Contacts of the helix formed by residues 79 - 107 (chain B) in PDB entry 1YWT
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 PRO 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLU* 1.3 95.4 + - + +
81B VAL* 3.5 7.7 - - - -
82B ARG* 3.7 10.8 + - + +
83B GLU* 3.1 36.1 + - - +
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Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ALA 5.0 0.5 - - - -
5A SER* 3.0 47.8 + - - +
8A GLN* 4.3 19.3 - - + +
9A LYS* 3.9 26.3 - - + +
12A LEU* 4.1 9.0 - - + -
79B PRO* 1.3 101.3 - - + +
81B VAL* 1.3 68.2 + - - +
83B GLU* 3.4 4.7 + - - +
84B TYR* 2.9 27.0 + - - +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLN* 5.2 3.8 - - - +
12A LEU* 3.7 22.2 - - + -
62B LEU* 3.8 16.3 - - + +
65B ILE* 4.0 19.1 - - + +
66B GLU* 3.7 39.7 - - + +
79B PRO 3.5 5.6 - - - -
80B GLU* 1.3 78.6 - - + +
82B ARG* 1.3 60.0 + - - +
84B TYR* 3.7 1.4 - - - +
85B ARG* 2.8 31.3 + - + +
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Residues in contact with ARG 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLU* 3.2 28.2 + - - +
79B PRO* 3.7 10.4 + - + +
80B GLU 3.3 0.4 - - - -
81B VAL* 1.3 79.7 - - - +
83B GLU* 1.3 67.4 + - - +
85B ARG* 3.1 18.1 + - - +
86B GLU* 2.9 51.0 + - - +
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.0 3.1 - - - +
5A SER* 6.1 0.2 - - - -
9A LYS* 3.0 33.5 + - - +
79B PRO* 3.1 22.7 + - - +
80B GLU* 3.4 6.6 + - - +
82B ARG* 1.3 79.2 - - + +
84B TYR* 1.3 61.4 + - - +
86B GLU* 3.6 14.3 + - - +
87B LYS* 3.2 19.6 + - - +
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Residues in contact with TYR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS* 4.6 14.5 - - + +
12A LEU* 4.2 10.1 - - + -
13A ALA* 3.7 24.4 - - + +
16A ALA* 4.6 1.8 - - + -
18A ARG* 3.4 17.2 + - - +
21A ASP* 2.6 41.7 + - + +
25A PHE* 3.8 25.1 - + - -
62B LEU* 3.6 33.9 - - + -
80B GLU 2.9 18.3 + - - +
81B VAL* 3.9 3.8 - - - +
83B GLU* 1.3 76.1 - - - +
85B ARG* 1.3 66.4 + - - +
87B LYS* 3.1 25.3 + - + -
88B VAL* 3.1 23.3 + - + +
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Residues in contact with ARG 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TRP* 3.9 21.5 - - + +
62B LEU* 4.1 24.1 - - + +
63B SER* 4.1 23.3 - - - +
66B GLU* 2.5 30.2 + - - +
81B VAL 2.8 21.8 + - - +
82B ARG* 3.1 25.0 + - - +
84B TYR* 1.3 72.5 - - - +
86B GLU* 1.3 76.5 + - - +
88B VAL* 3.3 3.7 + - - +
89B GLU* 2.8 61.8 + - - +
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Residues in contact with GLU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ARG* 2.9 49.8 + - - +
83B GLU* 3.7 13.8 - - - +
85B ARG* 1.3 99.6 + - - +
87B LYS* 1.3 57.0 + - - +
89B GLU* 3.4 9.5 - - - +
90B THR* 2.9 36.7 + - - +
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Residues in contact with LYS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 4.3 0.2 - - - +
21A ASP* 3.2 31.3 + - - -
25A PHE* 5.1 8.3 - - + -
83B GLU 3.2 11.0 + - - +
84B TYR* 3.1 29.0 + - + +
86B GLU* 1.3 78.8 - - - +
88B VAL* 1.3 62.7 + - + +
90B THR* 3.3 6.9 + - - -
91B GLU* 3.0 37.8 + - + +
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 3.8 31.0 - - - +
55B GLN* 3.7 30.0 - - + +
58B ALA* 4.0 5.4 - - + -
59B TRP* 4.0 17.5 - - + +
62B LEU* 3.7 18.6 - - + -
84B TYR* 3.1 23.0 + - + +
85B ARG 3.6 7.0 - - - +
87B LYS* 1.3 76.8 - - + +
89B GLU* 1.3 59.1 + - - +
91B GLU* 3.2 8.6 + - - +
92B LEU* 2.9 27.9 + - + +
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Residues in contact with GLU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TRP* 2.8 34.0 + - - +
85B ARG* 2.8 44.2 + - - +
86B GLU* 3.4 9.3 - - - +
88B VAL* 1.3 77.8 - - - +
90B THR* 1.3 58.2 + - - +
92B LEU* 3.2 6.0 + - - +
93B GLN* 2.9 43.5 + - - +
134B VAL* 3.6 35.1 - - + +
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Residues in contact with THR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLU* 2.9 21.8 + - - +
87B LYS* 3.6 6.5 - - - -
89B GLU* 1.3 76.5 - - - +
91B GLU* 1.3 63.0 + - - +
93B GLN* 3.4 16.4 + - + +
94B GLY* 3.1 18.7 + - - -
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Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 2.7 39.2 + - - -
55B GLN* 2.8 37.6 + - + +
87B LYS* 3.0 24.8 + - + +
88B VAL* 3.4 8.1 - - - +
90B THR* 1.3 78.8 - - - +
92B LEU* 1.3 62.9 + - - +
94B GLY* 3.3 9.5 + - - -
95B VAL* 3.4 11.5 + - + +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 4.3 5.6 - - + +
55B GLN* 3.6 24.5 - - + +
56B ARG* 3.6 46.2 - - + +
59B TRP* 5.1 4.5 - - + -
88B VAL 2.9 17.2 + - - +
89B GLU* 3.2 7.4 + - - +
91B GLU* 1.3 76.4 - - - +
93B GLN* 1.3 73.4 + - + +
95B VAL* 3.3 4.5 + - - +
96B CYS* 3.1 37.1 + - - -
130B TYR* 4.5 14.8 - - + +
131B LEU* 4.7 2.7 - - + -
134B VAL* 4.7 18.4 - - + -
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Residues in contact with GLN 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLU* 2.9 33.5 + - - +
90B THR* 3.7 18.1 + - - +
91B GLU 3.3 0.2 - - - -
92B LEU* 1.3 74.7 - - + +
94B GLY* 1.3 65.1 + - - +
96B CYS* 3.9 0.5 - - - +
97B ASP* 2.9 37.3 + - - +
131B LEU* 3.8 27.5 + - + +
134B VAL* 3.6 27.3 + - + +
135B ALA* 5.5 4.0 - - - +
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Residues in contact with GLY 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B THR 3.1 13.3 + - - -
91B GLU* 3.3 5.8 + - - -
92B LEU 3.1 0.6 - - - -
93B GLN* 1.3 78.0 - - - +
95B VAL* 1.3 60.2 + - - +
97B ASP* 3.4 6.4 + - - +
98B THR* 2.8 27.8 + - - -
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TYR* 3.8 30.7 - - + -
51B VAL* 4.2 17.9 - - + -
52B VAL* 4.6 14.1 - - + -
55B GLN* 3.7 22.9 - - - +
91B GLU* 3.4 12.9 + - + +
92B LEU 3.3 7.5 + - - +
94B GLY* 1.3 72.9 - - - +
96B CYS* 1.3 60.9 + - - +
98B THR* 3.0 9.1 + - - -
99B VAL* 2.8 30.3 + - + +
127B TYR* 5.0 0.4 - - + -
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Residues in contact with CYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 4.2 7.4 - - - -
92B LEU* 3.1 36.5 + - - +
93B GLN 3.9 0.2 - - - +
95B VAL* 1.3 76.1 - - - +
97B ASP* 1.3 58.7 + - - +
99B VAL* 3.8 1.0 - - - +
100B LEU* 2.8 36.7 + - - +
127B TYR* 3.9 37.2 - - + +
130B TYR* 4.0 12.8 - - - -
131B LEU* 3.5 28.7 - - + -
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Residues in contact with ASP 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B GLN* 2.9 28.9 + - - +
94B GLY* 3.8 6.1 - - - +
96B CYS* 1.3 75.5 - - - +
98B THR* 1.3 59.1 + - - +
100B LEU* 3.9 7.6 - - - +
101B GLY* 2.9 25.5 + - - -
131B LEU* 4.1 17.1 - - - +
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Residues in contact with THR 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 4.4 24.0 - - + +
48B TYR* 3.9 22.2 - - + +
94B GLY 2.8 19.5 + - - -
95B VAL* 3.0 12.5 + - - -
97B ASP* 1.3 75.1 - - - +
99B VAL* 1.3 65.8 + - - +
101B GLY* 3.3 1.6 + - - -
102B LEU* 3.0 26.8 + - + +
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TYR* 3.3 42.4 - - + -
95B VAL* 2.8 21.2 + - + +
96B CYS 3.8 3.1 - - - +
98B THR* 1.3 71.8 - - - +
100B LEU* 1.3 58.7 + - - +
102B LEU* 3.2 11.6 + - + +
103B LEU* 3.0 40.4 + - + +
123B MET* 3.7 20.2 - - + -
127B TYR* 3.6 42.6 - - + -
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B CYS 2.8 21.2 + - - +
97B ASP* 3.9 8.1 - - - +
99B VAL* 1.3 78.3 - - - +
101B GLY* 1.3 57.1 + - - +
103B LEU* 3.3 6.8 + - + +
104B ASP* 2.9 32.1 + - - +
124B LYS* 3.8 27.4 - - + +
127B TYR* 4.0 14.1 - - + -
128B TYR* 3.6 47.3 - - + +
131B LEU* 3.6 29.2 - - + -
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Residues in contact with GLY 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ASP 2.9 18.2 + - - -
98B THR* 3.8 1.3 - - - -
100B LEU* 1.3 74.7 - - - +
102B LEU* 1.3 63.5 + - - +
104B ASP* 4.0 4.5 - - - +
105B SER* 2.8 33.1 + - - -
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 3.9 39.3 - - + -
30B VAL* 3.8 28.5 - - + -
31B GLU* 4.1 15.7 - - + +
44B LEU* 4.3 14.1 - - + -
48B TYR* 4.2 24.0 - - + +
98B THR* 3.0 17.8 + - + +
99B VAL* 3.3 8.5 - - + +
101B GLY* 1.3 77.3 - - - +
103B LEU* 1.3 60.6 + - + +
106B HIS* 3.1 35.5 + - + +
107B LEU* 3.4 10.1 + - + +
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 3.0 39.1 + - + +
100B LEU* 3.6 10.3 - - + +
102B LEU* 1.3 79.1 - - + +
104B ASP* 1.3 62.0 + - - +
107B LEU* 3.3 28.8 + - + -
108B ILE* 2.8 40.0 + - + +
120B TYR* 3.8 30.7 - - + +
123B MET* 4.0 15.3 - - + +
124B LYS* 3.8 33.0 - - + +
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Residues in contact with ASP 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU 2.9 18.3 + - - +
101B GLY* 4.1 5.6 - - - +
103B LEU* 1.3 78.8 - - - +
105B SER* 1.3 59.6 + - - +
106B HIS 3.7 0.4 - - - -
108B ILE* 4.0 11.2 - - - +
110B GLU* 5.7 1.7 - - - +
124B LYS* 2.5 35.6 + - - +
128B TYR* 6.2 0.4 - - - -
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Residues in contact with SER 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLY 2.8 21.2 + - - -
104B ASP* 1.3 79.5 - - - +
106B HIS* 1.3 82.3 + - - +
110B GLU* 3.4 13.0 - - - +
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Residues in contact with HIS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 3.7 29.7 + - + +
31B GLU* 3.9 21.5 - - + +
33B GLY* 5.1 7.5 - - - +
35B GLU* 5.7 3.8 - - - +
102B LEU* 3.1 27.0 + - + +
104B ASP 3.7 1.0 - - - -
105B SER* 1.3 106.7 + - - +
107B LEU* 1.3 62.9 + - - +
110B GLU* 3.1 27.7 + - - +
249B CA 2.0 31.3 - - - -
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 4.0 15.9 - - + -
35B GLU* 5.8 2.9 - - - -
36B LEU* 4.0 17.0 - - + +
44B LEU* 3.7 24.7 - - + -
102B LEU* 3.6 21.8 - - + +
103B LEU* 3.3 30.4 + - + +
106B HIS* 1.3 84.3 - - + +
108B ILE* 1.3 69.6 + - - +
109B LYS 3.2 1.2 + - - -
110B GLU* 3.0 13.9 + - - +
111B ALA* 4.3 2.9 + - - +
120B TYR* 3.6 49.2 - - + +
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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