Contacts of the helix formed by residues 64 - 87 (chain A) in PDB entry 1TKY
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 ASP 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ILE 3.8 5.5 - - - +
60A ILE* 3.5 17.7 - - + -
61A THR* 2.9 37.0 + - - +
62A ALA 3.9 3.8 - - - +
63A LYS* 1.3 83.4 - - - +
65A GLU* 1.3 67.0 + - - +
66A GLU* 3.5 16.5 - - - +
67A GLY* 2.9 16.2 + - - +
68A LEU* 3.2 10.9 + - - +
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LYS 4.2 6.6 - - - +
64A ASP* 1.3 75.5 - - - +
66A GLU* 1.3 68.4 + - - +
68A LEU* 3.3 13.2 + - - +
69A GLU* 3.2 20.8 + - - +
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ARG* 2.8 38.3 + - - +
44A LEU* 4.3 20.0 - - + -
60A ILE* 4.1 21.7 - - + +
64A ASP* 3.5 17.5 - - - +
65A GLU* 1.3 87.0 + - + +
67A GLY* 1.3 61.3 + - - +
69A GLU* 3.4 7.7 + - - +
70A ILE* 3.0 30.7 + - + +
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Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ILE* 4.3 8.0 - - - +
60A ILE* 3.7 11.7 - - - +
61A THR 3.5 17.5 - - - -
62A ALA* 4.9 0.9 - - - -
64A ASP 2.9 10.8 + - - -
66A GLU* 1.3 80.9 - - - +
68A LEU* 1.3 56.5 + - - +
70A ILE* 3.3 6.6 + - - +
71A ILE* 3.0 38.5 + - - +
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ALA 4.8 5.6 + - - +
64A ASP 3.2 9.8 + - - +
65A GLU* 3.3 13.7 + - - +
67A GLY* 1.3 76.9 - - - +
69A GLU* 1.3 62.2 + - - +
71A ILE* 3.3 9.0 + - + +
72A ARG* 3.0 58.4 + - + +
222A ALA 3.9 0.7 - - - +
223A TRP* 3.7 31.4 - - + -
224A ALA* 3.9 12.1 - - + +
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 5.9 3.7 - - - +
65A GLU 3.2 10.5 + - - +
66A GLU* 3.7 10.8 - - - +
68A LEU* 1.3 81.2 - - - +
70A ILE* 1.3 59.3 + - + +
72A ARG* 3.3 11.3 + - - +
73A HIS* 2.9 26.4 + - + +
97A VAL* 3.6 27.4 - - + +
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Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ILE* 3.8 18.4 - - + -
37A ALA* 3.8 26.5 - - + -
44A LEU* 5.1 6.1 - - + -
60A ILE* 4.6 5.2 - - + -
66A GLU* 3.0 26.9 + - + +
67A GLY 3.6 4.0 - - - +
68A LEU 3.3 0.2 - - - -
69A GLU* 1.3 76.4 - - + +
71A ILE* 1.3 65.7 + - - +
73A HIS* 3.2 7.4 + - - +
74A SER* 2.9 22.5 + - - -
185A PRO* 3.6 31.4 - - + +
186A HIS 3.5 30.3 - - - -
187A VAL* 3.6 3.6 - - + +
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Residues in contact with ILE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ILE* 3.9 20.0 - - + -
62A ALA* 4.3 13.7 - - + -
67A GLY 3.0 21.6 + - - +
68A LEU* 3.6 11.4 - - + +
70A ILE* 1.3 75.8 - - - +
72A ARG* 1.3 65.3 + - - +
74A SER* 3.3 3.3 + - - -
75A CYS* 3.0 31.0 + - - -
187A VAL* 4.0 19.3 - - + -
192A PHE* 3.5 30.5 - - + +
193A CYS* 3.8 7.1 - - - -
195A HIS 5.5 0.4 - - - +
222A ALA* 4.6 5.4 - - + -
223A TRP 4.2 16.4 - - - +
224A ALA* 4.5 15.5 - - + +
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Residues in contact with ARG 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 3.0 47.0 + - + +
69A GLU* 3.5 9.3 - - - +
71A ILE* 1.3 75.7 - - - +
73A HIS* 1.3 62.7 + - - +
75A CYS* 3.1 13.2 + - - +
76A ALA 3.3 8.1 + - - -
97A VAL* 4.0 12.5 - - + +
98A ILE 4.5 1.0 + - - -
100A ASN* 3.1 48.7 + - - +
101A GLY* 3.4 31.1 - - - +
102A PHE* 3.7 10.5 - - - +
221A THR* 6.1 0.2 - - - -
222A ALA* 2.8 44.6 + - + +
223A TRP* 5.0 3.2 - - - +
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Residues in contact with HIS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLU* 2.9 15.3 + - + +
70A ILE* 3.2 8.3 + - - +
72A ARG* 1.3 74.6 - - - +
74A SER* 1.3 62.8 + - - +
76A ALA* 3.0 21.9 + - + +
77A HIS* 3.4 3.8 + - - -
95A GLY 3.6 11.1 + - - -
96A PRO* 4.4 5.6 - - + +
97A VAL* 3.4 26.1 - - + +
182A CYS* 3.3 29.8 - - - -
184A GLY* 5.2 5.2 + - - -
185A PRO 4.7 5.7 + - - +
186A HIS* 3.6 17.2 + + + +
500A A3S 3.1 31.8 + - - -
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ILE 2.9 14.2 + - - -
73A HIS* 1.3 76.5 - - - +
75A CYS* 1.3 59.1 + - - +
77A HIS* 3.1 7.9 + - - +
78A LEU* 2.9 25.5 + - - +
175A HIS* 4.5 3.3 - - - -
186A HIS* 2.8 25.3 + - - +
187A VAL* 2.9 42.8 + - - +
190A MET* 4.1 6.5 - - - +
193A CYS* 3.7 12.1 - - - -
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Residues in contact with CYS 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 3.0 19.7 + - - -
72A ARG 3.1 10.7 + - - +
74A SER* 1.3 74.4 - - - +
76A ALA* 1.3 66.0 + - - +
78A LEU* 3.2 10.7 + - + +
79A LEU* 3.0 19.4 + - - +
102A PHE* 3.6 23.2 - - + -
124A MET* 3.7 7.8 - - + +
193A CYS* 3.9 23.3 - - - -
195A HIS 5.1 0.4 - - - -
196A PHE* 4.0 20.6 - - + -
222A ALA* 3.7 20.4 - - - -
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Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ARG 3.3 5.3 + - - +
73A HIS* 3.0 14.6 + - + +
75A CYS* 1.3 77.4 - - - +
77A HIS* 1.3 62.0 + - - +
79A LEU* 3.1 10.5 + - - +
80A GLY 3.1 9.4 + - - -
95A GLY 3.7 25.6 - - - +
102A PHE* 3.9 23.9 - - + -
103A TYR 4.4 1.3 - - - +
104A TYR* 3.2 24.8 - - + -
500A A3S 4.0 3.6 - - - +
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Residues in contact with HIS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A HIS 3.4 0.8 + - - -
74A SER 3.1 9.0 + - - +
76A ALA* 1.3 79.4 - - - +
78A LEU* 1.3 56.6 + - - +
80A GLY 3.1 2.5 + - - +
81A HIS* 2.9 27.0 + - - +
173A TYR* 3.8 15.6 - + + +
175A HIS* 3.1 34.8 + - + +
178A TYR* 3.5 12.1 - - + -
180A ASP* 3.4 32.6 - - + +
182A CYS* 4.3 0.2 - - + -
186A HIS* 3.1 43.0 + + - -
500A A3S 2.8 37.6 + - - -
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A SER 2.9 12.9 + - - +
75A CYS* 3.4 11.7 - - - +
76A ALA 3.2 0.2 - - - -
77A HIS* 1.3 77.1 - - - +
79A LEU* 1.3 61.2 + - - +
81A HIS* 3.2 7.5 + - + +
82A ALA* 2.9 22.7 + - - +
124A MET* 3.6 32.1 - - + +
127A LEU* 4.0 10.8 - - + -
128A ALA* 3.8 20.0 - - + +
132A TYR* 4.0 19.3 - - - +
175A HIS* 4.8 0.6 - - - -
190A MET* 3.9 15.0 - - + -
193A CYS* 4.3 2.0 - - + +
196A PHE* 3.6 37.0 - - + -
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A CYS 3.0 12.2 + - - +
76A ALA* 3.3 10.1 - - - +
78A LEU* 1.3 77.4 - - - +
80A GLY* 1.3 61.9 + - - +
82A ALA* 3.3 1.2 + - - +
83A ILE* 2.8 42.0 + - + +
92A MET* 4.3 3.6 - - + -
102A PHE* 4.2 17.7 - - + -
104A TYR* 4.0 25.4 - - + -
106A VAL* 4.7 0.4 - - + -
120A LEU* 4.0 15.7 - - + +
124A MET* 3.8 17.2 - - + +
198A LEU* 4.2 7.9 - - + -
218A ILE* 3.8 40.6 - - + +
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Residues in contact with GLY 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ALA 3.1 5.2 + - - -
77A HIS 3.1 7.1 + - - -
79A LEU* 1.3 76.8 - - - +
81A HIS* 1.3 64.4 + - - +
83A ILE* 3.9 0.7 - - - -
84A LYS* 3.0 30.8 + - - +
92A MET* 3.5 27.3 - - - +
178A TYR* 3.4 16.6 - - - -
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Residues in contact with HIS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A HIS 2.9 12.0 + - - +
78A LEU* 3.4 11.9 - - + +
80A GLY* 1.3 76.7 - - - +
82A ALA* 1.3 63.1 + - - +
84A LYS* 3.6 2.6 + - - +
85A GLN* 3.4 27.1 + - - +
127A LEU* 3.7 18.2 - - + +
132A TYR* 3.2 31.1 - + - +
175A HIS* 3.5 14.1 + - + -
176A GLU* 2.9 25.6 + - - -
177A GLU* 3.4 33.6 + - - +
178A TYR* 3.5 29.3 - - + +
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LEU 2.9 8.9 + - - +
79A LEU 3.8 1.6 - - - +
81A HIS* 1.3 75.6 - - - +
83A ILE* 1.3 65.3 + - - +
85A GLN* 3.0 13.2 + - - +
86A LEU* 3.1 16.6 + - - +
120A LEU* 3.8 9.0 - - + -
123A ARG* 3.7 21.2 - - + +
124A MET* 3.6 33.0 - - + +
127A LEU* 3.7 11.9 - - + -
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Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU* 2.8 21.8 + - + +
80A GLY* 3.5 9.6 - - - +
82A ALA* 1.3 74.8 - - - +
84A LYS* 1.3 59.6 + - - +
86A LEU* 4.5 2.0 - - - +
87A TRP* 2.8 55.3 + - + +
90A THR* 4.1 15.0 - - + +
92A MET* 3.6 28.0 - - + -
106A VAL* 4.2 16.4 - - + -
108A LEU* 4.7 6.7 - - + -
112A LEU* 4.9 2.5 - - + -
120A LEU* 3.7 16.8 - - + -
218A ILE* 3.9 28.5 - - + -
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Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLY 3.0 21.6 + - - +
81A HIS 4.0 3.8 - - - +
83A ILE* 1.3 76.2 - - - +
85A GLN* 1.3 59.3 + - + +
87A TRP 4.1 3.1 - - - -
88A PRO* 3.1 46.7 + - - +
89A HIS 4.7 0.4 - - - -
90A THR* 2.8 33.1 + - - +
92A MET* 4.2 11.7 - - - -
151A ARG* 4.3 23.8 + - - +
153A GLU* 2.9 24.1 + - - +
177A GLU* 6.1 0.2 - - - +
178A TYR* 3.8 21.5 - - + -
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Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A HIS* 3.4 20.7 + - - +
82A ALA 3.0 7.4 + - - +
84A LYS* 1.3 81.6 - - + +
86A LEU* 1.3 64.0 + - - +
87A TRP 3.7 0.2 + - - -
88A PRO* 3.8 10.5 - - - +
123A ARG* 2.9 42.8 - - - +
127A LEU* 3.9 20.5 - - - +
176A GLU* 4.8 0.7 - - - +
177A GLU* 2.8 30.7 - - - +
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA 3.1 13.5 + - - +
85A GLN* 1.3 79.0 - - - +
87A TRP* 1.3 96.7 + - + +
88A PRO* 3.7 4.4 - - - +
119A ALA* 3.8 15.3 - - + +
120A LEU* 3.7 34.1 - - + +
123A ARG* 3.8 39.5 - - + +
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Residues in contact with TRP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ILE* 2.8 36.3 + - + +
84A LYS* 4.1 0.9 - - - -
86A LEU* 1.3 113.6 + - + +
88A PRO* 1.3 67.7 - - - +
89A HIS* 3.1 19.7 - + + -
90A THR* 2.8 37.1 + - - +
108A LEU* 3.9 19.5 - - + -
110A ARG* 4.2 19.8 - - + +
112A LEU* 3.9 11.7 - - + -
116A ASP* 3.7 50.5 - - + -
119A ALA* 5.1 3.4 - - + -
120A LEU* 4.7 5.2 - - + -
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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