Contacts of the helix formed by residues 72 - 93 (chain D) in PDB entry 7A62
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 72 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D GLN* 3.8 6.7 - - - +
70D LEU 3.7 0.6 - - - -
71D THR* 1.3 87.7 + - - +
73D HIS* 1.3 65.0 + - - +
74D LYS* 3.5 6.8 + - + +
75D SER* 2.8 44.8 + - - -
76D GLN* 3.0 28.6 + - - +
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Residues in contact with HIS 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D HIS* 4.1 30.0 + + - +
25D LEU* 4.3 14.9 - - + +
72D ASP* 1.3 74.9 - - - +
74D LYS* 1.3 61.7 + - + +
76D GLN* 3.0 13.5 + - - +
77D ARG* 2.8 68.9 + - + +
118D LEU* 3.9 20.0 - - + +
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Residues in contact with LYS 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LEU* 4.4 22.2 - - + +
26D PRO* 2.5 30.8 + - - +
27D ASN* 2.9 32.1 + - - +
28D PRO* 4.2 4.0 - - - -
29D GLN* 3.9 24.2 + - + +
72D ASP* 3.3 7.6 + - - +
73D HIS* 1.3 80.0 - - + +
75D SER* 1.3 62.7 + - - +
77D ARG* 3.9 6.9 - - - +
78D LEU* 3.1 24.3 + - - +
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Residues in contact with SER 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D GLN* 3.1 27.4 + - - +
32D LEU* 3.6 7.8 - - - +
33D PRO* 5.0 5.2 - - - +
70D LEU* 4.3 14.4 - - - -
71D THR* 4.1 12.4 + - - -
72D ASP* 2.8 41.9 + - - -
74D LYS* 1.3 73.5 - - - +
76D GLN* 1.3 56.8 + - - +
78D LEU* 3.4 0.9 + - - -
79D ALA* 3.0 28.6 + - - +
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Residues in contact with GLN 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D ILE* 5.8 3.2 + - - +
70D LEU* 4.2 23.2 + - + +
71D THR 6.0 0.2 - - - -
72D ASP 3.0 16.5 + - - +
73D HIS* 3.0 19.1 + - - +
75D SER* 1.3 74.5 - - - +
77D ARG* 1.3 61.4 + - - +
79D ALA* 3.2 4.0 + - - +
80D ARG* 2.8 30.7 + - - +
114D LEU* 3.8 30.0 - - + +
117D ALA* 4.6 14.1 - - - +
118D LEU* 3.9 22.8 - - + +
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Residues in contact with ARG 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PHE 5.8 0.6 + - - -
25D LEU* 4.0 33.6 - - + +
73D HIS* 2.8 58.8 + - + +
74D LYS* 3.9 4.5 - - - +
76D GLN* 1.3 73.4 - - - +
78D LEU* 1.3 62.8 + - - +
80D ARG* 3.3 6.9 + - - +
81D LEU* 3.0 22.9 + - - +
118D LEU* 4.2 13.5 - - - -
120D LEU* 5.6 6.0 - - - +
127D ALA* 2.8 42.4 + - - +
128D ASP* 4.6 9.1 + - - +
131D LEU* 4.2 8.9 - - - +
132D ALA* 3.8 19.1 - - + +
300D PRO* 5.0 12.8 - - - +
303D HIS* 6.1 2.0 - - - -
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Residues in contact with LEU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D GLN* 3.4 24.5 - - + +
30D GLU 3.4 30.1 - - - +
31D ASN 3.5 22.0 - - - +
32D LEU* 3.9 13.9 - - + +
40D MET* 4.8 1.6 - - + -
74D LYS 3.1 18.3 + - - +
75D SER 3.8 3.1 - - - +
77D ARG* 1.3 76.8 - - - +
79D ALA* 1.3 57.9 + - - +
81D LEU* 3.2 8.1 + - + +
82D VAL* 2.8 35.3 + - + +
132D ALA* 5.5 2.5 - - - +
151D LEU* 4.1 9.4 - - + -
152D PHE* 4.0 29.6 - - + -
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Residues in contact with ALA 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU* 4.2 12.3 - - + +
39D TRP* 4.6 7.9 - - + -
70D LEU* 3.6 31.9 - - + -
75D SER 3.0 17.8 + - - +
76D GLN 3.7 0.9 - - - +
78D LEU* 1.3 75.6 - - - +
80D ARG* 1.3 57.4 + - - +
82D VAL* 3.7 6.4 - - - +
83D LEU* 3.0 34.4 + - - +
114D LEU* 3.7 10.5 - - + -
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Residues in contact with ARG 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D GLN 2.8 20.2 + - - +
77D ARG* 3.6 6.5 - - - +
79D ALA* 1.3 74.8 - - - +
81D LEU* 1.3 56.3 + - - +
83D LEU* 4.2 2.6 - - - +
84D GLY* 2.8 26.7 + - - -
111D TYR* 4.2 15.8 + - + -
114D LEU* 3.5 15.8 - - + +
115D SER* 3.1 22.0 + - - +
118D LEU* 3.6 26.9 - - + -
120D LEU* 3.4 28.6 - - - +
121D PRO 2.8 23.0 + - - -
123D ILE 2.8 21.7 + - - -
125D VAL* 3.6 13.1 - - - +
128D ASP* 2.6 44.0 + - - +
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Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D ARG 3.0 13.8 + - - +
78D LEU* 3.2 11.4 + - + +
80D ARG* 1.3 73.7 - - - +
82D VAL* 1.3 65.1 + - - +
84D GLY* 3.3 0.7 + - - -
85D CYS* 2.9 44.5 + - - -
124D LEU* 4.2 1.3 - - + -
128D ASP* 3.2 41.3 + - + +
129D CYS* 3.9 9.4 - - - +
132D ALA* 3.8 10.8 - - + +
133D ASN* 3.7 39.0 - - + +
151D LEU* 4.4 3.8 - - + -
152D PHE* 3.7 23.6 - - + -
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Residues in contact with VAL 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU* 4.7 0.9 - - + -
39D TRP* 3.9 26.9 - - + +
40D MET* 3.9 20.9 - - + +
43D ALA* 3.7 20.5 - - + +
78D LEU* 2.8 28.9 + - + +
79D ALA* 3.7 8.3 - - - +
81D LEU* 1.3 73.5 - - - +
83D LEU* 1.3 57.8 + - - +
85D CYS* 3.8 2.6 - - - +
86D ILE* 3.0 43.9 + - + +
152D PHE* 3.8 27.1 - - + -
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Residues in contact with LEU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D TRP* 3.8 46.0 - - + -
67D ILE* 5.6 0.2 - - + -
79D ALA 3.0 20.3 + - - +
82D VAL* 1.3 73.5 - - - +
84D GLY* 1.3 61.0 + - - +
86D ILE* 3.5 7.1 + - + +
87D THR* 2.7 34.9 + - - +
107D ILE* 3.8 32.4 - - + +
110D PRO 4.3 1.1 - - - -
111D TYR* 3.7 48.2 - - + +
114D LEU* 4.2 12.3 - - + -
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Residues in contact with GLY 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ARG 2.8 17.7 + - - -
81D LEU 3.7 0.9 - - - -
83D LEU* 1.3 78.3 - - - +
85D CYS* 1.3 56.3 + - - +
87D THR* 3.3 3.4 + - - -
88D MET* 3.0 33.3 + - - +
111D TYR* 3.5 22.3 - - - -
124D LEU* 3.9 17.9 - - - +
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Residues in contact with CYS 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ALA* 5.1 4.3 - - + -
46D LEU* 3.9 19.2 - - + +
81D LEU* 2.9 40.1 + - - +
82D VAL* 3.8 4.7 - - - +
84D GLY* 1.3 72.6 - - - +
86D ILE* 1.3 67.2 + - - +
88D MET 3.5 0.7 + - - -
89D ALA* 3.1 24.6 + - - +
124D LEU* 4.0 8.7 - - - +
129D CYS* 5.7 1.1 - - - -
133D ASN* 5.9 0.9 - - - -
152D PHE* 4.2 22.0 - - + -
153D SER 5.9 0.2 - - - -
154D PHE* 3.7 26.5 - - + -
164D PHE* 6.6 0.2 - - - -
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Residues in contact with ILE 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D TRP* 3.5 33.7 - - + +
42D ILE* 4.1 15.0 - - + -
43D ALA* 4.1 17.0 - - + +
46D LEU* 4.7 4.0 - - + -
55D LEU* 4.7 1.3 - - + +
59D VAL* 3.8 26.7 - - + -
62D LEU* 5.4 1.3 - - + -
82D VAL* 3.0 28.4 + - + +
83D LEU* 3.9 11.4 - - + +
85D CYS* 1.3 75.1 - - - +
87D THR* 1.3 57.8 + - - +
89D ALA* 3.8 5.0 - - - +
90D TYR* 3.0 27.1 + - + +
103D LEU* 6.5 0.2 - - + -
107D ILE* 4.2 22.0 - - + -
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Residues in contact with THR 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D LEU 2.7 24.3 + - - -
84D GLY* 3.5 4.9 - - - +
85D CYS 3.1 0.2 - - - -
86D ILE* 1.3 73.8 - - - +
88D MET* 1.3 68.8 + - - +
90D TYR* 3.1 2.9 + - - +
91D VAL* 2.9 25.6 + - + +
103D LEU* 3.8 33.0 - - + +
107D ILE* 4.0 5.6 - - - +
111D TYR* 3.4 28.7 - - + +
122D PRO 5.2 0.2 - - - +
123D ILE* 5.7 1.1 - - - -
237D TRP* 4.1 26.0 - - + -
247D LEU* 4.8 0.7 - - + -
249D TYR* 5.6 0.4 - - + -
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Residues in contact with MET 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D GLY 3.0 17.0 + - - +
85D CYS 4.0 3.1 - - - +
87D THR* 1.3 77.0 - - - +
89D ALA* 1.3 58.6 + - - +
91D VAL* 3.3 1.5 + - - -
92D TRP* 2.9 37.6 + - + +
123D ILE* 4.0 22.4 - - + -
124D LEU* 3.9 25.8 - - + +
154D PHE* 4.1 9.4 - - + -
233D TYR* 3.2 32.7 - - - +
234D LEU* 3.8 11.7 - - - +
235D SER 3.2 28.9 - - - +
237D TRP* 3.6 21.1 - - + -
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Residues in contact with ALA 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 3.7 21.8 - - + -
50D ILE* 3.9 13.0 - - + -
55D LEU* 3.4 22.7 - - + +
85D CYS 3.1 18.3 + - - +
86D ILE 3.8 2.0 - - - +
88D MET* 1.3 76.1 - - - +
90D TYR* 1.3 58.6 + - - +
93D GLY* 2.7 30.7 + - - +
154D PHE* 4.6 3.5 - - + -
233D TYR* 4.3 11.0 - - - -
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Residues in contact with TYR 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LEU* 3.5 6.9 - - + +
56D ARG* 3.0 58.2 + - + +
59D VAL* 3.8 27.1 - - + -
60D GLU* 2.6 38.6 + - + +
86D ILE 3.0 19.1 + - - +
87D THR 3.1 4.2 + - - +
89D ALA* 1.3 77.1 - - - +
91D VAL* 1.3 59.2 + - + +
100D ARG* 3.6 29.7 - - + +
102D VAL 3.4 14.3 + - - -
103D LEU* 4.1 14.1 - - + -
104D PRO* 3.4 30.0 - - + +
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Residues in contact with VAL 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ARG* 2.9 15.6 + - - -
87D THR* 2.9 21.9 + - + +
88D MET 3.9 2.7 - - - +
90D TYR* 1.3 82.9 - - + +
92D TRP* 1.3 82.9 + - + +
99D VAL* 3.1 7.3 - - + +
100D ARG 3.1 30.0 + - - +
102D VAL 6.4 0.2 - - - -
103D LEU* 4.9 2.5 - - + -
237D TRP* 3.9 24.5 - - + -
243D LEU* 4.1 12.3 - - + -
247D LEU* 4.1 26.5 - - + -
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Residues in contact with TRP 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ARG* 3.6 1.8 - - - -
88D MET* 2.9 26.0 + - - +
91D VAL* 1.3 88.0 - - + +
93D GLY* 1.3 65.1 + - - +
94D LYS 3.1 0.5 + - - -
95D GLY* 2.9 16.3 + - - -
96D HIS 4.5 1.0 + - - -
97D GLY 5.2 0.5 + - - -
98D ASP 3.7 9.5 + - - +
99D VAL* 3.6 30.0 - - + +
232D ILE* 3.4 33.9 + - + +
233D TYR* 4.0 24.2 - - + -
235D SER* 2.8 34.7 + - - -
236D GLY 3.4 11.4 - - - -
237D TRP* 3.9 15.7 - + - -
240D ASN* 3.6 23.6 - - - -
242D GLN* 4.1 21.3 - - + -
243D LEU* 4.6 10.3 - - + -
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Residues in contact with GLY 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ILE* 3.6 13.6 - - - +
55D LEU* 5.5 1.6 - - - -
56D ARG* 3.2 25.7 - - - +
89D ALA 2.7 25.8 + - - -
92D TRP* 1.3 70.8 - - - +
94D LYS* 1.3 51.7 + - - -
98D ASP 4.5 0.2 - - - -
233D TYR* 2.6 32.6 + - - -
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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) + - + + + + + -
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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