Contacts of the helix formed by residues 74 - 103 (chain N) in PDB entry 1KYO
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 ASN 74 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72N VAL 3.1 1.6 + - - -
73N HIS* 1.3 77.9 - - - +
75N GLY* 1.3 65.3 + - - +
76N TYR* 3.1 17.2 + - - +
77N ILE* 2.8 25.4 + - + +
78N LEU* 2.8 24.5 + - + +
269O LEU* 4.9 8.9 - - - +
77P THR* 3.4 45.6 - - + +
80P SER* 3.4 12.6 + - - -
81P SER* 4.8 1.1 - - - -
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Residues in contact with GLY 75 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68N ILE* 3.2 31.1 - - - +
72N VAL* 2.7 23.4 + - - -
73N HIS 2.9 1.8 - - - -
74N ASN* 1.3 78.3 - - - +
76N TYR* 1.3 56.9 + - - +
78N LEU* 3.0 10.2 + - - +
79N ARG* 2.8 29.5 + - - +
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Residues in contact with TYR 76 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68N ILE 3.8 4.0 + - - -
69N MET* 4.0 43.0 + - + +
72N VAL 5.5 0.4 - - - -
74N ASN* 4.4 16.2 + - - -
75N GLY* 1.3 75.9 - - - +
77N ILE* 1.3 88.9 - - + +
80N TYR* 2.8 49.3 + + + +
244N VAL* 5.8 0.7 - - + -
245N PHE* 4.8 2.7 - + - -
262O GLU* 3.7 35.4 - - + -
265O GLU* 4.2 7.1 - - + +
266O ARG* 3.7 34.2 + - + -
269O LEU* 3.4 28.1 - - - +
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Residues in contact with ILE 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74N ASN* 2.8 29.2 + - + +
76N TYR* 1.3 112.4 - - + +
78N LEU* 1.3 65.3 + - + +
80N TYR* 4.8 3.4 - - - -
81N LEU* 3.0 43.9 + - + +
244N VAL* 4.7 5.7 - - + +
245N PHE* 3.9 33.2 - - + -
269O LEU* 4.2 8.3 - - + -
77P THR* 4.6 15.9 - - + -
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Residues in contact with LEU 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46N THR* 4.2 7.8 - - + +
49N PHE* 4.0 19.5 - - + +
50N MET* 3.8 25.7 - - + +
53N HIS* 5.8 0.9 - - + -
68N ILE* 5.5 0.9 - - + -
72N VAL* 5.0 4.0 - - + -
74N ASN 2.8 16.8 + - - +
75N GLY* 3.3 12.8 - - - +
77N ILE* 1.3 83.7 - - + +
79N ARG* 1.3 63.1 + - - +
81N LEU* 3.7 5.0 - - + +
82N HIS* 3.0 24.6 + - - +
77P THR* 5.5 5.4 - - + -
78P PHE* 3.3 40.2 - - + -
81P SER* 3.6 28.7 - - - +
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Residues in contact with ARG 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50N MET* 3.7 11.8 - - - -
65N VAL* 3.6 24.3 - - + +
66N GLU* 4.6 3.2 + - - -
68N ILE* 4.8 3.8 - - + -
69N MET* 3.4 37.9 - - + +
75N GLY 2.8 15.4 + - - +
76N TYR 3.9 0.2 - - - +
78N LEU* 1.3 74.3 - - - +
80N TYR* 1.3 65.3 + - - +
82N HIS* 3.3 2.9 + - - +
83N ALA* 2.9 30.4 + - - +
135N VAL* 4.2 11.7 - - - +
256N ASN* 5.8 0.4 + - - +
257N TYR* 3.9 30.3 + - - -
521N HEC 2.9 62.6 + - + +
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Residues in contact with TYR 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69N MET* 3.4 20.8 - - + +
76N TYR* 2.8 35.6 + + + +
79N ARG* 1.3 82.0 - - - +
81N LEU* 1.3 56.1 + - - +
83N ALA* 4.6 4.3 - - + -
84N ASN* 2.6 44.1 + - - +
244N VAL* 3.5 23.1 - - + +
248N PRO* 3.4 39.8 - - + +
249N ASN* 3.3 26.3 + - - -
257N TYR* 3.9 5.8 - - - -
182O LYS* 3.2 25.8 + - - +
260O GLU* 4.6 0.9 + - - -
262O GLU* 4.1 17.2 + - - -
266O ARG* 4.4 4.3 - - - -
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Residues in contact with LEU 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42N ILE* 3.8 18.2 - - + -
43N GLN* 4.1 0.9 + - - -
46N THR* 4.3 17.7 - - + -
77N ILE* 3.0 33.2 + - + +
78N LEU* 3.7 4.3 - - - +
80N TYR* 1.3 75.8 - - - +
82N HIS* 1.3 55.8 + - - +
85N GLY* 2.6 36.2 + - - -
240N LEU* 3.7 32.1 - - + -
244N VAL* 3.7 14.5 - - + +
78P PHE* 4.8 12.3 - - + -
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Residues in contact with HIS 82 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N GLN* 2.9 46.7 + - - +
46N THR* 2.8 24.1 + - - +
47N GLY* 3.9 3.1 + - - -
50N MET* 3.3 26.2 - - + -
78N LEU 3.0 10.3 + - - +
79N ARG 3.6 2.7 - - - +
81N LEU* 1.3 77.1 - - - +
83N ALA* 1.3 57.3 + - - +
86N ALA* 3.0 15.6 + - - +
521N HEC 2.0 94.6 + + + +
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Residues in contact with ALA 83 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79N ARG* 2.9 21.6 + - - +
80N TYR* 4.1 6.3 - - + +
82N HIS* 1.3 76.9 - - - +
84N ASN* 1.3 64.8 + - - +
86N ALA* 3.2 17.1 - - - +
87N SER* 3.5 7.6 + - - -
248N PRO 5.8 1.3 - - - +
521N HEC 3.5 36.7 + - + +
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Residues in contact with ASN 84 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80N TYR* 2.6 34.4 + - - +
83N ALA* 1.3 73.0 - - - +
85N GLY* 1.3 66.2 + - - +
86N ALA 3.0 2.0 - - - -
87N SER* 2.9 16.7 + - - +
88N PHE* 2.9 20.4 + - + -
240N LEU* 3.8 18.6 - - + -
243N PHE* 4.4 14.1 - - + +
244N VAL* 3.6 20.5 - - + +
247N SER 5.0 0.2 - - - +
248N PRO* 3.4 28.1 + - - +
251N LEU* 4.2 22.3 - - - +
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Residues in contact with GLY 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39N CYS* 4.9 5.3 - - - +
42N ILE* 5.1 2.2 - - - -
43N GLN* 3.3 18.9 + - - +
81N LEU 2.6 24.8 + - - -
84N ASN* 1.3 74.3 - - - +
86N ALA* 1.3 57.0 + - - +
88N PHE* 4.0 3.6 - - - +
89N PHE* 3.0 27.9 + - - +
236N PHE* 5.9 1.1 - - - -
240N LEU* 4.1 16.5 - - - +
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Residues in contact with ALA 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N GLN* 3.5 11.4 + - - +
82N HIS 3.0 12.2 + - - +
83N ALA 3.2 12.6 - - - +
84N ASN 3.0 0.6 - - - -
85N GLY* 1.3 77.6 - - - +
87N SER* 1.3 61.8 + - - +
89N PHE* 3.1 18.4 - - - +
90N PHE* 3.2 18.7 - - + -
274N TYR* 4.9 5.6 - - + +
521N HEC 3.8 37.2 - - + -
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Residues in contact with SER 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83N ALA 3.5 7.2 + - - -
84N ASN* 2.9 8.3 + - - -
86N ALA* 1.3 77.4 - - - +
88N PHE* 1.3 65.4 + - - +
90N PHE* 3.0 2.9 + - - -
91N MET* 3.0 19.1 + - - +
251N LEU* 3.8 26.9 + - - +
273N TRP* 2.6 45.0 + - - -
274N TYR* 3.9 12.5 - - - -
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Residues in contact with PHE 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39N CYS* 4.7 0.9 - - - -
84N ASN* 2.9 21.2 + - + +
85N GLY* 4.1 3.4 - - - +
87N SER* 1.3 73.7 - - - +
89N PHE* 1.3 68.4 + - - +
91N MET* 3.1 23.0 + - + +
92N VAL* 2.8 31.6 + - + +
236N PHE* 3.7 37.0 - + + -
239N ILE* 3.8 13.5 - - + -
240N LEU* 3.7 41.1 - - + -
243N PHE* 3.5 39.5 - + + -
251N LEU* 4.1 16.8 - - + -
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Residues in contact with PHE 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36N LEU* 3.6 19.4 - - + +
39N CYS* 3.9 18.1 - - + -
40N LEU* 3.9 30.1 - - + -
43N GLN* 4.0 12.8 - - + -
85N GLY 3.0 12.5 + - - +
86N ALA 3.1 13.5 - - - +
88N PHE* 1.3 77.6 - - - +
90N PHE* 1.3 54.8 + - + +
92N VAL* 3.6 0.6 + - - -
93N MET* 2.8 55.3 + - + +
124N THR* 4.5 14.4 - - + -
190N ILE* 5.5 0.4 - - + -
521N HEC 3.3 40.4 - - + -
522N HEC 4.1 14.1 - - + -
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Residues in contact with PHE 90 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86N ALA* 3.2 24.6 + - + -
87N SER 3.0 6.7 + - - +
89N PHE* 1.3 78.1 - - + +
91N MET* 1.3 58.3 + - - +
92N VAL 3.1 1.6 - - - -
93N MET* 3.7 7.8 - - + +
94N PHE* 2.8 54.3 + + + -
121N PHE* 4.8 9.2 - + - -
124N THR* 3.9 24.9 - - + -
125N ILE* 3.8 28.9 - - + -
128N ALA* 3.9 24.0 - - + -
273N TRP* 4.2 1.3 - - + -
274N TYR* 3.5 59.7 - + + -
275N LEU* 5.4 0.2 - - + -
521N HEC 5.3 2.7 - - + -
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Residues in contact with MET 91 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87N SER 3.0 17.0 + - - +
88N PHE* 3.1 38.6 + - + +
90N PHE* 1.3 75.0 - - - +
92N VAL* 1.3 64.1 + - + +
94N PHE* 3.6 5.9 + - - +
95N MET* 3.2 32.9 + - - +
243N PHE* 5.2 9.0 - - + -
251N LEU* 4.4 25.8 - - + -
273N TRP* 3.7 24.7 - - + -
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Residues in contact with VAL 92 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N MET* 3.7 33.2 - - + +
35N LEU* 4.0 15.0 - - + -
36N LEU* 3.5 21.3 - - + +
39N CYS* 5.1 1.8 - - - -
88N PHE* 2.8 19.4 + - + +
89N PHE* 3.9 3.1 - - - +
91N MET* 1.3 76.8 - - + +
93N MET* 1.3 65.3 + - - +
95N MET* 2.9 11.9 + - - +
96N HIS* 2.8 21.7 + - - +
236N PHE* 4.1 27.1 - - + -
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Residues in contact with MET 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36N LEU* 3.9 9.4 - - + -
89N PHE* 2.8 53.0 + - + +
90N PHE* 3.7 12.3 - - + +
92N VAL* 1.3 73.6 - - - +
94N PHE* 1.3 58.3 + - + +
96N HIS* 3.3 4.5 + - - +
97N MET* 2.8 47.9 + - - +
120N ILE* 4.8 1.6 - - + -
121N PHE* 3.8 32.5 - - + -
124N THR* 3.9 22.4 - - + +
522N HEC 3.7 37.7 - - + -
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Residues in contact with PHE 94 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90N PHE* 2.8 43.6 + + + +
91N MET* 3.8 9.2 - - - +
93N MET* 1.3 72.5 - - + +
95N MET* 1.3 59.5 + - + +
97N MET* 3.2 11.6 + - + +
98N ALA* 2.8 31.0 + - - +
121N PHE* 4.1 28.5 - + - -
273N TRP* 3.9 25.4 - + - -
274N TYR* 3.8 23.1 - - + -
277N PRO* 5.9 0.9 - - + -
278N PHE* 4.8 1.8 - + - -
333N PHE* 4.4 31.6 - + - -
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Residues in contact with MET 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N TRP* 3.8 36.9 - - + -
32N MET* 4.3 22.9 - - + +
91N MET* 3.2 22.5 + - - +
92N VAL* 2.9 14.1 + - - +
94N PHE* 1.3 78.3 - - + +
96N HIS* 1.3 62.5 + - - +
98N ALA* 2.9 9.3 + - - +
99N LYS* 2.8 27.2 + - - +
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Residues in contact with HIS 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N MET* 3.8 24.4 - - + +
33N GLY* 3.8 4.0 + - - -
36N LEU* 3.5 15.0 - - + -
92N VAL 2.8 15.3 + - - +
93N MET 3.4 8.3 - - - +
95N MET* 1.3 73.4 - - - +
97N MET* 1.3 63.0 + - - +
99N LYS* 3.6 11.9 + - - +
100N GLY* 3.4 14.2 + - - -
522N HEC 2.0 119.6 + + + +
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Residues in contact with MET 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93N MET* 2.8 28.2 + - - +
94N PHE* 3.5 13.2 - - + +
96N HIS* 1.3 72.2 - - - +
98N ALA* 1.3 58.0 + - - +
100N GLY* 3.3 3.5 + - - -
101N LEU* 2.9 34.2 + - + +
114N TRP* 4.1 11.5 - - + -
121N PHE* 3.8 39.5 - - + -
302N LEU* 3.6 31.6 - - + -
522N HEC 3.8 38.8 - - + -
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Residues in contact with ALA 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N TRP* 6.4 0.7 - - + -
94N PHE 2.8 20.9 + - - +
95N MET* 3.4 7.9 - - - +
97N MET* 1.3 69.9 - - - +
99N LYS* 1.3 66.5 + - - +
101N LEU* 3.0 11.0 + - - +
102N TYR* 2.8 26.3 + - - +
326N PHE* 4.0 16.8 - - + -
330N VAL* 5.7 4.0 - - + -
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Residues in contact with LYS 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N TRP* 2.8 62.1 + - + +
30N TRP* 3.3 27.9 - - + +
95N MET 2.8 18.2 + - - +
96N HIS* 3.8 13.6 + - + +
98N ALA* 1.3 72.2 - - - +
100N GLY* 1.3 77.9 + - - +
102N TYR* 3.2 3.8 + - - +
103N TYR* 2.9 47.4 + - + -
105N SER* 4.4 1.6 - - - +
522N HEC 3.1 48.8 + - + -
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Residues in contact with GLY 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96N HIS 3.4 4.2 + - - -
97N MET 3.3 6.6 + - - -
98N ALA 3.1 0.6 - - - -
99N LYS* 1.3 93.0 - - - +
101N LEU* 1.3 60.4 + - - +
104N GLY* 3.0 6.4 + - - -
105N SER* 2.9 42.3 + - - -
106N TYR* 3.7 3.7 - - - -
114N TRP* 4.6 8.1 - - - -
522N HEC 5.2 3.4 - - - -
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Residues in contact with LEU 101 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97N MET* 2.9 20.0 + - + +
98N ALA* 3.0 13.2 + - - +
100N GLY* 1.3 75.8 - - - +
102N TYR* 1.3 61.0 + - - +
106N TYR* 3.4 24.3 + - - -
114N TRP* 4.4 13.3 - - + -
302N LEU* 5.6 4.5 - - + -
305N LEU* 4.0 18.8 - - + -
316N ASN* 4.8 2.6 + - - -
326N PHE* 4.0 16.4 - - + -
329N PHE* 4.5 16.4 - - + -
362N TYR* 4.0 29.5 + - + +
363N PHE* 4.5 16.6 - - + -
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Residues in contact with TYR 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98N ALA 2.8 12.9 + - - +
99N LYS* 3.4 10.1 - - - +
101N LEU* 1.3 76.0 - - - +
103N TYR* 1.3 96.2 + + + +
104N GLY 3.1 9.9 + - - -
315N GLY* 3.6 0.9 - - - -
316N ASN* 3.2 61.3 + - + +
317N THR* 4.2 9.2 + - + +
323N LYS* 3.6 27.2 - - + +
326N PHE* 3.5 42.1 - + + -
327N PHE* 4.3 14.4 - + - -
55S GLN* 4.0 8.5 + - - -
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Residues in contact with TYR 103 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27N ASN* 3.0 24.3 + - - -
29N TRP* 4.2 12.9 + + - -
30N TRP* 3.6 29.6 - + + -
99N LYS* 2.9 40.7 + - + +
102N TYR* 1.3 98.2 - + - +
104N GLY* 1.3 63.1 + - - +
105N SER* 3.2 12.9 + - - +
207N SER* 5.0 4.4 + - - +
208N ASN 4.5 3.1 - - - +
209N PRO* 3.6 37.6 - - + +
211N GLY* 5.4 2.9 - - - -
314N ARG* 3.6 14.7 - - - +
315N GLY* 3.5 14.1 - - - -
317N THR* 4.0 10.1 - - + +
----------------------------------------------------------
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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