Contacts of the helix formed by residues 59 - 83 (chain B) in PDB entry 4K71
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 TRP 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ASN* 3.8 9.6 - - + +
418A MET* 3.5 27.6 - - + -
419A SER* 4.6 0.4 + - - -
422A THR* 3.0 29.3 + - + +
425A GLU* 4.3 5.1 + - - -
426A VAL* 5.3 3.3 - - + +
460A LEU* 3.9 14.6 - - + -
463A LEU* 3.4 40.6 - - + +
464A HIS* 3.9 29.2 - + + -
467A THR* 3.4 28.0 - - - +
57B VAL 3.5 0.6 + - - -
58B SER* 1.3 87.9 + - - +
60B TYR* 1.3 63.6 + - - +
61B TRP 3.4 2.2 - - - -
62B GLU* 3.4 29.7 + - + +
63B LYS* 2.9 44.2 + - - +
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Residues in contact with TYR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASN* 5.9 4.3 - - - -
35B TYR* 3.6 1.4 + - - -
56B GLN* 3.6 26.9 - - + +
57B VAL* 3.2 24.8 + - + +
58B SER 3.1 5.7 + - - -
59B TRP* 1.3 75.2 - - - +
61B TRP* 1.3 95.8 + + - +
63B LYS* 3.2 12.7 + - + +
64B GLU* 2.6 57.1 + - + +
162B ARG* 3.8 28.5 + - + +
165B GLU* 5.7 5.6 - - + -
166B HIS* 2.5 37.4 + + - -
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Residues in contact with TRP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A SER* 3.6 28.9 + - - -
421A PRO* 4.9 8.1 - - + -
35B TYR* 3.6 31.2 - + - -
36B LEU* 3.7 22.9 - - + -
45B ALA* 3.5 28.8 - - + +
46B GLU 3.4 15.0 - - - -
47B PRO* 3.4 45.8 - - + +
51B TRP* 5.3 6.4 + - + -
54B GLU* 5.1 2.9 + - - -
56B GLN* 4.1 17.4 - - + +
57B VAL 4.9 0.2 + - - -
59B TRP 3.4 0.2 - - - -
60B TYR* 1.3 99.7 - + - +
62B GLU* 1.3 59.3 + - - +
64B GLU* 3.2 10.2 + - + +
65B THR* 2.9 30.7 + - - -
166B HIS* 5.2 3.6 - + - -
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A GLN 5.3 0.7 - - - +
418A MET* 3.5 7.3 - - - +
419A SER* 2.7 40.2 + - - +
422A THR* 2.8 30.0 + - - +
467A THR* 3.6 23.1 - - - +
469A VAL* 3.6 25.2 - - + +
59B TRP* 3.4 29.0 - - + +
60B TYR 3.3 0.2 - - - -
61B TRP* 1.3 74.1 + - - +
63B LYS* 1.3 56.7 + - - +
65B THR* 3.2 9.8 + - - -
66B THR* 2.8 32.2 + - - -
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Residues in contact with LYS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ASP* 4.8 8.2 + - - -
109A ASN* 4.3 23.3 + - - +
463A LEU* 5.8 1.6 - - - +
467A THR* 4.0 22.6 - - + +
58B SER 5.0 0.2 + - - -
59B TRP* 2.9 36.2 + - - +
60B TYR* 3.5 11.9 - - + +
62B GLU* 1.3 72.3 - - - +
64B GLU* 1.3 65.8 + - - +
66B THR* 3.2 1.3 + - - -
67B ASP* 3.0 30.1 + - - +
162B ARG* 3.6 13.5 - - - +
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Residues in contact with GLU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B TYR* 2.7 33.0 + - - -
35B TYR* 2.7 16.6 + - - -
36B LEU* 3.4 14.6 - - + +
45B ALA* 3.9 15.3 - - + -
60B TYR* 2.6 54.0 + - + +
61B TRP* 3.2 9.8 + - + +
63B LYS* 1.3 76.0 - - - +
65B THR* 1.3 63.2 + - - +
67B ASP* 3.4 1.9 + - - +
68B LEU* 3.1 29.8 + - - +
154B PHE* 5.4 0.3 - - - -
162B ARG* 3.4 21.7 + - - +
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Residues in contact with THR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A PRO 5.1 0.2 - - - +
469A VAL* 4.8 11.4 - - + +
38B TYR* 4.3 4.1 - - + -
43B GLY 3.4 25.8 - - - +
44B GLU* 3.8 5.7 - - - +
45B ALA* 2.9 30.2 + - - +
61B TRP 2.9 15.9 + - - -
62B GLU* 3.2 12.5 + - - +
64B GLU* 1.3 78.2 - - - +
66B THR* 1.3 62.8 + - - +
68B LEU* 3.4 1.6 + - - +
69B ARG* 3.1 43.1 + - + +
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Residues in contact with THR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A LYS 4.3 13.9 - - - +
467A THR* 3.3 30.3 - - + -
468A PRO* 4.2 9.8 + - + +
62B GLU 2.8 21.1 + - - -
63B LYS* 3.2 4.9 + - - -
65B THR* 1.3 74.3 - - - +
67B ASP* 1.3 66.2 + - - +
69B ARG* 3.3 17.8 + - + +
70B ILE* 3.3 26.3 + - + +
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Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LYS* 3.0 17.0 + - - +
64B GLU* 3.9 4.0 - - - +
66B THR* 1.3 81.1 - - - +
68B LEU* 1.3 61.5 + - + +
70B ILE* 3.5 14.4 + - - +
71B LYS* 3.2 25.9 + - - +
154B PHE* 3.9 26.0 - - + -
158B SER* 4.5 6.1 + - - -
162B ARG* 2.8 32.5 + - - +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B TYR* 4.2 23.3 - - + -
11B LEU* 4.7 10.5 - - + -
24B PHE* 3.8 3.5 - - - -
26B VAL* 4.0 18.2 - - + -
36B LEU* 3.9 28.9 - - + -
38B TYR* 3.7 46.9 - - + -
45B ALA* 4.3 2.7 - - + -
64B GLU* 3.1 19.1 + - - +
65B THR 4.1 0.2 - - - +
66B THR 3.3 0.2 - - - -
67B ASP* 1.3 75.3 - - - +
69B ARG* 1.3 55.0 + - - +
71B LYS* 3.1 5.6 + - + +
72B GLU* 2.8 34.5 + - - +
154B PHE* 4.7 11.4 - - + -
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Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A PRO* 3.1 31.7 + - - +
469A VAL* 4.5 15.0 + - - +
38B TYR* 3.3 20.4 + - + +
42B ARG 5.2 0.6 + - - -
43B GLY* 2.9 32.8 + - - -
65B THR* 3.1 30.7 + - - +
66B THR* 3.3 9.5 + - + +
68B LEU* 1.3 71.9 - - - +
70B ILE* 1.3 65.6 + - + +
72B GLU* 3.3 8.1 - - - +
73B LYS* 3.2 27.8 + - - +
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Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B THR* 3.3 31.9 + - + +
67B ASP* 3.6 14.4 - - - +
68B LEU 3.3 0.2 - - - -
69B ARG* 1.3 77.1 - - + +
71B LYS* 1.3 68.8 + - + +
73B LYS* 3.2 12.6 + - + +
74B LEU* 3.1 33.0 + - + +
147B ALA* 6.2 2.0 - - - -
150B LYS* 4.3 41.7 - - + +
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.7 19.1 - - + -
24B PHE* 3.9 12.8 - - + -
67B ASP 3.2 16.5 + - - +
68B LEU* 3.1 13.7 + - + +
70B ILE* 1.3 85.7 - - + +
72B GLU* 1.3 63.2 + - - +
74B LEU* 3.2 14.0 + - + +
75B PHE* 2.9 37.5 + - + -
94B LEU* 3.5 21.8 - - + -
150B LYS* 4.9 1.6 + - - +
151B GLU* 2.7 33.7 + - - +
154B PHE* 3.6 36.0 - - + +
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Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.6 31.6 - - + -
38B TYR* 2.6 30.2 + - - -
40B SER* 3.3 34.2 - - - +
43B GLY* 5.5 0.2 - - - -
68B LEU 2.8 16.9 + - - +
69B ARG* 3.3 13.0 - - - +
70B ILE 3.2 0.2 - - - -
71B LYS* 1.3 71.8 - - - +
73B LYS* 1.3 66.0 + - + +
75B PHE* 3.2 1.7 + - - +
76B LEU* 3.0 41.1 + - + +
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Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ARG* 3.2 14.1 + - - +
70B ILE* 3.6 11.2 - - + +
72B GLU* 1.3 80.9 - - + +
74B LEU* 1.3 59.4 + - + +
76B LEU* 3.3 7.7 + - - +
77B GLU* 2.9 34.4 + - - +
144B GLN* 6.0 1.1 - - - +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 3.1 22.8 + - + +
71B LYS* 3.5 20.9 - - + +
73B LYS* 1.3 77.3 - - + +
75B PHE* 1.3 65.2 + - + +
77B GLU* 3.2 4.9 + - - +
78B ALA 3.2 9.7 + - - -
127B TRP* 4.6 11.2 - - + -
141B TRP* 2.8 52.5 + - + +
144B GLN* 3.5 33.7 - - - +
147B ALA* 4.2 26.2 - - + +
151B GLU* 5.8 2.5 - - + +
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Residues in contact with PHE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.7 39.0 - - + -
13B ALA* 3.7 25.6 - - + -
24B PHE* 3.7 15.0 - + + -
71B LYS* 2.9 28.5 + - + +
72B GLU 3.8 3.4 - - - +
74B LEU* 1.3 80.1 - - + +
76B LEU* 1.3 63.9 + - - +
78B ALA* 3.4 16.5 + - - +
79B PHE* 4.1 10.4 + - - -
90B LEU* 3.7 43.0 - - + +
92B GLY* 3.9 10.5 - - - -
94B LEU* 5.5 1.3 - - + -
110B PHE* 4.0 29.2 - + - -
141B TRP* 4.2 11.2 - + - -
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA* 4.3 11.7 - - + -
14B VAL 4.6 0.7 - - - +
23B ALA* 4.2 28.9 - - + +
24B PHE* 4.8 3.1 - - + -
40B SER* 6.0 1.1 - - - -
72B GLU* 3.0 40.4 + - + +
73B LYS* 4.0 5.2 - - - +
75B PHE* 1.3 75.4 - - + +
77B GLU* 1.3 63.2 + - - +
78B ALA 3.4 0.7 + - - -
79B PHE* 3.5 41.6 + - + +
80B LYS* 3.9 12.3 + - - +
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LYS* 2.9 18.8 + - - +
74B LEU 3.2 6.5 + - - +
76B LEU* 1.3 75.1 - - - +
78B ALA* 1.3 64.2 + - - +
80B LYS* 3.2 42.9 + - - +
81B ALA* 3.3 11.8 + - - +
140B ARG* 3.3 31.9 + - + +
141B TRP* 4.7 2.9 - - - +
144B GLN* 3.6 28.4 + - - +
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU 3.2 5.1 + - - -
75B PHE 3.4 13.2 - - - +
76B LEU 3.2 0.2 - - - -
77B GLU* 1.3 76.1 - - - +
79B PHE* 1.3 58.3 + - + +
81B ALA* 3.0 21.2 + - - +
82B LEU* 3.2 16.0 + - - +
90B LEU* 3.5 23.6 - - + -
137B ILE* 3.7 31.2 - - + +
140B ARG* 5.6 0.2 - - - -
141B TRP* 4.0 10.7 - - + +
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Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA* 3.5 27.4 - - + -
14B VAL 3.5 7.4 - - - -
15B SER* 3.4 39.3 - - - -
75B PHE 4.2 4.0 - - - -
76B LEU* 3.5 35.0 + - + +
77B GLU 3.3 0.8 - - - -
78B ALA* 1.3 75.5 - - + +
80B LYS* 1.3 56.4 + - + +
82B LEU* 3.3 11.1 + - + +
83B GLY* 2.7 31.2 + - - -
84B GLY 5.2 0.5 - - - +
88B TYR* 3.5 44.5 - + + -
90B LEU* 4.1 19.1 - - + -
112B LEU* 5.6 0.9 - - + -
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Residues in contact with LYS 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 4.2 12.8 - - - +
77B GLU* 3.2 44.1 + - - +
79B PHE* 1.3 74.5 - - + +
81B ALA* 1.3 64.8 + - - +
83B GLY* 3.5 11.8 + - - +
140B ARG* 3.7 21.1 + - - +
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLU 3.3 7.3 + - - +
78B ALA* 3.0 11.7 + - - +
80B LYS* 1.3 78.7 - - - +
82B LEU* 1.3 61.4 + - - +
136B ALA* 3.7 41.8 - - + +
137B ILE* 4.3 4.0 - - + +
140B ARG* 3.7 30.2 - - + +
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ALA 3.2 11.9 + - - +
79B PHE* 3.7 9.0 - - + +
81B ALA* 1.3 80.1 - - - +
83B GLY* 1.3 63.7 + - - +
88B TYR* 3.6 48.9 + - + +
112B LEU* 3.8 21.1 - - + -
133B GLU* 3.7 42.2 - - + +
136B ALA* 4.6 4.0 - - + -
137B ILE* 4.1 17.5 - - + -
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Residues in contact with GLY 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE 2.7 18.9 + - - -
80B LYS* 3.5 12.1 + - - -
81B ALA 3.5 1.4 - - - -
82B LEU* 1.3 76.3 - - - +
84B GLY* 1.3 64.1 + - - +
88B TYR* 2.6 29.5 + - - -
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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