Contacts of the helix formed by residues 103 - 128 (chain H) in PDB entry 3V3K
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 THR 103 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H LEU* 4.2 10.9 - - - +
101H GLY 5.8 1.3 - - - -
102H MET* 1.3 77.7 - - - +
104H ILE* 1.3 64.0 + - - +
105H GLU* 3.4 23.6 + - - +
106H ASP* 3.0 33.7 + - - +
107H ARG 3.5 4.2 + - - -
163J GLY 5.8 3.4 - - - +
166J ASP* 4.8 12.8 - - - +
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Residues in contact with ILE 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H PRO* 4.9 19.5 - - + +
98H LEU* 5.1 4.0 - - + -
103H THR* 1.3 71.6 - - - +
105H GLU* 1.3 59.8 + - + +
106H ASP 3.3 0.2 - - - -
107H ARG* 3.2 44.6 + - - +
108H ASP* 3.1 33.3 + - - +
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Residues in contact with GLU 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H THR* 3.2 13.7 + - - +
104H ILE* 1.3 78.3 - - + +
106H ASP* 1.3 57.2 + - - +
108H ASP* 4.0 7.3 - - - +
109H SER* 3.1 28.6 + - - -
112H ARG* 5.2 1.6 + - - -
166J ASP* 3.2 39.6 - - - +
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Residues in contact with ASP 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H VAL* 3.8 16.6 - - + +
101H GLY 5.2 0.2 - - - +
102H MET* 3.4 43.0 - - + +
103H THR* 3.0 37.9 + - - +
104H ILE 3.3 0.4 - - - -
105H GLU* 1.3 74.6 - - - +
107H ARG* 1.3 65.5 + - - +
109H SER* 2.7 20.3 + - - -
110H TYR* 3.5 5.2 + - - +
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Residues in contact with ARG 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H THR 3.2 26.3 + - - -
26H PRO* 3.4 21.4 + - - +
27H GLU 3.8 9.9 - - - +
28H SER* 3.9 1.3 + - - +
29H VAL* 3.3 29.7 - - - +
33H ASN* 4.4 12.9 - - - +
83H VAL* 4.2 1.7 - - - +
84H PHE* 3.9 29.3 - - + -
98H LEU* 4.4 7.6 - - + -
103H THR 3.5 6.0 + - - +
104H ILE* 3.2 37.0 + - - +
106H ASP* 1.3 77.6 - - - +
108H ASP* 1.3 87.7 + - - +
110H TYR* 3.2 7.1 + - - +
111H ILE* 3.2 31.2 + - + +
177H PRO* 4.8 1.3 - - + -
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Residues in contact with ASP 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H ASN* 5.3 0.7 + - - -
35H ASN* 4.1 30.0 + - + +
36H HIS* 2.9 33.6 + - + +
104H ILE* 3.1 23.4 + - - +
105H GLU* 4.1 7.0 - - - +
107H ARG* 1.3 103.9 + - - +
109H SER* 1.3 56.7 + - - +
111H ILE* 3.3 6.5 + - - +
112H ARG* 3.0 36.8 + - - +
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Residues in contact with SER 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H LYS* 3.2 23.2 + - - -
105H GLU 3.1 13.0 + - - -
106H ASP* 2.7 30.7 + - - -
108H ASP* 1.3 73.9 - - - +
110H TYR* 1.3 61.1 + - - +
112H ARG* 3.7 28.9 + - - +
113H ASP* 3.1 28.1 + - - +
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Residues in contact with TYR 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H LEU* 3.4 54.5 - - + +
79H LYS* 4.2 15.0 - - + +
80H ARG* 3.5 34.1 + - + -
83H VAL* 5.2 1.1 - - + -
84H PHE* 3.8 25.1 - + + -
106H ASP 4.0 7.4 - - - +
107H ARG 3.2 9.2 + - - +
109H SER* 1.3 80.7 + - - +
111H ILE* 1.3 61.4 + - + +
113H ASP* 3.1 6.9 + - - +
114H LEU* 2.8 48.4 + - + +
150H LEU* 5.0 2.9 - - - +
153H ASP* 2.7 30.8 + - - +
177H PRO* 4.3 10.5 - - + -
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Residues in contact with ILE 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H VAL* 3.8 9.0 - - + -
32H LEU* 4.3 3.8 - - + -
36H HIS* 3.1 46.9 - - + +
107H ARG* 3.2 27.9 + - + +
108H ASP* 3.3 9.2 + - - +
110H TYR* 1.3 82.1 - - + +
112H ARG* 1.3 56.2 + - - +
114H LEU* 3.4 7.9 - - + +
115H PHE* 2.7 33.1 + - + +
157H MET* 4.7 5.4 - - - -
176H VAL* 3.3 44.4 - - + +
177H PRO* 4.5 6.7 - - + -
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Residues in contact with ARG 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H ASN* 3.3 28.0 - - - +
36H HIS* 4.1 9.6 + - - +
37H PHE 3.6 16.3 + - - +
38H LEU* 4.0 6.8 - - - +
39H SER* 4.4 18.7 + - - +
41H GLU* 5.6 4.0 + - - -
42H LEU* 4.2 19.6 - - + +
105H GLU 5.2 1.2 + - - -
108H ASP* 3.0 19.4 + - - +
109H SER* 3.7 30.0 + - - +
111H ILE* 1.3 76.1 - - - +
113H ASP* 1.3 60.6 + - - +
115H PHE* 3.2 4.5 + - - +
116H PHE* 3.1 25.8 + - - +
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Residues in contact with ASP 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H LEU* 4.0 15.3 - - - +
72H PHE* 3.9 29.7 - - + -
76H LEU* 3.4 24.7 - - + +
79H LYS* 3.3 24.0 + - - +
109H SER 3.1 15.5 + - - +
110H TYR 3.1 5.4 + - - +
112H ARG* 1.3 79.1 + - - +
114H LEU* 1.3 61.9 + - - +
116H PHE* 3.4 7.1 + - - +
117H LEU* 3.4 24.3 + - - +
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Residues in contact with LEU 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H LEU* 4.5 3.7 - - + +
110H TYR* 2.8 37.8 + - + +
111H ILE* 3.4 13.9 - - + +
113H ASP* 1.3 75.3 - - - +
115H PHE* 1.3 62.8 + - - +
117H LEU* 3.5 7.5 + - + +
118H HIS* 3.3 20.3 + - - +
150H LEU* 4.1 19.5 - - + -
153H ASP* 3.7 30.5 - - + +
154H LEU* 4.1 9.5 - - + +
157H MET* 3.4 23.4 - - + +
176H VAL* 3.3 26.9 - - + +
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Residues in contact with PHE 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H LEU* 4.3 9.2 - - + -
36H HIS* 3.9 20.2 - - + +
37H PHE* 5.2 3.1 - + - -
38H LEU* 3.6 34.5 - - + -
111H ILE* 2.7 16.8 + - + +
112H ARG 3.2 9.6 + - - +
114H LEU* 1.3 71.6 - - - +
116H PHE* 1.3 57.9 + - - +
118H HIS* 3.3 3.7 + - - +
119H SER* 2.8 42.4 + - - -
157H MET* 3.4 31.8 - - + +
161H VAL* 4.2 15.5 - - + -
220K ARG* 3.5 45.8 - - - -
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Residues in contact with PHE 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H LEU* 3.8 8.4 - - + +
42H LEU* 3.4 39.7 - - + -
45H LYS* 4.1 12.1 - - + -
46H LEU* 3.6 26.4 - - + +
49H MET* 3.6 27.6 - - + -
69H LEU* 4.6 4.5 - - + -
72H PHE* 3.7 36.6 - + + -
112H ARG 3.1 11.8 + - - +
113H ASP* 3.5 13.0 - - - +
114H LEU 3.3 0.2 - - - -
115H PHE* 1.3 76.7 - - - +
117H LEU* 1.3 58.9 + - + +
119H SER* 3.3 5.7 + - - -
120H LEU* 3.0 55.7 + - + +
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Residues in contact with LEU 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H LEU* 4.1 12.1 - - + -
72H PHE* 4.2 12.3 - - + -
73H VAL* 3.8 26.7 - - + -
76H LEU* 4.2 19.1 - - + -
113H ASP 3.4 13.2 + - - +
114H LEU* 3.8 9.4 - - - +
115H PHE 3.4 0.4 - - - -
116H PHE* 1.3 79.8 - - + +
118H HIS* 1.3 62.0 + - - +
120H LEU* 4.0 1.3 - - + +
121H LYS* 3.2 24.6 + - - +
142H LEU* 3.4 33.7 - - + +
150H LEU* 4.0 28.3 - - + -
154H LEU* 4.0 14.0 - - + +
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Residues in contact with HIS 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H LEU 3.3 11.5 + - - +
115H PHE* 3.7 10.5 + - - +
116H PHE 3.3 0.4 - - - -
117H LEU* 1.3 78.3 - - - +
119H SER* 1.3 60.7 + - - +
121H LYS* 3.1 10.5 + - + +
122H VAL* 3.0 51.6 + - + +
154H LEU* 4.1 16.5 - - + +
157H MET* 3.9 18.4 - - + +
158H LYS* 3.7 41.3 - - + +
161H VAL* 4.0 28.9 - - + +
162H GLU* 4.3 8.4 + - + -
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Residues in contact with SER 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H LEU* 3.9 6.0 - - - +
46H LEU* 3.2 26.1 - - - +
115H PHE* 2.8 38.0 + - - -
116H PHE* 3.3 3.8 + - - -
118H HIS* 1.3 79.3 + - - +
120H LEU* 1.3 63.8 + - - +
122H VAL* 3.6 7.2 + - - +
123H LYS* 3.3 30.8 + - - +
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Residues in contact with LEU 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H LEU* 4.2 14.1 - - + +
49H MET* 3.8 30.3 - - + -
50H VAL* 5.3 6.4 - - + +
69H LEU* 4.1 14.8 - - + -
116H PHE* 3.0 49.8 + - + +
117H LEU* 4.0 4.0 - - - +
119H SER* 1.3 76.0 + - - +
121H LYS* 1.3 62.2 + - - +
123H LYS* 3.5 5.5 + - - +
124H ILE* 3.1 39.9 + - + +
138H VAL* 5.4 0.2 - - + -
142H LEU* 3.3 24.7 - - + -
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Residues in contact with LYS 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H LEU 3.2 18.3 + - - +
118H HIS* 3.1 11.5 + - + +
120H LEU* 1.3 75.4 - - - +
122H VAL* 1.3 59.6 + - - +
124H ILE* 3.5 3.1 + - - +
125H GLU* 3.0 47.2 + - - +
139H TYR* 4.0 11.2 - - + -
142H LEU* 2.8 48.7 + - + +
143H CYS* 3.5 27.6 - - - +
144H PRO* 4.9 1.4 - - - +
154H LEU* 5.3 8.9 - - + +
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Residues in contact with VAL 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H HIS* 3.0 46.1 + - + +
119H SER* 3.8 9.0 - - - +
120H LEU 3.3 0.2 - - - -
121H LYS* 1.3 78.3 - - + +
123H LYS* 1.3 59.6 + - + +
125H GLU* 3.4 12.8 + - - +
126H GLU* 3.1 38.7 + - + +
162H GLU* 4.4 12.8 - - - +
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Residues in contact with LYS 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H GLN* 4.7 5.9 - - - +
46H LEU* 3.4 25.2 - - + +
47H ASP* 3.7 14.6 + - - -
50H VAL* 3.5 40.9 - - + +
119H SER* 3.3 16.4 + - - +
120H LEU 3.9 4.0 - - - +
121H LYS 3.4 0.2 - - - -
122H VAL* 1.3 76.3 - - + +
124H ILE* 1.3 65.5 + - - +
126H GLU* 3.4 20.5 + - - +
127H SER* 3.3 23.6 + - - -
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Residues in contact with ILE 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H VAL* 6.2 3.8 - - + -
53H TYR* 3.8 42.4 - - + +
120H LEU* 3.1 40.9 + - + +
121H LYS* 3.9 4.9 - - - +
122H VAL 3.4 0.2 - - - -
123H LYS* 1.3 72.6 - - + +
125H GLU* 1.3 59.1 + - - +
127H SER* 3.2 7.8 + - - +
128H ARG* 3.0 30.6 + - - +
138H VAL* 4.2 20.0 - - + -
139H TYR* 3.6 28.0 - - + -
142H LEU* 4.1 9.2 - - + -
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Residues in contact with GLU 125 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H LYS* 3.0 36.4 + - - +
122H VAL* 3.6 10.4 - - - +
123H LYS 3.4 0.2 - - - -
124H ILE* 1.3 75.0 - - - +
126H GLU* 1.3 57.4 + - - +
128H ARG* 2.9 25.8 - - - +
129H GLN* 4.0 5.2 + - - +
139H TYR* 2.7 36.5 + - + +
158H LYS* 5.9 0.7 + - - -
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Residues in contact with GLU 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H VAL* 3.1 25.4 + - + +
123H LYS* 3.6 25.1 - - - +
124H ILE 3.2 0.4 - - - -
125H GLU* 1.3 75.5 - - - +
127H SER* 1.3 62.2 + - - +
129H GLN* 3.4 28.8 + - - +
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Residues in contact with SER 127 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H VAL* 5.5 3.3 + - - +
53H TYR* 4.5 16.8 - - - -
54H SER* 4.3 20.4 - - - -
123H LYS 3.3 12.7 + - - -
124H ILE* 3.2 11.4 + - - -
126H GLU* 1.3 79.4 - - - +
128H ARG* 1.3 58.4 + - - +
129H GLN* 3.1 9.9 + - - +
130H GLY 5.0 0.2 + - - -
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Residues in contact with ARG 128 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H TYR* 3.5 26.5 - - + +
124H ILE* 3.0 22.4 + - - +
125H GLU* 2.9 20.1 - - - +
127H SER* 1.3 72.9 - - - +
129H GLN* 1.3 59.5 + - - +
131H LYS 4.2 17.1 + - - +
132H GLU* 2.7 34.6 + - - +
134H SER* 4.0 18.3 - - - +
135H LYS* 4.3 4.9 - - - +
136H CYS* 3.5 17.6 - - - +
139H TYR* 3.2 46.9 - - - +
140H ASN* 5.1 0.8 + - - -
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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