Contacts of the helix formed by residues 102 - 128 (chain H) in PDB entry 1VEQ
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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H VAL* 3.8 18.2 - - + -
43H VAL 3.1 13.3 + - - +
44H GLY* 3.9 11.9 - - - -
45H PRO* 4.8 1.6 - - + -
46H ASN* 3.7 37.0 - - - +
47H PHE* 4.5 0.4 - - - +
50H VAL* 3.2 38.4 - - + -
101H THR* 1.3 75.7 - - - +
103H GLN* 1.3 72.8 + - + +
104H ALA 3.1 0.5 + - - -
105H HIS* 3.2 1.9 + - - +
106H LEU* 3.1 32.6 + - + +
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Residues in contact with GLN 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C PRO* 4.5 20.1 - - - +
46H ASN* 4.8 4.2 + - - +
101H THR* 3.5 11.0 - - - +
102H VAL* 1.3 90.3 - - + +
104H ALA* 1.3 65.3 + - - +
106H LEU* 3.4 4.1 + - - +
107H ALA* 2.9 26.4 + - - +
155H HIS* 4.0 21.2 + - - +
156H LEU* 4.0 19.3 - - + +
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Residues in contact with ALA 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H VAL* 4.8 6.5 - - + -
100H ASP* 3.5 28.7 - - + +
101H THR* 3.0 23.9 + - - +
102H VAL 3.1 0.2 + - - -
103H GLN* 1.3 78.2 - - - +
105H HIS* 1.3 65.4 + - - +
107H ALA* 3.2 5.4 + - - +
108H ALA* 3.0 20.8 + - - +
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Residues in contact with HIS 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H VAL* 3.9 20.5 - - + +
41H ASN* 3.2 23.7 + - + -
42H VAL* 3.6 22.7 - - + -
50H VAL* 6.5 0.4 - - + -
95H TYR* 2.6 39.6 + + - +
97H VAL* 3.0 30.3 - - + +
98H GLU 3.1 17.7 + - - -
100H ASP* 3.6 7.0 + - + -
101H THR 3.4 19.7 + - - -
102H VAL 3.2 5.2 + - - +
104H ALA* 1.3 79.0 - - - +
106H LEU* 1.3 56.2 + - + +
108H ALA* 2.8 3.0 + - - -
109H LEU* 2.5 37.3 + - + +
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Residues in contact with LEU 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H VAL* 6.5 0.9 - - + -
50H VAL* 3.9 11.4 - - + -
53H MET* 4.1 17.3 - - + -
54H ILE* 6.2 0.7 - - + -
102H VAL* 3.1 36.4 + - + +
103H GLN* 3.8 5.2 - - - +
105H HIS* 1.3 78.3 - - + +
107H ALA* 1.3 53.1 + - - +
109H LEU* 3.2 9.6 + - + -
110H ASP* 2.7 31.7 + - - +
152H VAL* 3.1 41.1 - - + +
155H HIS* 3.5 35.7 - - + -
156H LEU* 4.0 12.8 - - + -
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Residues in contact with ALA 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H GLN 2.9 18.7 + - - +
104H ALA* 3.5 4.5 - - - +
106H LEU* 1.3 74.0 - - - +
108H ALA* 1.3 65.2 + - - +
110H ASP* 2.9 21.3 - - - +
111H LEU* 3.0 13.5 - - + +
156H LEU* 3.8 20.6 - - + +
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Residues in contact with ALA 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H TYR* 3.6 23.1 - - + +
97H VAL* 4.1 12.8 - - + -
104H ALA 3.0 12.2 + - - +
105H HIS 2.8 6.4 + - - +
107H ALA* 1.3 75.7 - - - +
109H LEU* 1.3 61.8 + - - +
111H LEU* 3.3 20.0 + - - +
112H VAL* 3.1 18.1 + - - +
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Residues in contact with LEU 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H LEU* 5.6 0.2 - - + -
34H THR* 4.7 8.5 - - + -
35H LEU* 4.0 28.0 - - + -
38H VAL* 4.2 32.8 - - + -
54H ILE* 5.5 2.5 - - + -
95H TYR* 4.3 6.7 - - + -
105H HIS 2.5 19.5 + - - +
106H LEU* 3.5 14.4 - - + +
108H ALA* 1.3 69.6 - - - +
110H ASP* 1.3 70.6 + - - +
112H VAL* 3.0 28.4 + - + +
113H TYR* 3.0 27.4 + - + -
148H PHE* 4.3 17.0 - - + -
152H VAL* 4.3 10.5 - - + -
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Residues in contact with ASP 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H LEU 2.7 13.9 + - - +
107H ALA* 2.9 19.3 - - - +
109H LEU* 1.3 78.2 - - - +
111H LEU* 1.3 67.4 + - + +
113H TYR* 3.2 3.2 + - - +
114H ASN* 2.9 25.7 + - - +
149H GLN* 3.5 8.8 + - - +
152H VAL* 4.2 8.2 - - + +
153H ARG* 2.8 47.9 + - - +
156H LEU* 4.6 10.7 - - + +
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Residues in contact with LEU 111 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H ALA 3.0 20.6 - - - +
108H ALA* 3.3 11.9 + - - +
109H LEU 3.1 0.4 - - - -
110H ASP* 1.3 83.9 - - + +
112H VAL* 1.3 66.2 + - + +
114H ASN* 2.9 30.9 + - + +
115H GLY* 3.1 5.0 + - - -
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Residues in contact with VAL 112 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H ASP* 5.0 11.7 - - - +
31H LEU* 4.7 17.0 - - + -
34H THR* 5.3 8.1 - - + -
92H TRP* 5.7 6.1 - - + -
95H TYR* 4.3 14.8 - - + -
108H ALA 3.1 20.0 - - - +
109H LEU* 3.0 25.7 + - + +
111H LEU* 1.3 75.6 - - + +
113H TYR* 1.3 64.8 + - + +
115H GLY* 3.3 3.4 + - - -
116H VAL* 3.1 29.7 + - + +
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Residues in contact with TYR 113 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H LEU* 3.4 30.0 - - + +
35H LEU* 3.6 15.9 - - + +
57H GLN* 3.1 30.4 + - - +
109H LEU* 3.0 26.2 + - + +
110H ASP* 3.6 4.3 - - - +
112H VAL* 1.3 74.9 - - + +
114H ASN* 1.3 57.9 + - - +
116H VAL* 4.1 6.3 - - + -
117H ILE* 2.7 41.8 + - + +
145H LEU* 3.5 43.3 - - + -
148H PHE* 3.4 33.0 - + - -
149H GLN* 3.5 28.5 - - + +
152H VAL* 5.5 1.6 - - + -
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Residues in contact with ASN 114 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H ASP* 2.9 21.3 + - - +
111H LEU* 2.9 19.0 + - - +
113H TYR* 1.3 76.5 - - - +
115H GLY* 1.3 58.7 + - - +
117H ILE* 3.9 1.0 - - - +
118H GLU* 2.9 36.0 + - - +
149H GLN* 2.9 16.1 + - - +
153H ARG* 3.1 14.3 + - - +
7I PRO* 3.8 23.9 - - + +
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Residues in contact with GLY 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H TRP* 4.3 14.3 - - - -
111H LEU 3.1 7.3 + - - -
112H VAL* 3.3 4.7 + - - -
113H TYR 3.2 0.2 - - - -
114H ASN* 1.3 80.1 - - - +
116H VAL* 1.3 58.9 + - - +
118H GLU* 4.1 7.2 - - - -
119H ASP* 3.1 32.7 + - - +
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Residues in contact with VAL 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H THR* 4.0 30.7 - - + +
28H TYR* 4.7 11.2 - - + -
31H LEU* 4.6 31.2 - - + -
92H TRP* 4.7 7.2 - - + -
112H VAL* 3.1 22.2 - - + +
113H TYR* 3.0 11.1 + - + +
115H GLY* 1.3 79.3 - - - +
117H ILE* 1.3 60.0 + - + +
119H ASP* 3.8 2.2 + - - +
120H THR* 2.7 39.7 + - - +
145H LEU* 4.7 12.8 - - + -
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Residues in contact with ILE 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H TYR* 2.7 23.4 + - + +
114H ASN 4.0 2.0 - - - +
116H VAL* 1.3 71.7 - - + +
118H GLU* 1.3 58.4 + - - +
120H THR* 3.2 6.0 + - - -
121H ARG* 2.8 41.9 + - + +
142H ALA* 5.6 2.9 - - + -
145H LEU* 4.6 11.4 - - + -
146H GLU* 3.5 55.0 - - + +
149H GLN* 3.4 42.0 - - + +
6I ILE* 4.3 9.0 - - + -
7I PRO* 4.2 10.8 - - + +
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Residues in contact with GLU 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H ASN* 2.9 20.7 + - - +
115H GLY* 4.4 5.3 - - - +
117H ILE* 1.3 74.3 - - - +
119H ASP* 1.3 71.9 + - - +
120H THR 3.0 1.0 + - - -
121H ARG* 3.1 5.4 + - + +
122H LYS* 3.1 23.0 + - - +
7I PRO* 4.0 29.0 + - + +
8I GLY* 5.3 2.7 - - - +
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Residues in contact with ASP 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H LYS* 3.4 33.7 + - + -
24H GLN* 4.7 7.4 - - - +
27H THR* 5.2 9.5 + - + +
91H THR* 5.0 3.5 + - - -
92H TRP* 4.9 11.0 - - - -
115H GLY* 3.1 24.0 + - - +
116H VAL* 4.1 4.0 - - - +
118H GLU* 1.3 83.0 - - - +
120H THR* 1.3 61.1 + - - +
122H LYS* 3.8 6.1 + - - +
123H SER* 3.1 27.1 + - - -
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Residues in contact with THR 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H GLN* 2.6 25.5 + - - +
28H TYR* 4.7 2.3 + - - +
116H VAL* 2.7 27.0 + - - +
117H ILE* 3.3 7.6 - - - -
118H GLU 3.0 0.4 - - - -
119H ASP* 1.3 74.2 - - - +
121H ARG* 1.3 69.1 + - + +
123H SER* 2.8 17.1 + - - -
124H ILE* 2.8 28.6 + - + +
138H LEU* 3.7 28.3 - - + +
141H HIS* 5.8 0.2 - - + -
142H ALA* 4.4 14.1 - - + +
145H LEU* 5.7 4.5 - - + +
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Residues in contact with ARG 121 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H ILE* 2.8 28.9 + - + +
118H GLU* 3.5 6.3 - - + +
120H THR* 1.3 73.9 - - + +
122H LYS* 1.3 63.4 + - - +
124H ILE* 3.0 27.0 + - + +
125H GLU* 3.1 15.0 + - - +
142H ALA* 5.8 0.7 - - + -
146H GLU* 3.0 37.4 + - - +
6I ILE* 3.4 21.2 - - - +
7I PRO 4.2 11.4 + - - +
8I GLY* 5.1 9.3 + - - -
9I LEU* 4.2 19.7 - - - +
71I ARG* 3.9 5.1 - - - +
130I LEU 5.4 0.2 + - - -
131I ASP* 2.8 33.8 + - - +
132I LEU* 4.9 2.0 - - - +
133I VAL* 4.1 6.9 - - - +
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Residues in contact with LYS 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H GLU 3.1 12.2 + - - +
119H ASP* 3.9 6.7 - - - +
121H ARG* 1.3 78.8 - - - +
123H SER* 1.3 63.7 + - - +
124H ILE 3.1 0.3 + - - -
125H GLU* 3.3 6.7 + - - +
126H LYS* 3.0 37.8 + - - +
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Residues in contact with SER 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H LEU* 3.3 32.4 + - - +
23H LYS* 5.8 3.1 - - - +
24H GLN* 4.3 10.5 + - - -
119H ASP 3.1 12.6 + - - -
120H THR* 2.8 17.7 + - - -
122H LYS* 1.3 74.8 - - - +
124H ILE* 1.3 57.5 + - - +
126H LYS* 4.0 8.4 - - - +
127H LEU* 3.0 35.6 + - - +
138H LEU* 5.1 8.1 - - - -
----------------------------------------------------------
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Residues in contact with ILE 124 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120H THR* 2.8 35.0 + - + +
121H ARG* 3.0 17.5 + - - +
123H SER* 1.3 74.4 - - - +
125H GLU* 1.3 60.2 + - - +
126H LYS 3.1 0.7 - - - -
127H LEU* 2.7 34.4 + - - +
128H GLU 3.2 5.5 + - - -
135H GLN* 3.5 27.3 + - + +
138H LEU* 4.1 12.8 - - + +
139H ILE* 3.9 36.8 - - + +
142H ALA* 4.5 8.1 - - + -
132I LEU* 4.5 13.9 - - + -
133I VAL* 5.1 4.9 - - + -
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Residues in contact with GLU 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H ARG 3.1 7.8 + - - +
122H LYS* 3.8 8.7 - - - +
124H ILE* 1.3 80.8 - - - +
126H LYS* 1.3 61.6 + - - +
127H LEU 3.3 0.7 + - - -
128H GLU* 3.4 29.0 + - - +
129H ASP* 4.6 6.4 - - - +
135H GLN* 5.1 0.4 - - - +
132I LEU* 4.8 16.4 - - + +
----------------------------------------------------------
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Residues in contact with LYS 126 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H LEU* 4.5 25.6 - - + +
122H LYS* 3.0 28.7 + - - +
123H SER* 4.0 7.2 - - - +
125H GLU* 1.3 76.2 - - - +
127H LEU* 1.3 60.4 + - - +
129H ASP* 4.1 9.5 + - - +
130H LEU* 3.6 19.8 - - + +
----------------------------------------------------------
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Residues in contact with LEU 127 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H VAL* 4.0 26.2 - - + -
20H LEU* 4.1 10.8 - - + -
21H LEU* 5.0 7.2 - - + -
123H SER* 3.0 24.4 + - - +
124H ILE* 2.7 19.7 + - - +
126H LYS* 1.3 69.6 - - - +
128H GLU* 1.3 56.3 + - - -
129H ASP 2.8 12.4 + - - -
130H LEU* 2.8 35.4 + - + -
131H ASP 3.2 25.9 + - - +
134H SER* 3.2 28.7 - - - +
135H GLN* 4.2 9.2 - - + -
138H LEU* 4.5 11.9 - - + -
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Residues in contact with GLU 128 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G GLU* 4.2 13.7 - - - +
124H ILE 3.2 5.8 + - - +
125H GLU* 3.4 23.9 + - - +
127H LEU* 1.3 75.1 - - - +
129H ASP* 1.3 63.0 + - - +
130H LEU 5.2 0.2 - - - -
132H LEU* 4.5 23.3 - - + +
135H GLN* 3.3 29.3 + - - +
128I GLU* 4.1 17.6 - - - +
132I LEU* 4.8 14.9 - - - +
----------------------------------------------------------
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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