Contacts of the helix formed by residues 67 - 97 (chain D) in PDB entry 6C3P
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 67 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D LEU* 1.3 82.2 - - - +
68D TRP* 1.3 70.0 - - + +
69D PRO* 3.5 22.9 - - + +
70D HIS* 3.2 34.6 + - + +
71D THR* 3.1 18.5 + - - -
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Residues in contact with TRP 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PHE* 5.0 19.8 - + - -
56A LEU* 5.2 10.2 + - + -
57A GLN* 5.6 7.0 - - + +
60A PHE* 3.4 38.6 - + - -
162A ILE* 4.9 9.9 - - + -
66D LEU 3.4 2.4 + - - -
67D LYS* 1.3 71.9 - - + +
69D PRO* 1.3 72.6 - - + +
71D THR* 3.1 4.7 + - - -
72D LEU* 2.9 24.3 + - + +
167D ILE* 5.4 8.3 - - + -
170D LYS* 3.4 63.1 - - + +
171D THR* 4.2 2.0 - - - -
173D GLN* 5.5 3.1 - - + -
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Residues in contact with PRO 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LYS* 3.5 34.5 - - + +
68D TRP* 1.3 94.4 - - + +
70D HIS* 1.3 61.2 + - + +
72D LEU* 3.5 11.1 - - + +
73D LEU* 2.9 31.6 + - - +
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Residues in contact with HIS 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D LEU* 3.3 20.2 - - + -
67D LYS* 3.2 46.8 + - + +
69D PRO* 1.3 78.8 - - + +
71D THR* 1.3 58.9 + - - +
73D LEU* 3.3 7.4 + - + +
74D ILE* 2.9 37.4 + - + +
52H GLY* 3.4 42.1 + - - -
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Residues in contact with THR 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D LEU* 3.8 15.2 + - + +
66D LEU* 3.1 28.3 - - - +
67D LYS 3.1 7.0 + - - -
68D TRP* 3.6 7.2 - - + -
70D HIS* 1.3 73.6 - - - +
72D LEU* 1.3 65.6 + - - +
74D ILE* 3.1 10.0 + - - +
75D PHE* 3.0 50.9 + - + -
167D ILE* 5.0 3.8 - - + -
170D LYS* 3.7 29.4 + - + -
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 5.1 1.3 - - + -
158A MET* 3.7 35.4 - - + -
68D TRP 2.9 13.9 + - - +
69D PRO* 3.5 14.4 - - + +
71D THR* 1.3 75.0 - - - +
73D LEU* 1.3 69.0 + - + +
75D PHE* 3.1 6.7 + - - +
76D THR* 2.9 44.4 + - + +
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Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D PRO 2.9 20.4 + - - +
70D HIS* 3.6 8.5 - - + +
72D LEU* 1.3 80.1 - - + +
74D ILE* 1.3 64.3 + - + +
76D THR* 2.5 24.2 + - - +
77D MET* 2.9 39.2 + - + +
48H PHE* 4.6 19.7 - - + -
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Residues in contact with ILE 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D LEU* 4.5 15.7 - - + -
66D LEU* 4.8 11.9 - - + -
70D HIS* 2.9 27.9 + - + +
71D THR* 3.1 11.4 + - - +
73D LEU* 1.3 81.4 - - + +
75D PHE* 1.3 68.5 + - + +
77D MET* 3.8 3.4 - - - +
78D SER* 2.9 28.0 + - - -
45H PRO* 4.8 17.6 - - + +
48H PHE* 3.8 35.4 - - + +
49H ILE* 4.2 22.2 - - + -
52H GLY* 6.0 0.2 - - - -
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Residues in contact with PHE 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A MET* 4.1 20.2 - - + -
63D LEU* 3.5 29.8 - - + -
71D THR* 3.0 24.5 + - + +
72D LEU 3.7 5.6 - - - +
74D ILE* 1.3 80.7 - - + +
76D THR* 1.3 64.7 + - - +
78D SER* 2.3 26.1 + - - -
79D PHE* 3.0 14.9 + - + -
163D MET* 3.3 39.9 - - + -
166D CYS* 3.4 27.4 - - + -
167D ILE* 3.4 42.0 - - + -
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Residues in contact with THR 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 3.4 42.0 - - + -
158A MET* 5.3 1.3 - - + -
72D LEU* 2.9 34.9 + - + +
73D LEU* 2.5 29.5 + - - +
75D PHE* 1.3 76.4 - - + +
77D MET* 1.3 59.3 + - - +
79D PHE* 3.1 7.7 + - - +
80D LEU* 2.9 34.1 + - - +
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Residues in contact with MET 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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73D LEU* 2.9 25.5 + - + +
74D ILE* 4.0 3.8 - - - +
76D THR* 1.3 78.9 + - - +
78D SER* 1.3 61.0 + - - +
80D LEU* 3.6 9.1 - - + +
81D CYS* 2.9 32.0 + - + +
41H PHE* 6.1 2.9 - - + -
44H PHE* 3.5 38.4 - - + -
45H PRO* 5.1 5.8 - - + -
48H PHE* 3.4 37.7 - - + -
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Residues in contact with SER 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D ILE* 2.9 14.9 + - - -
75D PHE* 2.3 33.2 + - - -
77D MET* 1.3 76.1 - - - +
79D PHE* 1.3 58.7 + - - +
81D CYS* 3.0 14.0 - - - -
82D SER* 2.9 30.1 + - - -
159D ILE* 4.0 17.5 - - - +
163D MET* 3.6 17.7 - - - -
45H PRO* 4.4 12.9 - - - +
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Residues in contact with PHE 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 4.9 12.1 - - + -
157A LEU* 3.4 40.8 - - + -
158A MET* 4.7 13.5 - - + -
75D PHE 3.0 12.8 + - - -
76D THR* 3.1 9.2 + - - +
78D SER* 1.3 81.9 + - - +
80D LEU* 1.3 59.9 + - + +
82D SER* 3.4 1.7 + - - -
83D TRP* 2.9 59.9 + + + -
128D GLN* 4.8 7.4 - - - -
159D ILE* 4.2 28.7 - - + -
160D ASN* 4.8 13.0 - - + -
163D MET* 3.8 31.4 - - + -
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Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 3.9 30.5 - - + -
154A ILE* 3.6 25.8 - - + -
76D THR* 2.9 21.8 + - - +
77D MET* 3.6 15.9 - - + +
78D SER 3.3 0.2 - - - -
79D PHE* 1.3 77.1 - - - +
81D CYS* 1.3 56.9 + - - +
83D TRP* 3.2 8.9 + - + +
84D LEU* 2.9 46.2 + - + +
121D PHE* 4.6 11.0 - - + -
41H PHE* 6.1 0.7 - - + -
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Residues in contact with CYS 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 MET* 2.9 18.7 + - + +
78D SER* 3.0 29.4 - - - -
80D LEU* 1.3 75.5 - - - +
82D SER* 1.3 58.1 + - - +
84D LEU* 4.1 0.4 - - - +
85D LEU* 2.9 34.6 + - - +
159D ILE* 5.9 0.7 - - - -
41H PHE* 3.4 55.7 - - + +
44H PHE* 6.1 1.3 - - + -
45H PRO* 4.1 12.3 - - + -
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Residues in contact with SER 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D SER 2.9 17.9 + - - -
79D PHE* 3.8 3.4 - - - -
81D CYS* 1.3 81.7 - - - +
83D TRP* 1.3 61.0 + - - +
85D LEU* 4.1 3.8 - - - +
86D PHE* 3.1 40.7 + - - -
128D GLN* 2.7 34.5 + - - +
155D VAL* 4.3 8.1 - - - +
159D ILE* 4.2 12.8 - - - -
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Residues in contact with TRP 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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150A ILE* 3.9 32.1 - - + -
153A ASN* 3.9 23.3 - - + -
154A ILE* 4.4 8.1 - - + -
157A LEU* 4.9 4.9 - - + -
79D PHE* 2.9 46.3 + + + +
80D LEU* 3.7 16.8 - - + +
82D SER* 1.3 78.1 - - - +
84D LEU* 1.3 58.2 + - - +
85D LEU 3.3 0.2 + - - -
86D PHE 3.5 0.2 + - - -
87D ALA* 2.9 27.2 + - - +
121D PHE* 3.9 14.4 - + + -
124D SER* 3.6 13.0 - - - -
125D ILE* 3.9 26.9 - - + -
128D GLN* 2.9 45.4 - - + +
129D VAL* 3.4 23.4 - - + +
152D GLN* 5.0 0.2 - - - +
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Residues in contact with LEU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D LEU* 2.9 30.0 + - + +
81D CYS 4.1 2.2 - - - +
83D TRP* 1.3 76.6 - - - +
85D LEU* 1.3 63.3 + - - +
87D ALA* 3.3 4.1 - - - +
88D MET* 2.9 24.8 + - - +
117D PHE* 4.3 21.6 - - + -
121D PHE* 3.6 28.0 - - + -
37H VAL* 4.9 2.7 - - + +
41H PHE* 3.5 40.2 - - + -
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Residues in contact with LEU 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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81D CYS 2.9 19.4 + - - +
82D SER* 4.1 5.2 - - - +
84D LEU* 1.3 78.7 - - - +
86D PHE* 1.3 81.4 + - + +
88D MET* 3.2 4.9 + - - +
89D ALA* 3.0 26.1 + - + +
37H VAL* 4.6 12.3 - - + -
38H PHE* 4.2 43.5 - - + +
41H PHE* 4.8 11.6 - - + -
42H ILE* 5.4 4.7 - - + +
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Residues in contact with PHE 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D SER* 3.1 28.7 - - - +
83D TRP 3.5 1.2 + - - +
85D LEU* 1.3 91.4 - - + +
87D ALA* 1.3 60.2 + - - +
89D ALA* 3.3 7.9 - - + +
90D TRP* 2.8 35.5 + - - +
124D SER* 3.3 2.2 - - - -
128D GLN* 4.8 0.2 - - - -
148D ILE* 4.5 16.6 - - + -
151D VAL* 3.7 18.4 - - + -
152D GLN* 3.3 67.5 - - + +
155D VAL* 4.0 33.9 - - + -
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Residues in contact with ALA 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D TRP 2.9 16.0 + - - +
84D LEU* 3.1 10.1 + - - +
86D PHE* 1.3 74.4 - - - +
88D MET* 1.3 65.9 + - - +
90D TRP 3.3 0.2 + - - -
91D TRP* 2.9 26.0 + - - +
117D PHE* 3.7 9.9 - - + -
120D ALA* 3.5 6.2 - - - +
121D PHE* 3.6 40.2 - - + -
124D SER* 3.0 9.8 + - - +
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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
----------------------------------------------------------
84D LEU 2.9 12.2 + - - +
85D LEU 3.4 9.4 - - - +
87D ALA* 1.3 75.5 - - - +
89D ALA* 1.3 58.0 + - - +
91D TRP* 3.5 34.2 - - + +
92D LEU* 2.9 32.9 + - - +
117D PHE* 3.6 22.0 - - + -
30H ALA 5.4 0.4 - - - +
33H VAL* 4.4 13.7 - - + -
34H VAL* 4.1 29.4 - - + -
37H VAL* 3.8 37.9 - - + -
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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
----------------------------------------------------------
85D LEU* 3.0 16.0 + - + +
86D PHE* 3.3 18.4 - - + +
87D ALA 3.1 0.4 - - - -
88D MET* 1.3 78.4 - - - +
90D TRP* 1.3 62.3 + - - +
92D LEU* 3.6 7.2 - - - +
93D ILE* 2.9 29.7 + - + +
148D ILE* 4.5 25.6 - - + -
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Residues in contact with TRP 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D PHE 2.8 30.2 + - - +
87D ALA 3.9 2.7 - - - +
89D ALA* 1.3 73.2 - - - +
91D TRP* 1.3 63.8 + - - +
93D ILE* 3.1 9.5 + - + +
94D ALA* 2.9 23.8 + - - +
110D CYS* 6.2 0.4 - - + -
111D VAL* 4.9 13.4 - - + +
114D ILE* 4.3 5.8 - - + +
120D ALA* 4.1 11.4 - - + -
123D PHE* 3.3 38.9 - + + -
124D SER* 3.1 17.2 + - - +
127D VAL* 5.1 0.2 - - + -
138D VAL* 4.4 9.2 - - + -
145D ALA* 3.1 46.4 - - + -
148D ILE* 3.4 24.2 - - + +
149D LEU* 3.5 28.0 - - + -
152D GLN* 2.8 23.2 + - - -
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Residues in contact with TRP 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ALA 2.9 17.7 + - - +
88D MET* 3.5 33.9 - - + +
90D TRP* 1.3 76.7 - - - +
92D LEU* 1.3 75.0 + - + +
94D ALA* 3.3 7.0 + - + +
95D PHE* 2.9 30.5 + + + +
100D LEU* 3.7 27.2 - - + +
114D ILE* 4.8 2.2 - - + -
116D SER* 4.2 5.9 - - - +
117D PHE* 3.7 42.8 - + + +
120D ALA* 3.5 13.8 - - + +
5H PHE* 3.8 41.5 - + + -
30H ALA* 3.9 24.9 - - + -
33H VAL* 6.3 1.1 - - + -
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Residues in contact with LEU 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D MET 2.9 19.4 + - - +
89D ALA* 3.6 7.9 - - - +
91D TRP* 1.3 83.6 - - + +
93D ILE* 1.3 65.3 + - + +
95D PHE* 3.2 6.7 + - + +
96D ALA* 2.8 28.9 + - + +
27H PHE* 4.0 26.9 - - + -
30H ALA* 4.7 10.1 - - + -
31H LEU* 4.0 28.9 - - + +
34H VAL* 3.6 33.2 - - + -
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Residues in contact with ILE 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D ALA* 2.9 22.7 + - - +
90D TRP* 3.6 13.9 - - + +
92D LEU* 1.3 81.1 - - + +
94D ALA* 1.3 66.6 + - - +
96D ALA* 3.2 8.1 + - + +
97D HIS* 2.9 23.0 + - - +
110D CYS* 3.7 27.8 - - + -
142D CYS* 5.1 0.9 - - + -
144D LEU* 3.7 30.1 - - + -
145D ALA* 4.5 14.8 - - + +
148D ILE* 4.6 13.5 - - + -
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Residues in contact with ALA 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D TRP 2.9 7.0 + - - +
91D TRP* 3.7 6.7 - - + +
93D ILE* 1.3 78.3 - - - +
95D PHE* 1.3 59.8 + - - +
97D HIS* 3.5 4.9 + - - -
99D ASP* 3.0 43.3 + - + +
100D LEU* 4.0 10.0 + - + -
110D CYS* 5.1 5.4 - - - +
111D VAL* 5.0 4.2 - - + +
114D ILE* 3.4 37.9 - - + -
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Residues in contact with PHE 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D TRP* 2.9 27.3 + + + +
92D LEU* 3.7 7.9 - - + +
94D ALA* 1.3 77.2 - - - +
96D ALA* 1.3 64.0 + - - +
98D GLY* 3.2 10.4 + - - -
99D ASP 4.8 0.7 - - - +
100D LEU* 3.5 27.8 - - + +
5H PHE* 5.3 4.5 - + - -
6H CYS* 5.1 0.2 - - - -
16H ARG* 3.4 40.1 - - + +
18H ASP* 3.6 9.7 - - - +
24H ASN* 3.6 20.9 - - - -
26H CYS* 3.8 16.6 - - + -
27H PHE* 3.4 52.5 - + + -
30H ALA* 5.0 9.4 - - + -
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Residues in contact with ALA 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D LEU* 2.8 17.5 + - + +
93D ILE* 3.2 9.4 + - + +
95D PHE* 1.3 72.3 - - - +
97D HIS* 1.3 58.9 + - - +
98D GLY 3.0 5.2 - - - -
18H ASP* 3.0 16.4 - - - +
21H VAL* 4.0 17.4 - - + +
27H PHE* 3.5 30.0 - - + -
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Residues in contact with HIS 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ILE 2.9 16.4 + - - +
94D ALA 3.8 6.3 - - - +
95D PHE 3.3 0.4 - - - -
96D ALA* 1.3 74.8 - - - +
98D GLY* 1.3 62.3 + - - +
99D ASP* 3.6 19.3 + - + +
107D ALA* 4.9 12.3 - - + -
108D GLU 3.1 27.7 + - - -
109D PRO* 4.1 4.0 - - + -
110D CYS* 3.5 13.9 + - - -
141D GLU* 4.7 7.3 + - - +
142D CYS* 3.3 27.7 - - - -
18H ASP* 3.9 0.9 - - - -
----------------------------------------------------------
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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