Contacts of the helix formed by residues 42 - 70 (chain D) in PDB entry 1NF6
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 TYR 42 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LEU* 2.9 19.5 + - + +
38D ASP* 4.8 0.9 - - - +
40D MET* 3.5 45.8 - - + -
41D ASP* 1.3 79.6 - - - +
43D GLY* 1.3 54.2 + - - +
44D GLU 3.5 1.8 - - - -
45D LEU* 3.1 16.5 + - + -
46D ALA* 2.9 34.6 + - - +
88D VAL* 4.7 3.6 - - + -
151D ASP* 5.5 0.7 + - - -
154D LEU* 3.6 52.9 - - + +
157D ILE* 3.8 17.3 - - + -
158D ALA* 3.9 22.0 - - + -
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Residues in contact with GLY 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ASP* 4.9 0.7 - - - -
41D ASP* 3.4 7.6 + - - -
42D TYR* 1.3 71.0 - - - +
44D GLU* 1.3 62.9 + - - +
46D ALA* 3.1 4.2 + - - +
47D ALA* 2.9 25.5 + - - +
160D THR* 3.2 29.4 + - - -
161D PRO 3.3 9.2 - - - -
162D SER* 3.6 15.4 - - - -
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Residues in contact with GLU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D TYR 3.5 0.2 - - - -
43D GLY* 1.3 72.5 - - - +
45D LEU* 1.3 63.9 + - + +
47D ALA* 4.1 3.8 - - - +
48D ASN* 3.3 44.4 + - - +
156D LYS* 5.6 1.7 - - - -
157D ILE* 3.7 27.0 - - + +
160D THR* 2.8 24.4 + - - +
161D PRO 3.5 6.0 + - - +
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Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LEU* 3.7 16.4 - - + +
42D TYR* 3.1 19.5 + - + +
44D GLU* 1.3 78.0 - - + +
46D ALA* 1.3 65.4 + - - +
48D ASN* 4.1 0.7 - - - +
49D MET* 3.0 25.6 + - - +
88D VAL* 5.3 0.9 - - + -
92D TYR* 3.3 29.6 + - + +
138D TYR* 3.8 17.2 + - - +
142D ILE* 3.9 26.0 - - + -
146D ILE* 5.0 0.7 - - + -
153D TYR* 4.0 10.8 - - + +
154D LEU* 4.0 26.9 - - + -
157D ILE* 4.1 17.5 - - + +
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Residues in contact with ALA 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D HIS* 2.8 31.1 + - + +
37D LEU* 3.9 9.3 - - - +
38D ASP* 3.4 44.4 - - - +
42D TYR 2.9 17.2 + - - +
43D GLY 3.6 3.1 - - - +
45D LEU* 1.3 78.1 - - - +
47D ALA* 1.3 62.5 + - - +
49D MET* 3.4 1.9 + - - +
50D LYS 3.2 10.9 + - - -
162D SER* 4.6 0.9 - - - -
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Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D HIS* 5.1 0.4 - - - -
43D GLY 2.9 13.8 + - - +
44D GLU* 4.1 6.5 - - + +
46D ALA* 1.3 76.3 - - - +
48D ASN* 1.3 59.5 + - - +
50D LYS* 3.0 7.8 + - - +
51D LEU* 2.9 33.4 + - + +
161D PRO 4.9 1.1 - - - +
162D SER* 3.3 29.3 + - - +
163D SER 3.9 10.5 - - - +
164D THR* 3.7 10.5 - - + +
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Residues in contact with ASN 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C PHE* 3.6 20.1 - - + -
44D GLU* 3.3 33.2 + - - +
45D LEU 4.2 0.2 - - - +
47D ALA* 1.3 77.6 - - - +
49D MET* 1.3 64.1 + - - +
51D LEU* 3.5 22.4 - - - +
52D ILE* 3.0 31.2 + - - +
138D TYR* 3.2 34.5 + - + +
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Residues in contact with MET 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR* 3.2 29.5 - - - +
33D GLN* 3.3 18.2 - - + +
34D HIS* 3.8 13.0 - - + +
37D LEU* 4.1 6.7 - - + -
45D LEU 3.0 18.2 + - - +
46D ALA 3.7 4.5 - - - +
47D ALA 3.2 0.2 - - - -
48D ASN* 1.3 77.9 - - - +
50D LYS* 1.3 58.4 + - - +
52D ILE* 3.4 5.4 + - - +
53D ALA* 3.0 25.6 + - - +
91D ILE* 3.7 16.8 - - + -
92D TYR* 4.0 15.0 - - + +
95D ASP* 3.3 17.5 - - - +
138D TYR* 5.0 3.0 + - + -
139D TYR* 3.2 36.3 - - + -
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Residues in contact with LYS 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C GLU* 3.0 27.3 + - - +
1305C FEC 2.5 49.8 + - + -
31D MET* 4.0 15.3 - - + -
34D HIS* 3.7 20.4 + - + +
46D ALA 3.2 10.1 + - - +
47D ALA 3.0 9.3 + - - +
49D MET* 1.3 78.4 - - - +
51D LEU* 1.3 59.2 + - - +
53D ALA* 3.2 6.7 + - - +
54D ILE* 2.9 39.1 + - + +
164D THR* 3.6 9.8 + - + -
1401D SO4 2.5 35.4 + - - +
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Residues in contact with LEU 51 (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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169C LYS* 3.7 23.8 - - + +
170C GLY* 3.5 18.8 - - - +
171C PHE* 3.3 27.2 + - + +
47D ALA* 2.9 20.2 + - + +
48D ASN* 3.5 26.7 - - - +
50D LYS* 1.3 75.3 - - - +
52D ILE* 1.3 63.8 + - - +
54D ILE* 3.2 6.3 + - + +
55D ASP 3.0 15.6 + - - -
164D THR* 3.9 33.2 - - + +
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Residues in contact with ILE 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C PHE* 3.4 28.5 - - + -
30D TYR* 4.0 15.0 - - + -
48D ASN 3.0 21.9 + - - +
49D MET 3.7 3.6 - - - +
51D LEU* 1.3 75.6 - - - +
53D ALA* 1.3 66.3 + - - +
55D ASP* 2.9 15.0 + - - +
56D GLU* 3.1 12.0 + - - +
135D HIS* 3.9 30.5 - - + +
138D TYR* 3.6 33.2 - - + -
139D TYR* 3.4 32.8 - - + +
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Residues in contact with ALA 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ILE* 4.2 6.8 - - - +
30D TYR* 4.1 15.5 - - + -
31D MET* 3.7 32.1 - - + -
49D MET 3.0 14.6 + - - +
50D LYS 3.2 9.1 + - - +
52D ILE* 1.3 76.6 - - - +
54D ILE* 1.3 58.4 + - - +
56D GLU* 3.1 12.0 + - - +
57D MET* 2.9 35.2 + - + +
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Residues in contact with ILE 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C SER* 3.6 25.7 + - - +
169C LYS 3.5 27.8 - - - +
170C GLY* 4.4 0.9 - - - -
1305C FEC 4.0 27.5 - - + -
50D LYS* 2.9 44.2 + - + +
51D LEU* 3.6 12.1 - - + +
52D ILE 3.1 0.4 - - - -
53D ALA* 1.3 77.8 - - - +
55D ASP* 1.3 61.0 + - - +
57D MET* 3.4 26.3 + - + +
58D ARG* 3.2 20.3 + - - +
164D THR* 5.3 3.1 - - - +
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Residues in contact with ASP 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C GLY* 3.3 1.0 - - - -
171C PHE* 3.1 21.4 + - - +
172C VAL* 3.0 27.0 + - - +
51D LEU 3.0 7.1 + - - -
52D ILE 2.9 9.4 + - - +
54D ILE* 1.3 77.5 - - - +
56D GLU* 1.3 62.5 + - - +
58D ARG* 2.9 39.2 + - - +
59D HIS* 3.0 30.1 + - - +
135D HIS* 2.7 34.5 + - + -
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Residues in contact with GLU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLU* 3.2 21.7 - - - +
26D ALA* 3.9 17.8 - - + +
27D ILE* 3.9 15.5 - - + -
30D TYR* 3.7 13.3 - - + -
52D ILE 3.1 14.5 + - - +
53D ALA* 3.1 6.9 + - - +
55D ASP* 1.3 72.7 - - - +
57D MET* 1.3 59.9 + - - +
59D HIS* 2.9 25.8 + - - +
60D ALA* 2.8 30.8 + - - +
99D GLU* 3.3 11.1 - - - +
132D GLU* 3.3 3.6 - - - +
135D HIS* 3.5 3.6 + - - -
200D FE 2.1 30.2 - - - -
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Residues in contact with MET 57 (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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1305C FEC 2.4 101.5 - - + +
27D ILE* 3.7 31.1 - - + +
31D MET* 4.4 6.5 - - + -
53D ALA* 2.9 30.1 + - + +
54D ILE* 3.5 27.8 - - + +
55D ASP 3.2 0.2 - - - -
56D GLU* 1.3 77.3 - - - +
58D ARG* 1.3 56.4 + - - +
60D ALA* 3.5 2.1 + - - +
61D GLU* 3.1 27.5 + - - +
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Residues in contact with ARG 58 (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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167C ALA* 5.1 8.7 - - - +
168C SER* 2.9 42.5 + - - +
170C GLY* 4.0 5.9 - - - +
172C VAL* 4.2 10.7 + - - +
1305C FEC 5.4 2.9 - - + +
54D ILE 3.2 6.0 + - - +
55D ASP* 2.9 45.0 + - - +
57D MET* 1.3 75.4 - - - +
59D HIS* 1.3 62.7 + - + +
61D GLU* 3.4 19.2 + - - +
62D ASN* 2.8 43.7 + - - +
127D ARG* 4.2 17.5 - - - +
131D GLU* 3.7 20.8 + - - -
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Residues in contact with HIS 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLU* 2.7 35.2 + - + +
55D ASP* 3.0 25.5 + - - +
56D GLU* 2.9 23.5 + - - +
58D ARG* 1.3 79.0 - - + +
60D ALA* 1.3 66.0 + - - +
62D ASN* 3.0 1.7 + - - +
63D PHE* 2.8 30.9 + - + -
127D ARG* 4.9 3.1 - - - -
128D ILE* 3.7 39.8 - - + +
131D GLU* 2.6 38.6 + - + +
132D GLU* 3.3 15.9 - - - -
135D HIS* 4.2 2.9 - + - -
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Residues in contact with ALA 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1305C FEC 4.7 4.0 - - + -
20D ARG* 2.9 37.5 + - + +
23D GLU* 3.8 19.2 - - + +
24D LEU* 4.5 7.2 - - + -
27D ILE* 4.3 13.0 - - + -
56D GLU 2.8 19.2 + - - +
57D MET* 3.7 5.8 - - - +
59D HIS* 1.3 73.3 - - - +
61D GLU* 1.3 57.7 + - - +
63D PHE* 3.5 3.0 + - - +
64D ALA 3.0 19.6 + - - -
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Residues in contact with GLU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C HIS* 4.3 6.1 + - - +
35C TYR* 3.5 22.8 + - + +
50C LYS* 2.8 39.6 + - - +
1305C FEC 3.5 22.9 - - + +
57D MET 3.1 17.6 + - - +
58D ARG* 3.5 21.0 - - - +
60D ALA* 1.3 74.1 - - - +
62D ASN* 1.3 64.7 + - - +
64D ALA* 3.5 1.2 + - - +
65D GLU* 2.9 50.2 + - - +
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Residues in contact with ASN 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D ARG* 2.8 40.9 + - - +
59D HIS* 3.9 6.5 - - - +
61D GLU* 1.3 77.9 - - - +
63D PHE* 1.3 62.1 + - - +
65D GLU* 3.0 19.0 + - - +
66D ARG* 2.8 32.1 + - - +
124D LEU* 4.0 22.6 - - + +
127D ARG* 3.1 30.8 - - - +
128D ILE* 4.5 2.0 - - + +
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Residues in contact with PHE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LEU* 3.7 24.5 - - + +
19D ALA* 3.6 20.4 - - + -
20D ARG* 3.9 22.9 - - + -
23D GLU* 3.6 30.3 - - + -
59D HIS 2.8 24.1 + - - +
60D ALA 3.6 4.7 - - - +
62D ASN* 1.3 78.1 - - - +
64D ALA* 1.3 55.4 + - - +
66D ARG* 3.2 2.6 + - - +
67D ILE* 2.9 35.0 + - - +
106D TYR* 3.7 13.2 - + - -
124D LEU* 4.3 12.6 - - + -
125D PHE* 3.7 28.0 - + - -
128D ILE* 3.7 25.4 - - + -
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Residues in contact with ALA 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TYR* 3.7 23.1 - - + -
20D ARG* 3.5 17.2 - - - +
60D ALA 3.0 18.6 + - - +
61D GLU 3.7 5.8 - - - +
63D PHE* 1.3 74.3 - - - +
65D GLU* 1.3 64.2 + - - +
67D ILE* 3.3 12.2 + - - +
68D LYS* 3.1 26.9 + - - +
74D PRO* 3.9 13.6 - - + +
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Residues in contact with GLU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C HIS* 4.9 4.7 + - - -
35C TYR* 4.4 14.6 - - + -
38C ASP* 3.8 20.5 - - - +
61D GLU* 2.9 39.6 + - - +
62D ASN* 3.0 25.0 + - - +
64D ALA* 1.3 76.2 - - - +
66D ARG* 1.3 59.1 + - - +
68D LYS* 3.2 9.1 + - - +
69D GLU* 3.0 33.7 + - + +
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Residues in contact with ARG 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LEU* 3.9 12.3 - - + -
62D ASN 2.8 16.0 + - - +
63D PHE 3.7 3.4 - - - +
65D GLU* 1.3 75.8 - - - +
67D ILE* 1.3 62.7 + - - +
69D GLU* 2.6 46.8 + - - +
70D LEU* 3.3 39.9 + - - +
118D ASP* 3.2 22.6 + - - -
120D VAL* 3.6 25.4 - - + +
121D THR* 3.1 21.8 + - + +
124D LEU* 3.6 25.6 - - + -
133E GLN* 3.0 21.4 + - - -
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Residues in contact with ILE 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ILE* 3.9 13.0 - - + +
16D LEU* 3.5 35.7 - - + +
17D ASN* 3.5 28.3 - - - +
20D ARG* 4.1 4.7 - - - -
63D PHE 2.9 28.4 + - - +
64D ALA* 3.6 6.5 - - - +
65D GLU 3.2 0.2 - - - -
66D ARG* 1.3 77.8 - - - +
68D LYS* 1.3 59.7 + - - +
70D LEU* 3.3 10.9 + - - +
71D GLY 3.3 0.2 + - - -
72D GLY* 2.9 48.8 + - - -
73D GLU 3.6 6.3 - - - +
74D PRO* 3.7 18.8 - - + -
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Residues in contact with LYS 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ASN 5.3 0.4 - - - -
35C TYR* 3.8 32.5 - - + +
36C SER* 3.6 22.6 + - - +
39C ASP* 3.6 46.2 + - + +
64D ALA 3.1 14.8 + - - +
65D GLU* 3.3 13.0 - - - +
67D ILE* 1.3 75.1 - - - +
69D GLU* 1.3 64.8 + - + +
71D GLY* 2.9 14.7 + - - -
72D GLY 4.0 11.1 + - - +
73D GLU* 4.0 12.7 + - - -
74D PRO* 4.2 22.0 - - + -
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Residues in contact with GLU 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASP* 4.9 4.3 - - - +
9D LYS* 5.7 1.4 - - - -
65D GLU* 3.0 20.6 + - + +
66D ARG* 2.6 50.9 + - - +
67D ILE 3.4 0.2 - - - -
68D LYS* 1.3 76.9 - - + +
70D LEU* 1.3 59.7 + - - +
71D GLY 3.3 0.9 + - - -
120D VAL* 4.8 2.1 - - - +
133E GLN* 4.2 13.6 + - - +
137E THR* 3.9 25.1 + - + +
140E GLU* 5.3 5.4 - - - +
----------------------------------------------------------
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Residues in contact with LEU 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LYS* 3.5 44.8 - - + +
12D VAL* 3.3 35.2 - - + -
13D ILE* 3.7 23.0 - - + +
16D LEU* 3.6 19.1 - - + -
66D ARG* 3.3 34.7 + - - +
67D ILE 3.3 8.7 + - - +
68D LYS 3.1 1.0 - - - -
69D GLU* 1.3 77.4 - - - +
71D GLY* 1.3 60.5 + - - +
72D GLY 3.4 0.4 + - - -
118D ASP* 4.1 7.2 - - - +
121D THR* 4.2 2.5 - - - +
----------------------------------------------------------
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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).
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