Contacts of the helix formed by residues 101 - 128 (chain B) 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 THR 101 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 4.4 6.9 - - - +
44B GLY* 5.5 1.8 - - - -
45B PRO* 5.6 9.9 - - + -
100B ASP* 1.3 87.8 + - - +
102B VAL* 1.3 72.4 + - + +
103B GLN* 4.0 22.7 - - + +
104B ALA* 2.9 23.4 + - - +
105B HIS* 3.1 9.5 + - - -
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 3.8 12.6 - - + -
43B VAL 3.8 5.4 + - - +
44B GLY* 5.4 1.3 - - - -
45B PRO* 6.0 1.5 - - + +
46B ASN* 3.5 15.9 - - + +
47B PHE* 3.4 36.6 - - + +
50B VAL* 3.6 26.6 - - + +
100B ASP 3.7 2.2 + - - -
101B THR* 1.3 73.0 - - + +
103B GLN* 1.3 68.8 + - + +
105B HIS* 2.9 7.7 + - - +
106B LEU* 2.9 37.9 + - + +
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Residues in contact with GLN 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B THR* 3.1 16.2 - - + +
102B VAL* 1.3 82.2 - - + +
104B ALA* 1.3 54.8 + - - +
105B HIS 2.7 11.8 + - - -
106B LEU* 4.5 6.3 - - + +
107B ALA* 2.9 28.9 + - + +
155B HIS* 5.9 14.3 - - - -
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B VAL* 4.2 8.2 - - + +
100B ASP* 3.1 36.8 - - + +
101B THR* 2.9 19.6 + - - +
103B GLN* 1.3 79.0 - - - +
105B HIS* 1.3 55.7 + - - +
107B ALA* 4.6 3.3 - - - +
108B ALA* 3.5 20.0 + - - +
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Residues in contact with HIS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 4.0 13.3 - - + +
41B ASN* 2.9 29.3 + - + -
42B VAL* 3.5 25.6 - - + -
50B VAL* 6.1 2.0 - - + -
95B TYR* 2.7 29.6 + + - +
97B VAL* 3.4 13.9 - - + +
98B GLU 2.7 25.2 + - - -
100B ASP* 3.3 15.3 + - + +
101B THR 3.1 19.2 + - - -
102B VAL 2.9 6.5 + - - +
103B GLN 2.7 5.3 + - - -
104B ALA* 1.3 72.3 - - - +
106B LEU* 1.3 57.9 + - + +
107B ALA 3.1 1.1 - - - -
108B ALA* 2.8 2.8 + - - +
109B LEU* 2.5 38.6 + - + +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B VAL* 3.9 21.5 - - + -
53B MET* 4.0 26.2 - - + -
54B ILE* 6.1 0.4 - - + -
102B VAL* 2.9 40.1 + - + +
103B GLN* 4.0 4.7 - - - +
105B HIS* 1.3 72.3 - - + +
107B ALA* 1.3 54.8 + - - +
109B LEU* 3.5 13.9 - - + +
110B ASP* 2.6 37.6 + - - +
152B VAL* 3.5 25.1 - - + +
154B ALA* 4.8 9.9 - - + +
155B HIS 4.3 18.4 - - - +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B GLN* 2.9 17.9 + - + +
104B ALA* 4.6 4.0 - - - +
106B LEU* 1.3 77.7 - - - +
108B ALA* 1.3 60.9 + - - +
110B ASP* 3.4 9.5 - - - +
111B LEU* 3.4 26.8 + - + +
155B HIS 5.4 3.9 + - - +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B TYR* 3.6 11.4 - - + +
97B VAL* 3.6 26.2 - - + -
104B ALA 3.5 15.3 + - - +
105B HIS 2.8 12.7 + - - +
107B ALA* 1.3 73.0 - - - +
109B LEU* 1.3 59.6 + - - +
111B LEU* 3.0 28.9 + - - +
112B VAL* 3.1 13.2 + - - +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 5.7 0.2 - - + -
34B THR* 4.7 9.2 - - + -
35B LEU* 4.0 31.9 - - + -
38B VAL* 4.3 19.5 - - + -
54B ILE* 4.5 15.7 - - + -
95B TYR* 4.0 11.4 - - + +
105B HIS* 2.5 19.9 + - + +
106B LEU* 3.5 15.5 - - + +
108B ALA* 1.3 69.7 - - - +
110B ASP* 1.3 64.8 + - - +
112B VAL* 2.9 28.1 + - + +
113B TYR* 3.0 24.9 + - + -
148B PHE* 4.3 14.6 - - + -
152B VAL* 4.5 9.4 - - + -
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Residues in contact with ASP 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU 2.6 21.6 + - - +
107B ALA* 3.4 12.4 - - - +
109B LEU* 1.3 72.7 - - - +
111B LEU* 1.3 70.2 + - - +
113B TYR* 3.4 3.3 + - - +
114B ASN* 3.2 12.0 + - - -
149B GLN* 3.0 33.2 + - - +
152B VAL* 3.5 19.2 - - + +
153B ARG* 3.2 36.3 + - + +
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ALA* 3.5 17.3 - - + +
108B ALA* 3.0 16.4 + - - +
110B ASP* 1.3 86.8 - - - +
112B VAL* 1.3 61.9 + - - +
114B ASN* 3.4 25.1 - - + +
115B GLY* 3.7 3.8 + - - -
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.7 30.5 - - + -
34B THR* 5.1 7.2 - - + -
92B TRP* 6.2 4.3 - - + -
95B TYR* 4.2 29.4 - - + +
108B ALA 3.1 7.8 + - - +
109B LEU* 2.9 19.1 + - + +
111B LEU* 1.3 74.8 - - - +
113B TYR* 1.3 69.6 + - + +
114B ASN 3.2 0.7 + - - -
115B GLY* 3.2 12.5 + - - -
116B VAL* 3.4 16.0 + - + +
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Residues in contact with TYR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.4 34.5 - - + +
35B LEU* 3.6 7.7 - - + +
57B GLN* 2.4 44.7 + - - +
61B VAL* 3.8 0.2 - - - +
109B LEU* 3.0 25.3 + - + +
110B ASP* 3.8 8.1 - - - +
112B VAL* 1.3 80.5 - - + +
114B ASN* 1.3 63.0 + - - +
116B VAL* 3.2 9.2 + - + +
117B ILE* 2.8 33.5 + - + +
145B LEU* 3.7 36.8 - - + -
148B PHE* 3.4 23.6 - + - -
149B GLN* 3.7 22.4 - - + +
152B VAL* 5.5 1.3 - - + -
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Residues in contact with ASN 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASP* 3.2 18.2 + - - -
111B LEU* 3.4 21.2 - - + +
112B VAL 3.1 0.2 - - - -
113B TYR* 1.3 76.1 - - - +
115B GLY* 1.3 58.4 + - - +
116B VAL 2.9 1.2 + - - -
117B ILE* 3.3 3.0 + - - +
118B GLU* 2.9 33.7 + - - +
149B GLN* 3.1 30.5 + - - +
153B ARG* 3.7 15.5 + - - +
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Residues in contact with GLY 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TRP* 5.5 5.0 - - - -
111B LEU 3.7 4.2 + - - -
112B VAL 3.2 7.0 + - - -
114B ASN* 1.3 76.4 - - - +
116B VAL* 1.3 61.4 + - - +
118B GLU* 3.9 18.6 - - - -
119B ASP* 3.4 25.8 - - - +
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B THR* 3.7 32.7 - - + +
28B TYR* 5.3 2.7 - - + -
31B LEU* 4.4 16.2 - - + -
92B TRP* 6.2 4.0 - - + -
112B VAL* 3.4 25.8 - - + +
113B TYR* 3.2 12.5 + - + +
114B ASN 3.0 0.6 - - - -
115B GLY* 1.3 80.9 - - - +
117B ILE* 1.3 57.7 + - + +
118B GLU 3.1 0.9 - - - -
119B ASP* 3.2 3.7 + - - +
120B THR* 2.7 47.6 + - - +
145B LEU* 4.6 19.5 - - + -
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TYR* 2.8 22.2 - - + +
114B ASN* 3.8 2.9 - - - +
116B VAL* 1.3 74.7 - - + +
118B GLU* 1.3 53.5 + - - +
120B THR* 3.5 7.4 - - - -
121B ARG* 2.6 42.6 + - + +
142B ALA* 6.0 2.5 - - + -
145B LEU* 4.3 8.3 - - + +
146B GLU* 3.1 63.3 - - + +
149B GLN* 3.1 35.7 - - + +
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Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASN* 2.9 20.2 + - - +
115B GLY* 3.9 13.4 + - - -
117B ILE* 1.3 77.7 - - - +
119B ASP* 1.3 67.8 + - - +
121B ARG* 3.7 6.4 - - - +
122B LYS* 3.2 50.2 + - - +
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Residues in contact with ASP 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLN* 4.8 7.0 - - - +
27B THR* 5.0 7.0 + - + +
91B THR* 4.8 10.4 - - - +
92B TRP* 4.4 18.9 - - - -
115B GLY 3.4 16.8 - - - +
116B VAL* 3.2 8.2 + - - +
118B GLU* 1.3 89.1 - - - +
120B THR* 1.3 59.6 + - - +
122B LYS* 3.0 19.4 + - - +
123B SER* 2.8 33.0 + - - -
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Residues in contact with THR 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLN* 2.8 33.6 + - - +
27B THR* 5.3 0.3 - - - +
28B TYR* 4.8 2.5 - - - +
116B VAL* 2.7 36.1 + - - +
117B ILE* 3.5 8.5 - - - -
119B ASP* 1.3 71.7 - - - +
121B ARG* 1.3 61.2 + - - +
123B SER* 3.6 3.8 + - - -
124B ILE* 3.1 24.0 + - - +
138B LEU* 3.9 25.3 - - + +
142B ALA* 3.9 21.3 - - + +
145B LEU* 4.5 7.8 - - + +
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 2.6 23.7 + - + +
118B GLU* 3.7 6.7 - - - +
120B THR* 1.3 71.2 - - - +
122B LYS* 1.3 65.6 + - - +
124B ILE* 3.4 16.8 + - + +
125B GLU* 3.2 45.0 + - - +
142B ALA* 5.9 1.6 - - + -
146B GLU* 4.1 18.0 + - - +
13D LYS* 6.4 1.3 - - - -
71D ARG* 4.4 2.8 - - - +
130D LEU 4.8 3.8 + - - -
131D ASP* 2.6 46.7 + - - +
132D LEU* 3.2 27.5 - - - +
133D VAL* 3.4 23.8 - - + +
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Residues in contact with LYS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLU* 3.2 43.0 + - - +
119B ASP* 3.0 20.2 + - - +
121B ARG* 1.3 74.6 - - - +
123B SER* 1.3 52.3 + - - +
125B GLU* 3.1 15.4 + - - +
126B LYS* 2.7 45.6 + - + +
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 4.1 30.3 + - - +
24B GLN* 4.2 7.7 + - - -
119B ASP* 2.8 18.4 + - - +
120B THR* 3.9 7.6 - - - -
122B LYS* 1.3 72.5 - - - +
124B ILE* 1.3 64.0 + - - +
126B LYS* 3.4 11.6 + - - +
127B LEU* 3.1 28.0 + - - +
138B LEU* 4.1 19.7 - - - -
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B THR 3.1 17.1 + - - +
121B ARG* 3.7 17.7 - - - +
122B LYS 3.2 0.4 - - - -
123B SER* 1.3 74.4 - - - +
125B GLU* 1.3 55.2 + - - +
127B LEU* 2.7 19.7 + - - -
135B GLN* 2.6 38.5 + - - +
138B LEU* 3.5 35.7 - - + +
139B ILE* 3.8 18.8 - - + -
142B ALA* 3.7 18.4 - - + -
132D LEU* 3.5 31.4 - - + -
133D VAL* 4.4 10.1 - - + -
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ARG* 3.2 36.9 + - - +
122B LYS* 3.1 13.0 + - - +
124B ILE* 1.3 79.3 - - + +
126B LYS* 1.3 59.3 + - - +
127B LEU 3.0 5.4 + - - -
128B GLU* 3.3 18.1 + - - +
129B ASP* 4.8 1.2 + - - +
13D LYS* 5.2 12.3 + - - +
129D ASP* 5.5 6.7 - - - +
132D LEU* 5.3 4.9 - - + -
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Residues in contact with LYS 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 3.3 38.7 - - + +
23B LYS* 5.0 6.2 - - - +
122B LYS* 2.7 30.2 + - + +
123B SER* 3.4 9.6 - - - +
125B GLU* 1.3 72.3 - - - +
127B LEU* 1.3 58.9 + - - +
129B ASP* 4.7 3.3 + - - +
130B LEU* 3.2 28.2 + - + +
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 4.0 20.9 - - + -
20B LEU* 3.8 25.6 - - + -
21B LEU* 4.9 4.3 - - + -
123B SER 3.1 18.3 + - - +
124B ILE* 2.7 14.1 + - - +
126B LYS* 1.3 70.6 - - - +
128B GLU* 1.3 56.5 + - - +
129B ASP 2.8 12.6 + - - -
130B LEU* 2.9 33.7 + - + +
131B ASP* 3.2 25.9 + - + +
132B LEU* 4.3 1.2 + - - +
134B SER* 4.3 7.9 - - - -
135B GLN* 3.2 31.0 + - + +
138B LEU* 4.2 19.1 - - + -
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 4.8 9.9 - - - +
124B ILE 3.3 1.0 + - - +
125B GLU* 3.3 13.0 + - - +
127B LEU* 1.3 76.1 - - - +
129B ASP* 1.3 68.0 + - - +
132B LEU* 3.4 25.9 - - - +
135B GLN* 2.9 29.5 - - - +
128D GLU* 3.3 24.8 - - - +
129D ASP* 6.0 2.0 - - - +
132D LEU* 3.8 18.7 - - + +
----------------------------------------------------------
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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