Contacts of the helix formed by residues 42 - 70 (chain P) 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 P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P LEU* 2.9 21.0 + - + +
38P ASP* 4.8 0.6 - - - +
40P MET* 3.5 46.9 - - + -
41P ASP* 1.3 80.9 - - - +
43P GLY* 1.3 55.0 + - - +
44P GLU 3.5 1.6 - - - -
45P LEU* 3.2 17.6 + - + -
46P ALA* 2.8 33.7 + - - +
88P VAL* 4.3 9.9 - - + -
154P LEU* 3.9 38.8 - - + +
157P ILE* 3.7 18.6 - - + -
158P ALA* 3.8 22.9 - - + -
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Residues in contact with GLY 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P ASP* 5.4 0.7 - - - -
41P ASP 3.5 5.5 + - - -
42P TYR* 1.3 71.5 - - - +
44P GLU* 1.3 63.1 + - - +
46P ALA* 3.0 3.7 + - - +
47P ALA* 2.8 25.6 + - - +
160P THR* 2.9 31.7 + - - -
161P PRO 3.3 12.2 - - - +
162P SER* 3.7 10.1 - - - -
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Residues in contact with GLU 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43P GLY* 1.3 71.5 - - - +
45P LEU* 1.3 60.4 + - + +
47P ALA* 3.8 4.0 - - - +
48P ASN* 3.1 46.5 + - - +
153P TYR* 5.1 2.8 + - - -
156P LYS* 4.8 6.6 + - - +
157P ILE* 3.1 31.8 - - + +
160P THR* 2.9 28.3 + - - +
161P PRO 3.6 5.0 + - - -
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Residues in contact with LEU 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P LEU* 3.7 17.5 - - + +
42P TYR* 3.2 22.4 + - + +
43P GLY 3.1 0.6 - - - -
44P GLU* 1.3 81.1 - - + +
46P ALA* 1.3 59.0 + - - +
48P ASN* 3.7 1.0 + - - +
49P MET* 3.0 30.1 + - - +
88P VAL* 5.6 1.8 - - + -
92P TYR* 3.5 28.7 + - + +
138P TYR* 3.8 16.8 + - - +
142P ILE* 4.1 24.5 - - + -
146P ILE* 5.5 0.7 - - + -
153P TYR* 4.4 6.7 - - + +
154P LEU* 4.0 26.7 - - + -
157P ILE* 3.8 17.5 - - + -
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Residues in contact with ALA 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34P HIS* 2.7 33.1 + - + +
37P LEU* 3.7 11.3 - - + +
38P ASP* 3.6 40.4 - - - +
42P TYR 2.8 17.6 + - - +
43P GLY 3.6 3.8 - - - +
45P LEU* 1.3 75.6 - - - +
47P ALA* 1.3 62.8 + - - +
49P MET* 3.4 1.0 + - - +
50P LYS 3.0 10.7 + - - -
162P SER* 4.5 2.2 - - - -
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Residues in contact with ALA 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34P HIS* 5.1 0.4 - - - -
43P GLY 2.8 20.8 + - - +
44P GLU* 3.8 5.6 - - - +
46P ALA* 1.3 72.9 - - - +
48P ASN* 1.3 65.2 + - - +
50P LYS* 3.1 5.9 + - - +
51P LEU* 2.9 29.1 + - + +
161P PRO 4.7 1.3 - - - +
162P SER* 3.4 22.6 + - - +
163P SER 3.8 13.2 - - - +
164P THR* 3.7 12.2 - - + +
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Residues in contact with ASN 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171O PHE* 3.9 16.0 - - + -
44P GLU* 3.1 27.7 + - - +
45P LEU 4.3 0.2 - - - +
47P ALA* 1.3 78.7 - - - +
49P MET* 1.3 61.4 + - - +
51P LEU* 3.2 20.2 + - - +
52P ILE* 3.0 29.4 + - - +
138P TYR* 3.2 43.5 + - + +
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Residues in contact with MET 49 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P TYR* 3.2 30.8 - - - +
33P GLN* 3.6 13.2 - - + +
34P HIS* 3.9 11.4 - - + +
37P LEU* 4.0 14.4 - - + -
45P LEU 3.0 21.1 + - - +
46P ALA 3.6 4.5 - - - +
48P ASN* 1.3 76.6 - - - +
50P LYS* 1.3 62.1 + - - +
52P ILE* 3.6 4.9 + - - +
53P ALA* 3.1 21.8 + - - +
91P ILE* 3.8 17.9 - - + -
92P TYR* 4.1 7.4 - - + +
95P ASP* 3.2 23.6 - - - +
138P TYR* 4.9 2.6 + - + -
139P TYR* 3.2 33.7 - - + -
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Residues in contact with LYS 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61O GLU* 3.0 28.6 + - - +
2502O FEC 2.7 46.9 + - - -
31P MET* 4.2 13.0 - - + -
34P HIS* 3.5 30.0 + - + +
46P ALA 3.0 6.4 + - - +
47P ALA 3.1 7.6 + - - +
49P MET* 1.3 72.4 - - - +
51P LEU* 1.3 60.7 + - - +
53P ALA* 3.1 8.3 + - - +
54P ILE* 2.9 37.8 + - + +
164P THR* 3.6 11.1 + - + -
2601P SO4 2.3 37.5 + - - +
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Residues in contact with LEU 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169O LYS* 3.7 23.3 - - + +
170O GLY* 3.5 12.9 - - - +
171O PHE* 3.4 26.2 + - + +
47P ALA* 2.9 19.4 + - + +
48P ASN* 3.6 25.6 - - - +
50P LYS* 1.3 77.0 - - - +
52P ILE* 1.3 60.8 + - - +
54P ILE* 3.1 10.9 + - + +
55P ASP 3.1 16.6 + - - -
163P SER 6.1 0.2 - - - +
164P THR* 3.7 34.1 - - + +
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Residues in contact with ILE 52 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171O PHE* 3.5 31.0 - - + -
30P TYR* 3.9 16.2 - - + -
48P ASN 3.0 18.1 + - - +
49P MET* 3.9 3.6 - - - +
51P LEU* 1.3 73.4 - - - +
53P ALA* 1.3 68.1 + - - +
55P ASP* 3.1 11.3 + - - +
56P GLU* 3.1 13.3 + - - +
135P HIS* 3.6 33.2 - - + +
138P TYR* 3.6 32.5 - - + -
139P TYR* 3.4 34.3 - - + +
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Residues in contact with ALA 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27P ILE* 4.1 6.7 - - - +
30P TYR* 4.0 16.4 - - + -
31P MET* 3.7 29.2 - - + +
49P MET 3.1 15.5 + - - +
50P LYS 3.1 8.9 + - - +
52P ILE* 1.3 78.1 - - - +
54P ILE* 1.3 63.8 + - - +
56P GLU* 3.0 21.7 + - - +
57P MET* 3.0 19.6 + - + +
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Residues in contact with ILE 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168O SER* 3.7 26.1 - - - +
169O LYS 3.4 27.4 - - - +
170O GLY* 4.4 0.9 - - - -
2502O FEC 4.0 30.3 - - + +
50P LYS* 2.9 43.4 + - + +
51P LEU* 3.5 13.0 - - + +
52P ILE 3.1 0.4 - - - -
53P ALA* 1.3 77.6 - - - +
55P ASP* 1.3 61.5 + - - +
57P MET* 3.2 31.6 + - + +
58P ARG* 3.2 12.1 + - - +
164P THR* 5.4 2.5 - - - +
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Residues in contact with ASP 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170O GLY* 3.1 4.2 - - - -
171O PHE* 3.0 22.3 + - - +
172O VAL* 3.0 24.4 + - - +
51P LEU 3.1 7.8 + - - -
52P ILE 3.1 9.3 + - - +
54P ILE* 1.3 75.9 - - - +
56P GLU* 1.3 56.5 + - - +
58P ARG* 2.5 46.9 + - - +
59P HIS* 2.9 33.6 + - - +
135P HIS* 2.7 32.6 + - + -
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Residues in contact with GLU 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23P GLU* 2.9 23.5 - - - +
26P ALA* 4.1 13.6 - - + +
27P ILE* 3.9 14.6 - - + -
30P TYR* 3.5 15.1 - - + -
52P ILE 3.3 11.4 - - - +
53P ALA* 3.0 7.7 + - - +
55P ASP* 1.3 73.4 - - - +
57P MET* 1.3 54.8 + - - +
59P HIS* 2.8 38.5 + - - +
60P ALA* 2.8 34.0 + - - +
99P GLU* 3.3 11.6 - - - +
132P GLU* 3.2 1.9 - - - +
135P HIS* 3.4 6.9 + - - -
200P FE 2.1 30.5 - - - -
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Residues in contact with MET 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2502O FEC 2.4 115.2 - - + +
27P ILE* 3.6 26.7 - - + +
31P MET* 4.4 7.4 - - + -
53P ALA* 3.0 28.5 + - + +
54P ILE* 3.2 21.8 - - + +
56P GLU* 1.3 75.2 - - - +
58P ARG* 1.3 58.1 + - - +
60P ALA* 3.5 2.1 + - - +
61P GLU 3.0 21.3 + - - -
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Residues in contact with ARG 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167O ALA* 6.0 2.6 - - - +
168O SER* 3.2 36.7 + - - +
170O GLY* 4.0 3.6 - - - +
172O VAL* 4.0 9.6 + - - +
2502O FEC 5.8 1.6 - - + -
54P ILE 3.2 5.5 + - - +
55P ASP* 2.5 51.7 + - - +
57P MET* 1.3 78.3 - - - +
59P HIS* 1.3 55.5 + - - +
61P GLU* 3.8 16.1 - - - +
62P ASN* 2.5 57.2 + - - +
131P GLU* 3.0 34.7 + - - -
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Residues in contact with HIS 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23P GLU* 3.1 24.3 + - + +
55P ASP* 2.9 25.7 + - - +
56P GLU* 2.8 32.2 + - - +
58P ARG* 1.3 79.1 + - - +
60P ALA* 1.3 67.3 + - - +
62P ASN* 3.1 8.8 + - - +
63P PHE* 2.8 29.9 + - + -
128P ILE* 3.7 33.3 - - + +
131P GLU* 2.5 39.6 + - + +
132P GLU* 3.3 15.8 + - - -
135P HIS* 4.1 5.2 - + - -
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Residues in contact with ALA 60 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2502O FEC 4.4 5.4 - - + -
20P ARG* 3.2 30.7 + - + +
23P GLU* 3.9 17.6 - - + +
24P LEU* 4.4 4.7 - - + -
27P ILE* 4.4 12.6 - - + -
56P GLU 2.8 18.1 + - - +
57P MET 3.6 6.5 - - - +
59P HIS* 1.3 73.4 - - - +
61P GLU* 1.3 56.7 + - - +
63P PHE* 3.1 8.9 + - - +
64P ALA 2.9 25.6 + - - -
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Residues in contact with GLU 61 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31O MET* 4.3 1.0 - - - +
34O HIS* 4.2 8.3 + - - -
35O TYR* 3.4 18.7 + - + -
50O LYS* 3.0 37.8 + - - +
2501O SO4 4.7 5.6 + - - -
2502O FEC 3.3 34.2 - - + +
57P MET 3.0 9.2 + - - +
58P ARG* 3.8 17.8 - - - +
60P ALA* 1.3 75.4 - - - +
62P ASN* 1.3 61.9 + - - +
64P ALA* 3.3 1.9 + - - +
65P GLU* 2.8 54.5 + - - +
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Residues in contact with ASN 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58P ARG* 2.5 51.2 + - - +
59P HIS* 3.7 10.5 - - - +
61P GLU* 1.3 77.5 - - - +
63P PHE* 1.3 67.7 + - - +
65P GLU* 3.6 17.7 + - - +
66P ARG* 3.4 21.0 + - - +
124P LEU* 3.6 27.1 - - + +
128P ILE* 4.5 9.3 - - + +
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Residues in contact with PHE 63 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P LEU* 3.7 27.6 - - + +
19P ALA* 3.5 21.1 - - + -
20P ARG* 3.9 27.4 - - + -
23P GLU* 3.6 24.0 - - + -
59P HIS 2.8 24.1 + - - -
60P ALA 3.4 5.6 - - - +
62P ASN* 1.3 78.5 - - - +
64P ALA* 1.3 63.5 + - - +
66P ARG* 3.2 4.5 + - - +
67P ILE* 3.0 27.2 + - - +
106P TYR* 3.8 10.5 - + - -
124P LEU* 4.0 12.8 - - + -
125P PHE* 3.7 29.4 - + - -
128P ILE* 3.5 26.7 - - + -
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Residues in contact with ALA 64 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35O TYR* 3.5 40.4 - - + -
20P ARG* 3.7 8.5 - - - +
60P ALA 2.9 13.6 + - - +
61P GLU 3.3 1.1 + - - +
63P PHE* 1.3 76.4 - - - +
65P GLU* 1.3 58.6 + - - +
67P ILE* 3.4 13.7 + - - +
68P LYS* 3.1 32.4 + - - +
74P PRO* 3.7 13.8 - - + +
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Residues in contact with GLU 65 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34O HIS* 5.1 2.9 + - - -
35O TYR* 4.5 11.2 - - + -
38O ASP* 3.9 17.6 - - - +
2501O SO4 5.2 5.0 + - - -
61P GLU* 2.8 43.9 + - + +
62P ASN* 4.0 16.8 - - - +
63P PHE 3.2 0.4 - - - -
64P ALA* 1.3 76.3 - - - +
66P ARG* 1.3 58.0 + - - +
68P LYS* 3.3 9.0 + - - +
69P GLU* 3.0 34.1 + - + +
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Residues in contact with ARG 66 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133K GLN* 3.0 26.7 + - - -
16P LEU* 3.9 12.6 - - + -
62P ASN 3.4 14.2 + - - +
63P PHE 3.2 4.4 + - - +
65P GLU* 1.3 76.5 - - - +
67P ILE* 1.3 66.8 + - - +
69P GLU* 3.0 35.4 + - - +
70P LEU* 2.9 46.8 + - - +
118P ASP* 2.6 32.5 + - - -
120P VAL* 3.6 23.2 - - - +
121P THR* 2.6 30.0 + - + +
124P LEU* 4.0 14.1 - - + -
2615P GOL 4.8 3.6 - - - -
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Residues in contact with ILE 67 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P ILE* 4.4 13.0 - - + +
16P LEU* 3.5 38.6 - - + +
17P ASN* 3.6 26.7 - - - +
20P ARG* 4.4 6.7 - - - -
63P PHE 3.0 24.8 + - - +
64P ALA* 3.5 11.4 - - - +
66P ARG* 1.3 76.5 - - - +
68P LYS* 1.3 57.7 + - - +
70P LEU* 2.9 17.3 + - - +
71P GLY 3.0 0.2 + - - -
72P GLY* 2.9 48.7 + - - +
73P GLU 3.8 13.5 - - - +
74P PRO* 3.9 3.8 - - + -
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Residues in contact with LYS 68 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32O ASN 5.3 0.4 - - - -
35O TYR* 4.0 21.1 - - + +
36O SER* 3.6 41.7 + - - +
39O ASP* 4.0 36.0 + - + +
64P ALA 3.1 17.3 + - - +
65P GLU* 3.4 11.7 - - - +
66P ARG 3.2 0.2 - - - -
67P ILE* 1.3 77.4 - - - +
69P GLU* 1.3 57.1 + - + +
71P GLY* 2.8 21.1 + - - -
72P GLY 3.4 16.2 + - - +
73P GLU* 4.0 12.1 + - - -
74P PRO* 3.7 22.9 - - + -
----------------------------------------------------------
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Residues in contact with GLU 69 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133K GLN* 3.9 15.8 + - - +
137K THR* 4.0 25.4 + - + +
140K GLU* 5.4 3.5 - - - +
39O ASP* 4.9 2.7 + - - -
9P LYS* 5.2 3.3 - - - -
65P GLU* 3.0 20.9 + - + +
66P ARG* 3.0 44.6 + - - +
68P LYS* 1.3 76.0 - - + +
70P LEU* 1.3 62.4 + - - +
71P GLY 3.3 0.6 + - - -
120P VAL* 5.0 1.6 - - - +
----------------------------------------------------------
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Residues in contact with LEU 70 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P LYS* 3.5 46.0 - - + +
12P VAL* 3.7 21.3 - - + -
13P ILE* 3.6 21.8 - - + +
16P LEU* 3.8 14.6 - - + -
66P ARG* 2.9 39.2 + - - +
67P ILE 2.9 9.2 + - - +
69P GLU* 1.3 80.7 - - - +
71P GLY* 1.3 59.9 + - - +
72P GLY 3.5 0.2 - - - -
118P ASP* 3.7 17.0 - - - +
121P THR* 3.9 4.7 - - - +
2615P GOL 4.1 10.5 - - - +
----------------------------------------------------------
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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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