Contacts of the helix formed by residues 65 - 92 (chain D) in PDB entry 3AEF
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 CYS 65 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ASN* 3.3 27.0 + - - +
64D PRO* 1.3 75.1 - - - +
66D SER* 1.3 65.8 + - - +
67D ALA* 4.0 10.3 - - - +
68D MET* 3.6 27.8 - - - +
69D ASP* 3.0 26.8 + - - +
127D CYS* 4.4 0.7 - - - +
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Residues in contact with SER 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D CYS* 1.3 72.7 - - - +
67D ALA* 1.3 56.5 + - - +
68D MET 3.0 4.3 - - - -
69D ASP* 2.6 39.5 + - - +
70D TYR* 3.0 33.3 + - - -
120D ASN* 4.9 6.4 + - - +
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Residues in contact with ALA 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D CYS* 3.6 10.8 - - - -
66D SER* 1.3 77.9 - - - +
68D MET* 1.3 58.5 + - + +
70D TYR* 3.7 8.3 + - - +
71D SER* 2.7 36.7 + - - -
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Residues in contact with MET 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D LEU* 3.8 26.0 - - + -
59D ALA* 4.5 10.3 - - + -
60D ALA* 3.6 30.1 - - + +
63D ASN* 3.5 25.8 - - - +
65D CYS* 3.6 29.0 + - - +
66D SER 3.0 0.2 - - - -
67D ALA* 1.3 86.5 - - + +
69D ASP* 1.3 62.2 + - - +
71D SER* 4.2 4.6 - - - +
72D LEU* 3.3 27.5 + - - +
127D CYS* 4.5 3.8 - - - -
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Residues in contact with ASP 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D CYS 3.0 15.7 - - - +
66D SER* 2.6 25.6 + - - +
68D MET* 1.3 72.3 - - - +
70D TYR* 1.3 56.3 + - + +
72D LEU* 3.6 6.8 + - - +
73D ALA* 3.1 20.1 + - - +
120D ASN* 3.4 31.1 + - + +
124D VAL 4.9 1.7 - - - +
125D GLY* 4.2 9.6 - - - -
126D ILE* 3.4 16.9 + - - +
127D CYS* 2.9 40.7 + - - +
128D LYS 5.5 0.2 + - - -
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Residues in contact with TYR 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D SER* 3.0 44.2 + - - +
67D ALA* 4.3 6.5 - - - +
69D ASP* 1.3 73.1 - - - +
71D SER* 1.3 55.2 + - - +
72D LEU 3.1 1.6 - - - -
73D ALA* 2.9 4.7 + - - +
74D ALA* 2.7 35.9 + - - +
113D PHE* 4.7 2.2 - - + -
117D CYS* 3.8 33.0 - - + -
120D ASN* 3.5 27.4 - - + +
121D TYR* 3.2 39.9 + - + +
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Residues in contact with SER 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D LEU* 3.7 26.6 - - - +
67D ALA* 2.7 22.7 + - - +
68D MET* 4.2 6.4 - - - +
70D TYR* 1.3 76.8 - - - +
72D LEU* 1.3 52.8 + - - +
74D ALA* 3.3 6.2 + - - +
75D ALA* 2.8 38.1 + - - +
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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
----------------------------------------------------------
53D LEU* 4.8 5.8 - - + -
56D LEU* 3.8 34.1 - - + +
57D LEU* 3.8 21.1 - - + -
60D ALA* 4.2 15.9 - - + -
68D MET 3.3 18.8 + - - +
69D ASP 3.6 5.4 - - - +
70D TYR 3.1 0.2 - - - -
71D SER* 1.3 79.9 - - - +
73D ALA* 1.3 57.2 + - - +
76D LEU* 2.8 42.1 + - + +
126D ILE* 3.7 33.4 - - + -
127D CYS* 4.7 4.5 - - - -
1306D EPH 4.0 21.1 - - + -
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Residues in contact with ALA 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D ASP 3.1 14.1 + - - +
70D TYR* 2.9 11.2 + - - +
72D LEU* 1.3 74.1 - - - +
74D ALA* 1.3 67.3 + - - +
77D THR* 3.1 29.3 + - - +
113D PHE* 3.9 14.4 - - + -
116D LEU* 3.9 34.1 - - + -
117D CYS* 4.9 2.2 - - - +
120D ASN* 4.0 10.1 - - - +
126D ILE* 4.3 2.6 - - + +
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Residues in contact with ALA 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D TYR 2.7 15.7 + - - +
71D SER* 3.6 10.1 - - - +
73D ALA* 1.3 73.9 - - - +
75D ALA* 1.3 59.3 + - - +
77D THR* 3.7 2.1 + - - -
78D LEU* 2.9 33.3 + - - +
113D PHE* 3.6 20.8 - - + -
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Residues in contact with ALA 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D VAL* 5.2 10.4 - - + +
52D LEU* 5.3 8.3 - - + -
53D LEU* 3.8 18.2 - - + +
56D LEU* 3.7 22.9 - - + -
71D SER 2.8 20.8 + - - +
72D LEU 4.4 0.2 - - - +
74D ALA* 1.3 72.9 - - - +
76D LEU* 1.3 57.5 + - - +
78D LEU* 4.5 4.5 - - - -
79D HIS* 2.8 36.0 + - - +
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Residues in contact with LEU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C VAL* 3.8 34.9 - - + +
1305C HEM 3.9 32.9 - - + +
53D LEU* 3.6 24.8 - - + +
57D LEU* 5.2 4.0 - - + -
72D LEU* 2.8 30.7 + - + +
73D ALA* 4.0 2.5 - - - +
75D ALA* 1.3 76.9 - - - +
77D THR* 1.3 57.8 + - + +
79D HIS* 4.1 0.9 - - - +
80D GLY* 3.0 24.8 + - - -
116D LEU* 4.8 4.5 - - + -
126D ILE* 4.9 4.7 - - + -
1306D EPH 3.9 36.1 - - + -
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Residues in contact with THR 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C VAL* 4.5 3.6 - - + -
73D ALA 3.1 19.3 + - - +
74D ALA 3.7 2.1 + - - -
76D LEU* 1.3 74.7 - - - +
78D LEU* 1.3 58.0 + - - +
80D GLY* 4.7 1.3 - - - -
81D HIS* 2.6 37.0 + - - +
109D SER* 4.6 9.1 + - - -
112D THR* 3.7 25.4 - - + -
113D PHE* 3.5 28.8 - - - +
116D LEU* 3.6 24.9 - - + -
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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
----------------------------------------------------------
49D VAL* 3.8 20.6 - - + -
74D ALA 2.9 19.9 + - - +
75D ALA* 4.0 3.6 - - - +
77D THR* 1.3 75.5 + - - +
79D HIS* 1.3 66.2 + - - +
81D HIS* 3.3 9.8 + - + +
82D TRP* 3.0 72.3 + - + +
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Residues in contact with HIS 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1305C HEM 2.1 85.6 + + + -
46D GLU* 4.7 1.0 + - - +
49D VAL* 4.1 19.7 - - + +
50D SER* 3.3 31.4 + - - -
53D LEU* 3.7 19.9 - - + +
75D ALA 2.8 22.4 + - - +
76D LEU 4.1 0.7 - - - +
78D LEU* 1.3 72.6 - - - +
80D GLY* 1.3 62.9 + - - +
82D TRP* 3.3 4.2 + - - +
83D GLY* 3.0 20.6 + - - -
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Residues in contact with GLY 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C SER* 3.7 21.0 + - - -
1305C HEM 4.4 9.6 - - - -
76D LEU 3.0 19.2 + - - -
77D THR* 3.7 1.8 - - - -
79D HIS* 1.3 77.7 - - - +
81D HIS* 1.3 62.5 + - - +
83D GLY* 3.2 1.6 + - - -
84D ILE* 3.1 30.0 + - - +
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Residues in contact with HIS 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D THR 2.6 23.2 + - - +
78D LEU* 3.6 12.1 - - + +
80D GLY* 1.3 73.9 - - - +
82D TRP* 1.3 80.2 + + - +
85D GLY* 3.1 17.7 + - - -
102D LYS* 5.0 4.2 - - + +
105D LEU* 3.6 43.3 - - + +
106D LEU* 3.9 28.2 - - + +
109D SER* 2.6 30.6 + - - +
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Residues in contact with TRP 82 (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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42D HIS* 3.3 36.1 + + - -
45D GLY* 3.7 16.2 - - - -
46D GLU* 3.6 51.8 - - + +
49D VAL* 3.9 20.4 - - + -
78D LEU* 3.0 48.5 + - + +
79D HIS* 4.0 3.1 - - - +
81D HIS* 1.3 92.5 - + - +
83D GLY* 1.3 64.6 + - - +
85D GLY* 3.3 3.0 + - - -
86D GLN* 3.2 26.0 + - - +
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Residues in contact with GLY 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1305C HEM 3.5 39.1 - - - +
79D HIS* 3.0 13.5 + - - -
80D GLY 3.2 2.9 + - - -
82D TRP* 1.3 73.8 - - - +
84D ILE* 1.3 65.4 + - - +
86D GLN* 3.1 19.3 + - - +
87D VAL* 3.2 8.5 + - - +
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Residues in contact with ILE 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ILE* 4.2 25.8 - - + +
53C SER* 4.4 16.6 - - - -
1305C HEM 3.8 18.3 - - + +
80D GLY 3.1 13.8 + - - +
83D GLY* 1.3 71.1 - - - +
85D GLY* 1.3 56.4 + - - +
87D VAL* 3.0 11.4 + - + +
88D VAL* 2.7 46.2 + - + +
105D LEU* 3.7 34.3 - - + -
108D LEU* 6.2 2.0 - - + -
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Residues in contact with GLY 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D HIS 3.1 15.1 + - - -
82D TRP* 3.5 7.4 - - - -
83D GLY 3.1 1.2 - - - -
84D ILE* 1.3 75.8 - - - +
86D GLN* 1.3 49.4 + - - +
88D VAL* 3.2 2.8 + - - +
89D THR* 2.5 43.7 + - - +
102D LYS* 3.9 12.0 - - - -
105D LEU* 3.5 11.3 - - - +
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Residues in contact with GLN 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TYR* 5.4 3.2 + - - +
214B ARG* 2.7 38.8 + - - +
216B HIS* 4.4 9.4 - - + -
46C ARG* 4.2 5.8 - - - +
1305C HEM 4.1 14.4 - - - +
42D HIS* 3.9 12.5 + - - -
43D TRP* 5.9 1.8 - - - -
46D GLU* 2.7 36.2 + - - +
47D ARG* 5.2 1.6 - - - +
82D TRP 3.2 13.4 + - - +
83D GLY* 3.1 9.5 + - - +
85D GLY* 1.3 73.1 - - - +
87D VAL* 1.3 56.9 + - - +
89D THR* 3.3 6.5 + - - +
90D ASP* 2.9 35.2 + - - -
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Residues in contact with VAL 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ARG* 3.2 37.5 - - - +
50C ILE* 4.3 23.6 - - + -
1305C HEM 4.2 9.2 - - + -
83D GLY 3.2 11.0 + - - +
84D ILE* 3.0 17.6 + - + +
86D GLN* 1.3 72.5 - - - +
88D VAL* 1.3 71.0 + - + +
90D ASP* 3.3 1.1 + - - +
91D TYR* 3.1 45.5 + - + +
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Residues in contact with VAL 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D ILE* 2.7 37.8 + - + +
85D GLY 3.5 3.6 - - - +
87D VAL* 1.3 75.6 - - + +
89D THR* 1.3 59.9 + - - +
90D ASP 3.1 0.2 + - - -
92D VAL* 2.8 49.8 + - + +
98D GLN* 4.2 9.4 - - + -
101D ALA* 3.8 33.0 - - + -
102D LYS* 4.2 18.8 - - - +
105D LEU* 4.9 6.7 - - + -
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Residues in contact with THR 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ASN* 4.3 1.7 + - - -
209B PRO* 5.0 5.2 - - + +
210B PHE* 3.8 29.6 - - - -
214B ARG* 3.3 24.3 + - - +
85D GLY 2.5 39.0 + - - +
86D GLN* 3.3 12.3 + - - +
88D VAL* 1.3 75.4 - - - +
90D ASP* 1.3 59.9 + - - +
92D VAL 4.7 3.0 + - - +
93D ARG* 6.1 0.2 - - - -
98D GLN* 3.2 20.6 - - - +
102D LYS* 3.6 19.1 - - - +
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Residues in contact with ASP 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B SER* 5.6 2.9 - - - -
173B TRP* 4.2 7.5 - - + +
174B ASN* 2.7 28.1 + - - +
214B ARG* 2.7 35.6 + - - +
216B HIS* 2.7 26.3 + - - -
46C ARG* 2.8 21.3 + - - +
86D GLN 2.9 15.7 + - - +
87D VAL 3.6 5.4 - - - +
88D VAL 3.1 0.2 - - - -
89D THR* 1.3 79.5 - - - +
91D TYR* 1.3 77.9 + - + +
92D VAL 5.4 0.2 - - - -
93D ARG* 4.5 4.9 - - - -
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Residues in contact with TYR 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B TRP* 3.5 40.8 + + + -
46C ARG* 3.1 36.2 + - - +
50C ILE* 6.0 1.8 - - + -
87D VAL* 3.1 34.6 + - + +
90D ASP* 1.3 86.0 - - + +
92D VAL* 1.3 64.9 + - + +
93D ARG* 3.3 16.1 + - - +
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Residues in contact with VAL 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D VAL* 2.8 47.4 + - + +
89D THR 4.9 2.5 - - - +
90D ASP 3.7 0.6 - - - -
91D TYR* 1.3 75.2 - - + +
93D ARG* 1.3 59.3 + - - +
94D GLY 3.8 1.0 + - - -
97D LEU* 3.8 42.0 - - + +
98D GLN* 3.8 30.5 - - + +
101D ALA* 4.6 8.1 - - + -
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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