Contacts of the helix formed by residues 107 - 130 (chain H) in PDB entry 6BAA
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 TYR 107 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88H GLU 5.6 0.2 - - - -
89H ILE* 3.5 20.6 - - + +
92H GLY* 3.7 31.0 - - - -
93H ILE* 3.7 25.6 - - + +
96H ASP* 3.2 29.0 + - + -
102H ARG* 5.2 6.2 + - - +
103H HIS 3.3 26.2 - - - -
104H LEU* 4.1 15.8 - - - +
106H LEU* 1.3 81.0 - - + +
108H MET* 1.3 88.7 + - + +
109H PRO* 2.9 7.2 - - - -
110H ALA* 3.4 8.2 + - - +
111H GLY 3.3 14.2 + - - -
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Residues in contact with MET 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104H LEU* 3.0 35.3 + - + +
105H HIS* 5.2 0.4 - - - -
107H TYR* 1.3 98.2 - - + +
109H PRO* 1.3 69.2 - - + +
111H GLY* 3.1 5.7 + - - +
112H MET* 2.9 45.7 + - + +
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Residues in contact with PRO 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H ASP* 4.1 26.2 - - + +
32H ASN* 4.9 9.2 - - + -
33H VAL* 4.4 13.0 - - + +
36H HIS* 3.7 12.9 + - - -
105H HIS* 3.2 27.6 - - + +
106H LEU 4.2 1.3 - - - -
107H TYR* 2.9 15.5 - - - +
108H MET* 1.3 95.3 - - + +
110H ALA* 1.3 62.5 + - - +
112H MET* 3.2 11.7 + - + +
113H ALA 3.1 16.1 + - - -
153H LYS* 5.8 5.8 - - - +
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Residues in contact with ALA 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H LEU* 4.2 11.4 - - + +
88H GLU* 4.7 13.5 - - + +
89H ILE* 3.8 23.9 - - + +
106H LEU 5.9 0.2 - - - +
107H TYR* 3.6 11.7 - - - +
108H MET 3.2 0.4 - - - -
109H PRO* 1.3 81.3 - - - +
111H GLY* 1.3 62.2 + - - +
113H ALA* 2.9 19.7 + - - +
114H PHE* 3.1 12.6 + - - +
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Residues in contact with GLY 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H ILE* 3.4 17.4 - - - +
107H TYR 3.3 5.8 + - - -
108H MET* 3.1 10.9 + - - -
110H ALA* 1.3 78.6 - - - +
112H MET* 1.3 62.7 + - - +
114H PHE* 3.1 10.3 + - - +
115H MET* 3.1 25.9 + - - +
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Residues in contact with MET 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D MET* 5.6 1.8 - - - -
33H VAL* 4.1 16.6 - - + +
36H HIS* 3.7 15.2 - - + +
37H VAL* 3.7 27.8 - - + -
40H LEU* 5.1 8.4 - - + +
108H MET* 2.9 51.8 + - + +
109H PRO* 3.7 12.1 - - + +
110H ALA 3.2 0.4 - - - -
111H GLY* 1.3 76.3 - - - +
113H ALA* 1.3 52.1 + - - +
115H MET* 3.3 9.8 + - + +
116H ALA* 2.7 35.0 + - - +
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Residues in contact with ALA 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H HIS* 3.2 37.0 - - + +
85H LEU* 3.4 19.6 - - + +
109H PRO 3.1 6.6 + - - +
110H ALA* 2.9 14.6 + - - +
112H MET* 1.3 76.3 - - - +
114H PHE* 1.3 52.7 + - - +
116H ALA* 3.4 1.7 - - - +
117H ALA* 2.6 37.6 + - - +
142H TYR* 5.4 0.3 + - - -
175H LEU* 6.1 0.9 - - + -
179H TYR* 4.5 6.2 + - - +
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Residues in contact with PHE 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82H LEU* 3.9 35.9 - - + -
85H LEU* 3.4 16.5 - - + +
86H VAL* 4.5 22.7 - - + -
89H ILE* 5.6 4.5 - - + -
110H ALA 3.1 10.1 + - - +
111H GLY* 3.4 11.9 - - - +
113H ALA* 1.3 77.6 - - - +
115H MET* 1.3 83.3 + - - +
117H ALA* 3.3 4.2 + - - +
118H ILE* 3.2 40.6 + - + +
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Residues in contact with MET 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H LEU* 4.5 14.6 - - + -
111H GLY 3.1 14.5 + - - +
112H MET* 3.6 11.4 - - + +
114H PHE* 1.3 97.0 - - + +
116H ALA* 1.3 63.8 + - - +
118H ILE* 3.4 13.5 + - + +
119H THR* 3.2 29.2 + - + +
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Residues in contact with ALA 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H HIS* 3.5 26.5 - - + -
39H LEU* 4.0 3.8 - - + +
40H LEU* 3.4 14.3 - - + +
112H MET 2.7 21.4 + - - +
113H ALA* 3.1 5.1 + - - +
115H MET* 1.3 72.0 - - - +
117H ALA* 1.3 53.4 + - - +
119H THR* 2.6 22.7 + - - -
120H SER* 2.6 25.8 + - - -
142H TYR* 4.0 12.8 - - - +
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Residues in contact with ALA 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H THR* 5.4 2.3 - - + +
81H LEU* 3.7 18.6 - - + -
82H LEU* 3.4 29.3 - - + +
85H LEU* 4.7 0.7 - - + -
113H ALA 2.6 21.8 + - - +
114H PHE* 3.6 4.7 - - - +
115H MET 3.3 0.2 - - - -
116H ALA* 1.3 73.6 - - - +
118H ILE* 1.3 63.4 + - - +
120H SER* 2.5 25.0 + - - +
121H VAL* 3.1 12.6 + - - +
142H TYR* 5.5 1.1 - - - -
143H TRP* 5.5 2.9 - - + -
179H TYR* 5.6 2.2 - - - +
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Residues in contact with ILE 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H LEU* 4.0 21.3 - - + -
114H PHE* 3.2 40.8 + - + +
115H MET* 3.4 15.0 + - + +
116H ALA 3.3 0.2 - - - -
117H ALA* 1.3 76.7 - - - +
119H THR* 1.3 59.3 + - + +
121H VAL* 3.2 11.5 - - + +
122H VAL* 2.9 39.6 + - + +
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Residues in contact with THR 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H LEU* 4.2 10.6 - - - +
40H LEU* 3.4 24.4 - - + +
43H THR* 5.0 1.1 - - - -
44H PHE* 5.4 10.1 - - + -
47H LEU* 4.9 17.3 - - + +
115H MET* 3.2 14.1 + - + +
116H ALA* 2.6 29.5 + - - -
118H ILE* 1.3 73.9 - - + +
120H SER* 1.3 55.3 + - - +
121H VAL 2.9 5.2 + - - -
122H VAL* 3.1 5.1 + - - +
123H TYR* 2.9 35.4 + - - +
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Residues in contact with SER 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H LEU* 3.6 22.7 - - - -
78H THR* 5.2 3.3 - - - +
116H ALA 2.6 17.6 + - - -
117H ALA* 2.5 26.7 + - - +
119H THR* 1.3 72.0 + - - +
121H VAL* 1.3 58.7 + - - +
123H TYR* 4.4 7.1 - - - +
124H TYR* 3.9 15.0 + - - +
139H LEU* 4.2 12.5 - - - +
142H TYR* 4.7 0.2 - - - -
143H TRP* 3.6 32.3 - - - -
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Residues in contact with VAL 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H ARG* 5.5 2.9 - - + -
75H TRP* 3.6 35.0 - - + -
78H THR* 3.8 31.0 - - + +
82H LEU* 6.1 2.2 - - + -
117H ALA 3.1 13.5 + - - +
118H ILE* 3.2 21.8 - - + +
119H THR 3.0 0.6 - - - -
120H SER* 1.3 79.8 - - - +
122H VAL* 1.3 64.5 + - + +
123H TYR 3.3 1.1 - - - -
124H TYR* 3.3 12.5 + - + +
125H HIS* 2.9 25.5 + - - +
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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
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47H LEU* 4.9 9.0 - - + -
118H ILE* 2.9 33.1 + - + +
119H THR* 4.1 4.9 - - - +
121H VAL* 1.3 77.7 - - + +
123H TYR* 1.3 61.8 + - - +
125H HIS* 3.0 11.0 + - + +
126H ASN* 2.9 44.9 + - - +
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Residues in contact with TYR 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H LEU* 5.6 1.6 - - + -
43H THR* 3.7 37.5 - - + +
46H ILE* 4.7 14.0 - - + +
47H LEU* 3.8 26.3 - - + +
119H THR 2.9 18.3 + - - +
120H SER* 4.5 4.5 - - - -
122H VAL* 1.3 77.2 - - - +
124H TYR* 1.3 54.1 + - - +
126H ASN* 3.2 3.0 + - + +
127H ILE* 3.0 28.7 + - + +
135H LEU* 2.3 58.2 + - + +
136H LEU* 4.7 2.2 - - + -
138H ALA* 4.2 9.7 - - + +
139H LEU* 3.7 40.2 - - + -
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Residues in contact with TYR 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68H PHE* 3.3 33.2 - + + +
69H PRO 5.2 0.2 + - - -
70H GLY 4.7 1.9 + - - -
71H HIS* 3.3 28.1 - - + +
74H ARG* 3.3 51.0 + - + +
75H TRP* 4.6 14.4 - + - -
120H SER 3.9 13.5 + - - +
121H VAL* 3.3 14.8 + - + +
122H VAL 3.2 0.6 - - - -
123H TYR* 1.3 78.5 - - - +
125H HIS* 1.3 60.5 + - - +
127H ILE* 3.2 13.4 - - + +
128H GLU* 2.9 50.8 + - - +
136H LEU* 5.7 8.1 - - + -
139H LEU* 4.5 10.3 - - + -
189H VAL* 5.6 2.9 - - + +
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Residues in contact with HIS 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54H GLN* 6.3 1.1 - - - -
65H TRP* 4.1 19.0 - + - -
75H TRP* 4.0 15.0 - + + -
121H VAL 2.9 14.2 + - - +
122H VAL* 3.0 15.3 + - + +
124H TYR* 1.3 77.1 - - - +
126H ASN* 1.3 60.1 + - - +
128H GLU* 3.4 9.3 + - + +
129H THR* 2.4 51.2 + - + -
223H ASN* 3.1 44.2 + - + +
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Residues in contact with ASN 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LEU* 5.9 2.9 - - - +
47H LEU* 3.9 15.6 - - + +
50H GLY* 5.8 7.6 - - - -
54H GLN* 4.0 21.0 - - - +
122H VAL* 2.9 36.3 + - - +
123H TYR* 3.8 5.8 - - + +
124H TYR 3.2 0.2 - - - -
125H HIS* 1.3 82.6 + - - +
127H ILE* 1.3 63.4 + - - +
128H GLU 3.2 0.2 - - - -
129H THR* 3.3 19.2 + - - +
130H SER* 3.3 13.7 + - - +
135H LEU* 5.9 0.4 - - - -
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Residues in contact with ILE 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68H PHE* 3.2 27.2 - - + -
123H TYR* 3.0 19.6 + - + +
124H TYR* 3.2 28.3 - - + +
126H ASN* 1.3 77.7 - - - +
128H GLU* 1.3 59.9 + - - +
130H SER 2.8 23.2 - - - +
131H ASN* 3.8 0.5 - - - -
132H PHE* 3.3 33.4 - - + +
135H LEU* 3.7 20.8 - - + +
136H LEU* 3.6 43.7 - - + +
139H LEU* 5.8 0.4 - - + -
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Residues in contact with GLU 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H TRP* 5.3 6.4 - - + -
66H LEU* 3.0 38.0 + - + +
67H HIS* 2.5 44.1 + - + +
68H PHE* 3.5 20.6 - - + +
71H HIS* 3.6 11.0 + - - -
75H TRP* 4.0 15.8 + - - -
124H TYR* 2.9 42.0 + - - +
125H HIS* 3.6 7.7 - - + +
126H ASN 3.2 0.2 - - - -
127H ILE* 1.3 76.5 - - - +
129H THR* 1.3 65.9 + - - +
130H SER 4.7 0.2 - - - -
131H ASN* 4.4 5.0 - - - +
223H ASN* 6.1 1.1 - - - -
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Residues in contact with THR 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D GLU* 4.4 3.1 - - - +
54H GLN* 5.3 8.5 - - - +
61H HIS* 5.6 10.5 - - + +
64H THR* 3.8 23.7 - - - +
65H TRP* 4.5 21.2 - - + -
66H LEU* 4.8 0.7 + - - +
125H HIS* 2.4 44.3 + - + -
126H ASN* 3.4 18.3 + - - +
127H ILE 3.2 0.4 - - - -
128H GLU* 1.3 80.3 - - - +
130H SER* 1.3 61.7 + - - +
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Residues in contact with SER 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D GLU* 2.7 42.6 + - - +
53D GLY* 4.0 13.0 + - - -
55D PHE* 5.2 5.0 - - - +
56D LEU* 5.8 10.4 - - - +
126H ASN 3.3 7.0 + - - +
127H ILE* 2.8 16.9 - - - +
129H THR* 1.3 81.5 - - - +
131H ASN* 1.3 64.5 + - - +
132H PHE* 3.2 6.3 + - - +
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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