Contacts of the helix formed by residues 13 - 40 (chain H) 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 LYS 13 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LYS* 1.3 93.9 - - + +
14H ALA* 1.3 66.3 + - - +
15H SER 3.7 0.2 - - - -
16H ASP* 3.2 13.2 + - + +
17H VAL* 3.2 28.4 + - + +
129H ASP 5.5 5.1 + - - -
130H LEU* 5.2 26.9 + - + +
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Residues in contact with ALA 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LYS* 3.3 12.1 - - + +
13H LYS* 1.3 72.1 - - - +
15H SER* 1.3 57.8 + - - +
16H ASP 2.7 4.5 + - - -
17H VAL* 2.7 30.1 + - - +
18H ALA* 3.1 12.3 + - - +
75H LEU* 4.7 14.8 - - + +
76H GLY 5.5 3.4 - - - +
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Residues in contact with SER 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LYS 4.6 3.7 + - - +
13H LYS 3.7 0.2 - - - -
14H ALA* 1.3 75.1 - - - +
16H ASP* 1.3 66.3 + - - +
17H VAL 3.5 0.2 - - - -
18H ALA* 4.4 11.0 - - - -
19H ASP* 3.1 21.1 - - - +
77H LYS* 5.6 6.0 - - - +
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Residues in contact with ASP 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LYS 3.8 19.9 - - - +
13H LYS* 3.3 14.9 - - + +
14H ALA 2.7 0.6 + - - -
15H SER* 1.3 87.5 - - - +
17H VAL* 1.3 62.8 + - + +
18H ALA 3.7 0.2 - - - -
19H ASP* 4.7 8.7 + - - +
20H LEU* 4.7 10.4 - - - +
127H LEU* 5.6 0.5 - - - +
130H LEU* 5.7 6.4 - - + +
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Residues in contact with VAL 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H LYS* 3.2 19.7 - - + +
14H ALA* 2.7 9.2 + - - +
16H ASP* 1.3 80.2 - - + +
18H ALA* 1.3 56.5 + - - +
19H ASP 3.3 2.0 - - - -
20H LEU* 2.9 26.4 + - - +
21H LEU* 3.4 24.5 + - + -
75H LEU* 5.6 3.6 - - + -
127H LEU* 4.3 21.5 - - + -
130H LEU* 4.4 25.6 - - + -
131H ASP* 4.3 24.2 - - + +
134H SER* 5.1 0.9 - - - +
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Residues in contact with ALA 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H ALA 3.1 11.9 + - - +
15H SER* 4.5 9.2 - - - -
16H ASP 3.7 0.2 - - - -
17H VAL* 1.3 72.8 - - - +
19H ASP* 1.3 55.3 + - - +
20H LEU 2.8 15.4 + - - -
21H LEU* 3.3 6.8 + - - +
22H GLN* 3.0 28.5 + - - +
72H ILE* 4.7 10.5 - - + +
77H LYS* 4.5 24.7 - - + -
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Residues in contact with ASP 19 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H SER 3.1 23.6 - - - +
16H ASP* 4.8 7.1 - - - +
17H VAL 3.3 0.6 - - - -
18H ALA* 1.3 75.6 - - - +
20H LEU* 1.3 66.4 + - + +
22H GLN* 4.5 4.7 - - - -
23H LYS* 3.3 41.4 + - - +
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Residues in contact with LEU 20 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ASP 4.7 9.2 - - - +
17H VAL 2.9 10.2 + - - +
18H ALA 2.8 3.2 + - - -
19H ASP* 1.3 92.8 - - + +
21H LEU* 1.3 57.8 + - - +
22H GLN 3.1 4.3 - - - -
23H LYS* 3.1 13.7 + - + +
24H GLN* 2.9 29.3 + - - +
123H SER* 4.8 18.4 + - - +
126H LYS* 4.3 31.0 - - + +
127H LEU* 3.5 42.0 - - + -
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Residues in contact with LEU 21 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H VAL* 3.4 21.0 + - + +
18H ALA* 3.3 5.2 + - - +
20H LEU* 1.3 76.9 - - - +
22H GLN* 1.3 55.7 + - - +
24H GLN* 3.7 6.7 - - + +
25H LEU* 2.9 28.1 + - - +
68H VAL* 3.8 14.2 - - + +
71H ARG* 3.6 28.9 - - + +
72H ILE* 3.5 21.7 - - + +
75H LEU* 4.6 4.3 - - + -
127H LEU* 4.6 12.3 - - + -
134H SER* 3.4 32.5 - - - +
138H LEU* 4.2 22.4 - - + -
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Residues in contact with GLN 22 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H ALA 3.0 17.9 + - - +
19H ASP* 4.6 5.8 - - - +
21H LEU* 1.3 74.0 - - - +
23H LYS* 1.3 58.7 + - + +
24H GLN 2.8 9.9 + - - -
25H LEU* 2.9 25.1 + - - +
26H SER* 2.9 25.3 + - - -
72H ILE* 3.8 5.0 - - + +
78H SER 4.0 3.8 - - - +
79H PRO* 3.7 12.5 - - - +
80H LYS* 3.1 49.6 + - - +
85H ALA* 5.3 2.2 + - - +
89H ASP* 4.0 14.8 - - + +
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Residues in contact with LYS 23 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ASP* 3.3 32.2 + - - +
20H LEU* 3.1 15.6 + - + +
22H GLN* 1.3 74.1 - - + +
24H GLN* 1.3 54.2 + - - +
26H SER* 4.6 1.6 - - - -
27H THR* 2.8 26.0 + - - -
89H ASP* 3.5 47.9 - - + +
91H THR* 5.0 11.0 - - + -
92H TRP* 4.9 3.5 - - - -
119H ASP* 6.0 0.7 - - - +
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Residues in contact with GLN 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H LEU 2.9 14.8 + - - +
21H LEU* 3.7 11.4 - - + +
22H GLN 2.8 0.6 - - - -
23H LYS* 1.3 82.0 + - - +
25H LEU* 1.3 62.4 + - - +
26H SER 3.4 0.7 - - - -
27H THR* 3.5 17.5 + - - +
28H TYR* 2.8 55.0 + - + +
68H VAL* 4.1 4.0 - - + -
119H ASP* 4.9 4.0 - - - +
120H THR* 3.4 24.0 + - - +
123H SER* 4.9 13.3 + - - -
138H LEU* 3.4 38.5 - - + +
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Residues in contact with LEU 25 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H LEU 2.9 17.9 + - - +
22H GLN* 3.5 21.8 - - - +
24H GLN* 1.3 78.1 - - - +
26H SER* 1.3 58.8 + - - +
28H TYR* 3.4 4.8 + - - +
29H ASN* 2.8 52.5 + - - +
65H ALA* 3.9 6.0 - - - +
68H VAL* 3.5 15.9 - - + +
69H ALA* 3.4 36.3 - - + -
79H PRO* 3.5 21.3 - - + -
80H LYS 3.7 17.7 - - - +
81H GLY* 4.2 1.6 - - - -
86H ILE* 6.4 0.2 - - + -
40J TRP* 4.2 8.7 - - + -
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Residues in contact with SER 26 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H GLN* 2.9 9.5 + - - -
23H LYS* 4.6 2.0 - - - -
25H LEU* 1.3 80.8 - - - +
27H THR* 1.3 57.5 + - - +
29H ASN* 3.8 7.6 - - - +
30H ASP* 2.7 34.7 + - - +
85H ALA 4.0 6.1 - - - -
86H ILE* 3.0 40.2 + - - +
89H ASP* 3.5 24.5 + - - -
92H TRP* 4.3 5.1 - - - -
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Residues in contact with THR 27 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H LYS 2.8 22.5 + - - -
24H GLN* 3.5 24.3 + - - +
26H SER* 1.3 78.5 - - - +
28H TYR* 1.3 68.3 + - + +
30H ASP* 3.7 1.7 - - - +
31H LEU* 2.8 28.9 + - - +
92H TRP* 3.1 28.0 - - + -
116H VAL* 3.7 40.1 - - + +
119H ASP* 4.4 5.4 + - + +
120H THR* 4.8 0.9 - - - +
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Residues in contact with TYR 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H GLN* 2.8 40.2 + - + +
25H LEU 3.4 6.1 + - - +
26H SER 3.3 0.2 - - - -
27H THR* 1.3 86.1 - - + +
29H ASN* 1.3 57.4 + - - +
31H LEU* 3.4 5.5 - - + +
32H HIS* 2.8 35.3 + - - +
61H VAL* 3.5 13.9 - - + +
64H TYR* 3.3 28.7 - + + -
65H ALA* 3.7 12.8 - - - +
68H VAL* 3.7 13.7 - - + -
116H VAL* 5.2 1.1 - - + -
120H THR* 4.6 0.6 - - - +
138H LEU* 4.0 5.9 - - - +
141H HIS* 2.4 50.9 + + - +
145H LEU* 3.6 27.4 - - + +
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Residues in contact with ASN 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H LEU* 2.8 26.2 + - - +
26H SER* 3.2 10.9 + - - +
28H TYR* 1.3 74.0 - - - +
30H ASP* 1.3 59.8 + - - +
32H HIS* 3.3 17.2 + - + +
33H LEU* 3.0 35.2 + - - +
65H ALA* 3.3 21.7 - - - +
81H GLY* 4.0 17.6 - - - -
86H ILE* 4.2 14.8 - - + +
33J LEU* 4.0 16.1 - - + +
40J TRP* 3.8 22.4 - - - -
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Residues in contact with ASP 30 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H SER* 2.7 19.4 + - - +
29H ASN* 1.3 73.1 - - - +
31H LEU* 1.3 62.6 + - - +
33H LEU* 4.4 0.8 - - - +
34H THR* 3.3 28.1 + - - -
86H ILE* 4.3 8.5 - - + +
90H ARG* 4.2 10.6 - - - -
92H TRP* 3.4 37.1 + - + -
93H ASP 5.5 0.7 - - - +
94H ASP* 4.5 4.0 - - - +
95H TYR* 5.6 3.3 + - - +
112H VAL* 6.0 1.9 - - - +
82J THR* 5.4 0.5 - - - +
83J PRO* 3.1 36.5 - - + +
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Residues in contact with LEU 31 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H THR 2.8 19.7 + - - +
28H TYR* 3.4 10.5 - - + +
29H ASN 3.1 0.2 - - - -
30H ASP* 1.3 77.3 - - - +
32H HIS* 1.3 64.8 + - - +
34H THR* 3.3 7.3 + - + -
35H LEU* 3.2 34.0 + - + +
61H VAL* 3.6 15.9 - - + -
112H VAL* 3.9 23.6 - - + -
113H TYR* 3.3 48.0 - - + +
116H VAL* 4.2 20.0 - - + -
145H LEU* 4.6 8.7 - - + -
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Residues in contact with HIS 32 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H TYR 2.8 21.3 + - - +
29H ASN* 3.3 29.2 + - - +
31H LEU* 1.3 71.8 - - - +
33H LEU* 1.3 96.0 + - + +
35H LEU* 3.0 29.6 + - + +
36H LYS* 3.3 8.2 + - - +
58H VAL* 4.2 17.1 - - + +
61H VAL* 3.5 16.2 - - + -
62H ARG* 4.1 35.1 + - + +
65H ALA* 5.1 3.4 - - + -
32J HIS* 4.5 15.9 - + - -
33J LEU* 4.3 13.7 - - + +
62J ARG* 4.9 6.4 + - - -
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Residues in contact with LEU 33 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H ASN 3.0 16.6 + - - +
30H ASP* 4.4 3.8 - - - +
32H HIS* 1.3 97.2 + - + +
34H THR* 1.3 58.6 + - - +
36H LYS* 3.8 8.4 + - + +
37H HIS 3.3 12.1 + - - -
40H TRP* 5.9 1.3 - - + -
86H ILE* 5.3 2.7 - - + -
29J ASN* 3.7 25.1 - - + +
32J HIS* 4.8 5.4 - - + +
33J LEU* 3.6 34.1 - - + -
81J GLY 3.3 39.3 - - - +
82J THR* 5.4 0.4 - - - -
83J PRO* 4.3 18.8 - - + -
86J ILE* 3.9 13.5 - - + -
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Residues in contact with THR 34 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H ASP* 3.3 24.5 + - - -
31H LEU* 3.3 6.4 + - - +
32H HIS 3.1 0.6 - - - -
33H LEU* 1.3 77.4 - - - +
35H LEU* 1.3 56.3 + - + +
37H HIS* 3.1 8.5 + - - +
38H VAL* 2.8 32.4 + - - +
95H TYR* 3.4 42.0 - - + +
109H LEU* 4.4 12.1 - - + -
112H VAL* 4.7 10.4 - - + +
82J THR* 3.4 21.5 - - - +
83J PRO* 4.9 0.2 - - - +
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Residues in contact with LEU 35 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H LEU* 3.2 43.0 + - + +
32H HIS* 3.0 18.1 + - + +
34H THR* 1.3 75.0 - - + +
36H LYS* 1.3 52.1 + - - +
38H VAL* 2.8 11.9 - - + +
39H HIS* 2.7 34.5 + - - +
54H ILE* 3.8 14.3 - - + +
57H GLN* 3.9 13.0 - - + -
58H VAL* 3.4 37.7 - - + +
61H VAL* 4.4 1.1 - - + -
109H LEU* 4.3 16.6 - - + -
113H TYR* 4.0 16.8 - - + +
148H PHE* 4.9 4.7 - - + -
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Residues in contact with LYS 36 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H HIS* 3.3 7.1 + - - +
33H LEU* 4.0 12.1 - - + +
35H LEU* 1.3 77.8 - - - +
37H HIS* 1.3 64.0 + - - +
39H HIS* 2.9 23.1 + - + +
40H TRP* 3.0 38.5 + - + +
55H ASP* 4.5 15.3 - - - -
58H VAL* 4.0 26.2 - - + -
62H ARG* 3.6 24.9 - - - +
62J ARG* 4.7 6.7 + - - +
66J ASP* 2.8 47.2 + - - +
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Residues in contact with HIS 37 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H LEU 3.3 12.4 + - - +
34H THR* 3.1 13.3 + - - +
36H LYS* 1.3 76.8 - - - +
38H VAL* 1.3 60.2 + - - +
40H TRP* 3.2 18.0 + - - +
41H ASN* 2.6 31.5 + - - +
95H TYR* 3.8 33.0 + + - -
96H SER 5.3 0.4 - - - -
97H VAL 3.4 20.3 + - - -
98H GLU* 4.8 6.8 + - - -
78J SER* 5.8 0.7 - - - -
79J PRO 3.3 21.1 + - - -
80J LYS* 3.4 11.2 - - + -
81J GLY* 2.7 34.9 + - - +
82J THR* 4.1 10.8 - - + -
----------------------------------------------------------
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Residues in contact with VAL 38 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H THR* 2.8 20.3 + - + +
35H LEU* 2.8 29.8 - - - +
37H HIS* 1.3 73.6 - - - +
39H HIS* 1.3 52.8 + - - +
41H ASN* 2.7 23.6 + - - -
42H VAL* 2.9 23.2 + - + +
50H VAL* 4.8 1.8 - - + -
54H ILE* 3.7 15.3 - - + -
95H TYR* 4.0 9.9 - - + +
105H HIS* 3.2 50.5 - - + +
109H LEU* 4.0 21.1 - - + -
----------------------------------------------------------
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Residues in contact with HIS 39 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H LEU 2.7 17.7 + - - +
36H LYS* 2.9 25.3 + - + +
38H VAL* 1.3 71.9 - - - +
40H TRP* 1.3 71.5 + + - +
41H ASN 3.3 0.6 + - - -
42H VAL* 3.8 5.8 - - - +
51H HIS* 3.1 62.8 + + - -
54H ILE* 4.0 20.9 - - + -
55H ASP* 3.4 35.9 + - - -
66J ASP* 5.7 2.5 - - - -
70J GLU* 6.6 0.2 - - - -
----------------------------------------------------------
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Residues in contact with TRP 40 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E TRP* 5.1 8.2 - - - -
33H LEU* 5.9 1.1 - - + -
36H LYS* 3.0 35.3 + - + +
37H HIS* 3.6 14.6 - - - +
38H VAL 3.0 1.0 + - - -
39H HIS* 1.3 91.7 + + - +
41H ASN* 1.3 65.1 + - - +
42H VAL 4.0 0.4 - - - -
43H VAL* 5.5 0.5 - - - +
51H HIS* 5.8 0.2 - - - -
99H ARG* 5.6 0.7 - - - +
25J LEU* 3.8 38.1 - - + -
29J ASN* 4.5 9.6 - - - -
65J ALA* 4.6 2.0 - - + -
66J ASP* 3.0 49.6 + - - +
69J ALA* 3.5 21.8 - - + -
70J GLU* 5.0 9.9 - - + +
73J ALA* 4.0 19.6 - - + +
79J PRO* 3.8 24.9 - - + -
81J GLY* 4.1 15.7 - - - -
----------------------------------------------------------
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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).
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