1.3 68.8 + - + +
115C GLY* 3.0 17.3 + - - -
116C VAL* 3.1 23.5 + - + +
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Residues in contact with TYR 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 3.5 30.0 - - + +
35C LEU* 3.5 7.4 - - + +
57C GLN* 2.6 44.1 + - - +
109C LEU* 3.0 32.0 + - + +
112C VAL* 1.3 79.2 - - + +
114C ASN* 1.3 66.6 + - - +
115C GLY 2.9 2.2 - - - -
116C VAL* 4.2 7.6 - - + +
117C ILE* 2.7 47.2 + - + +
145C LEU* 3.6 25.6 - - + -
148C PHE* 3.2 26.4 - + - -
149C GLN* 3.3 26.9 - - + -
152C VAL* 5.1 1.6 - - + -
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Residues in contact with ASN 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ASP* 3.1 30.4 + - - -
111C LEU* 3.1 37.1 - - + +
113C TYR* 1.3 74.3 - - - +
115C GLY* 1.3 57.3 + - - +
117C ILE* 4.2 3.6 - - - +
118C GLU* 3.3 22.2 + - - +
149C GLN* 4.4 11.2 + - - +
153C ARG* 4.2 16.2 + - - +
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Residues in contact with GLY 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C LEU 3.3 3.0 + - - -
112C VAL 3.0 8.2 + - - -
113C TYR 2.9 2.0 + - - -
114C ASN* 1.3 77.7 - - - +
116C VAL* 1.3 65.3 + - - +
118C GLU* 3.0 17.2 + - - +
119C ASP* 3.0 23.5 + - - -
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Residues in contact with VAL 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C THR* 4.2 29.8 - - + +
28C TYR* 4.7 7.9 - - + -
31C LEU* 4.1 28.7 - - + -
92C TRP* 5.7 5.6 - - + +
112C VAL* 3.1 24.2 + - + +
113C TYR* 3.9 10.5 - - + +
115C GLY* 1.3 72.7 - - - +
117C ILE* 1.3 59.5 + - - +
119C ASP* 3.6 1.8 + - - +
120C THR* 2.4 40.6 + - - +
145C LEU* 4.1 24.5 - - + -
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Residues in contact with ILE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C TYR* 2.7 59.6 + - + +
114C ASN* 4.2 4.0 - - - +
116C VAL* 1.3 74.2 - - + +
118C GLU* 1.3 67.3 + - + +
120C THR* 3.5 6.5 - - - -
121C ARG* 3.1 56.1 + - - +
142C ALA* 5.9 1.2 - - - +
145C LEU* 3.9 15.7 - - + +
146C GLU* 3.5 24.9 - - + +
149C GLN* 3.6 25.8 - - + +
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Residues in contact with GLU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ASN 3.3 16.5 + - - +
115C GLY* 3.0 8.7 + - - +
117C ILE* 1.3 78.1 - - + +
119C ASP* 1.3 74.8 + - - +
121C ARG* 2.7 23.2 + - + +
122C LYS* 2.8 19.2 + - + -
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Residues in contact with ASP 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN* 4.9 7.0 - - - +
27C THR* 4.7 12.2 + - + +
91C THR* 4.6 16.4 - - - +
92C TRP* 4.6 10.9 - - - -
115C GLY* 3.0 19.9 + - - +
116C VAL* 4.0 3.6 - - - +
118C GLU* 1.3 83.3 - - - +
120C THR* 1.3 66.9 + - - +
122C LYS* 2.8 30.9 + - - +
123C SER* 3.1 6.9 + - - -
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Residues in contact with THR 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN* 3.6 33.0 + - - +
27C THR* 6.1 0.2 - - - +
28C TYR* 4.8 2.7 - - - +
116C VAL* 2.4 34.9 + - - +
117C ILE* 3.5 7.0 - - - -
119C ASP* 1.3 76.3 - - - +
121C ARG* 1.3 57.0 + - - +
123C SER* 3.3 2.2 + - - -
124C ILE* 2.9 40.6 + - + +
138C LEU* 3.5 28.9 - - + +
141C HIS* 5.2 0.4 - - + -
142C ALA* 3.9 16.4 - - + +
145C LEU* 4.9 4.3 - - + +
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Residues in contact with ARG 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ILE* 3.1 38.2 + - - +
118C GLU* 2.7 17.2 + - + +
120C THR* 1.3 68.4 - - - +
122C LYS* 1.3 52.9 + - - +
123C SER 2.6 16.4 + - - -
124C ILE* 3.7 10.1 - - + +
125C GLU* 2.7 27.4 + - - +
142C ALA* 5.7 3.6 - - + -
146C GLU* 2.7 34.4 + - - +
149C GLN* 5.8 0.6 + - - -
75E LEU* 5.7 5.7 - - - +
131E ASP* 5.8 2.3 + - - -
133E VAL* 5.9 3.8 - - + -
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Residues in contact with LYS 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C GLU* 2.8 21.6 + - + +
119C ASP* 3.0 13.2 - - - +
121C ARG* 1.3 67.9 - - - +
123C SER* 1.3 56.1 + - - +
125C GLU* 3.1 37.1 - - - +
126C LYS* 4.1 13.4 - - + +
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Residues in contact with SER 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 3.7 29.6 + - - +
24C GLN* 4.7 5.6 + - - -
119C ASP 3.2 17.0 - - - -
120C THR* 3.4 7.4 - - - -
121C ARG 2.6 8.3 + - - -
122C LYS* 1.3 73.5 - - - +
124C ILE* 1.3 59.5 + - - -
125C GLU 3.0 1.5 - - - +
126C LYS* 2.9 20.7 + - - +
127C LEU* 3.1 23.5 + - - +
138C LEU* 4.1 12.1 - - - +
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Residues in contact with ILE 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C THR* 2.9 24.8 + - + +
121C ARG* 3.8 8.1 - - + +
123C SER* 1.3 74.8 - - - +
125C GLU* 1.3 61.0 - - - +
127C LEU* 3.4 7.4 + - - -
128C GLU* 4.9 0.2 - - - +
135C GLN* 2.4 47.0 + - + +
138C LEU* 3.3 45.2 - - + +
139C ILE* 3.4 31.9 - - + -
142C ALA* 3.8 15.3 - - + -
132E LEU* 4.4 11.3 - - + +
133E VAL* 5.1 4.5 - - + -
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Residues in contact with GLU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ARG 2.7 17.3 + - - +
122C LYS* 3.1 46.5 - - - +
124C ILE* 1.3 79.9 - - - +
126C LYS* 1.3 66.2 + - - +
127C LEU 3.4 0.6 + - - -
128C GLU* 4.8 7.6 + - - +
129C ASP* 5.5 1.9 - - - +
132E LEU* 6.5 0.2 - - - -
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Residues in contact with LYS 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 3.9 26.4 - - + +
122C LYS* 4.1 17.9 - - + +
123C SER* 2.9 13.6 + - - +
125C GLU* 1.3 92.7 - - - +
127C LEU* 1.3 56.3 + - - +
128C GLU 3.8 0.7 - - - -
129C ASP* 4.2 6.3 - - - +
130C LEU* 3.5 23.5 - - - +
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Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C VAL* 3.9 29.6 - - + +
20C LEU* 3.8 21.5 - - + -
21C LEU* 4.8 3.4 - - + -
123C SER 3.1 16.3 + - - +
124C ILE* 3.4 5.3 + - - +
125C GLU 3.4 1.4 - - - -
126C LYS* 1.3 77.8 - - - +
128C GLU* 1.3 59.1 + - - +
129C ASP 3.2 2.7 - - - -
130C LEU* 2.7 40.5 + - + -
131C ASP 3.2 16.0 + - - +
134C SER* 4.1 6.7 - - - -
135C GLN* 3.9 32.3 - - + +
138C LEU* 3.8 26.0 - - + -
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Residues in contact with GLU 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ILE 4.9 1.3 - - - +
125C GLU* 4.8 6.8 + - - +
126C LYS 3.8 1.2 - - - -
127C LEU* 1.3 76.0 - - - +
129C ASP* 1.3 71.2 + - - +
130C LEU 3.3 0.9 + - - +
132C LEU* 3.1 36.1 - - + +
135C GLN* 3.1 30.8 + - - +
128E GLU* 5.9 2.9 - - - +
132E LEU* 4.1 18.3 - - - +
128J GLU* 3.2 22.6 - - - +
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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