Contacts of the helix formed by residues 38 - 63 (chain A) in PDB entry 1NNQ
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 PHE 38 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ALA* 2.8 18.2 + - + +
34A GLU 4.4 0.2 + - - -
36A GLU* 3.7 37.5 - - + -
37A GLY* 1.3 77.4 - - - +
39A PRO* 1.3 60.0 - - - +
40A ASN 3.3 2.9 - - - -
41A ILE* 3.2 18.9 + - + -
42A ALA* 3.0 25.3 + - - +
69B THR* 3.8 23.1 - - - -
70B PRO* 5.5 2.7 - - + -
128B ALA* 4.2 19.5 - - + -
131B GLY* 3.8 17.5 - - - -
132B GLU 3.5 30.3 - - - -
133B ASP* 3.5 21.1 - - - +
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Residues in contact with PRO 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLU* 4.9 12.3 - - + +
37A GLY* 3.4 10.5 - - - +
38A PHE* 1.3 88.6 - - - +
40A ASN* 1.3 63.6 + - - +
42A ALA* 3.3 10.3 - - + +
43A LYS* 3.0 42.1 + - - +
133B ASP* 3.0 12.1 - - + +
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Residues in contact with ASN 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PRO* 1.3 79.2 - - - +
41A ILE* 1.3 60.0 + - - +
43A LYS* 3.4 24.5 + - - +
44A LEU* 2.9 25.1 + - - +
133B ASP* 3.0 20.8 + - - +
134B ILE* 2.9 38.2 + - + +
135B GLU* 4.5 4.0 - - - +
136B ILE 4.1 19.9 + - - +
137B LYS* 5.7 0.5 - - - -
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Residues in contact with ILE 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ALA* 3.9 3.6 - - + -
38A PHE* 3.2 18.2 + - + +
40A ASN* 1.3 72.4 - - - +
42A ALA* 1.3 60.6 + - - +
44A LEU* 3.1 9.3 + - + +
45A PHE* 2.9 53.7 + - + -
69B THR* 3.9 16.8 - - + -
73B LEU* 4.1 11.7 - - + -
124B ALA* 3.9 18.6 - - + +
128B ALA* 3.8 29.4 - - + -
132B GLU 4.6 1.3 - - - +
133B ASP* 3.2 15.6 + - - +
134B ILE* 3.7 18.8 - - + +
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 3.4 29.0 - - - +
33A ALA* 3.9 6.7 - - - +
34A GLU* 4.0 11.2 - - + +
38A PHE 3.0 13.3 + - - +
39A PRO* 3.3 14.6 - - + +
41A ILE* 1.3 77.7 - - - +
43A LYS* 1.3 58.8 + - - +
45A PHE 3.4 0.7 + - - -
46A ARG* 3.0 44.8 + - - +
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Residues in contact with LYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PRO* 3.0 31.1 + - - +
40A ASN* 3.4 24.8 + - - +
41A ILE 3.3 0.2 - - - -
42A ALA* 1.3 71.7 - - - +
44A LEU* 1.3 66.1 + - - +
46A ARG* 3.3 11.8 + - + +
47A ALA* 3.0 26.2 + - - +
136B ILE 5.8 0.7 - - - +
137B LYS 5.1 4.9 - - - +
139B VAL* 4.7 7.3 - - + +
170B PHE* 4.8 8.8 - - + +
171B GLU* 3.6 40.7 + - - +
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASN 2.9 14.8 + - - +
41A ILE* 3.1 11.4 + - + +
43A LYS* 1.3 76.9 - - - +
45A PHE* 1.3 62.7 + - - +
47A ALA* 3.8 0.9 - - - +
48A ILE* 3.1 46.2 + - + +
73B LEU* 5.3 1.1 - - + -
120B LEU* 4.0 31.2 - - + +
121B TYR* 4.3 18.8 - - + -
124B ALA* 4.0 27.8 - - + -
134B ILE* 4.1 15.0 - - + -
139B VAL* 4.4 23.3 - - + +
150B VAL* 4.8 5.2 - - + -
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Residues in contact with PHE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 3.5 35.4 - + + +
29A PHE* 3.6 51.8 - + + -
30A ALA* 3.7 6.1 - - + -
33A ALA* 4.4 2.7 - - + -
41A ILE* 2.9 42.6 + - + -
42A ALA 3.5 7.2 - - - +
44A LEU* 1.3 73.4 - - - +
46A ARG* 1.3 57.1 + - - +
48A ILE* 3.6 0.7 + - - -
49A ALA* 2.9 28.6 + - - +
69B THR* 4.8 4.3 - - + -
72B ASN* 4.5 3.8 - - + -
73B LEU* 3.5 31.4 - - + -
76B GLY* 5.8 0.4 - - - -
121B TYR* 3.5 34.3 - + - -
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 4.8 17.5 + - + +
30A ALA* 3.7 13.0 - - + +
31A GLU* 3.7 29.5 - - - +
34A GLU* 4.4 12.7 - - - +
42A ALA* 3.0 40.4 + - - +
43A LYS* 3.3 10.0 + - - +
45A PHE* 1.3 74.9 - - - +
47A ALA* 1.3 58.4 + - - +
49A ALA* 3.3 8.9 + - - +
50A TYR* 3.0 24.6 + - - +
170B PHE* 4.1 16.2 - - + -
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS 3.0 17.2 + - - +
44A LEU 3.8 2.9 - - - +
46A ARG* 1.3 74.2 - - - +
48A ILE* 1.3 66.2 + - - +
50A TYR* 3.0 13.9 + - - +
51A ALA 3.1 9.2 + - - -
139B VAL* 3.7 29.2 - - + -
141B ILE* 3.6 11.7 - - + +
170B PHE* 3.6 34.9 - - + -
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Residues in contact with ILE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 3.8 4.3 - - + -
44A LEU* 3.1 32.0 + - + +
45A PHE 4.0 0.2 - - - +
47A ALA* 1.3 76.2 - - + +
49A ALA* 1.3 62.1 + - - +
51A ALA* 3.0 8.4 + - - +
52A GLU* 3.0 29.9 + - - +
80B GLU* 4.3 0.2 - - - +
117B HIS* 3.6 53.6 - - + +
120B LEU* 4.3 7.0 - - + -
121B TYR* 3.3 44.2 - - + +
141B ILE* 5.0 0.9 - - - -
148B THR* 4.6 7.4 - - + -
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A HIS* 2.6 51.6 + - + +
26A TYR* 3.9 8.0 - - + -
27A LEU* 4.0 17.3 - - + -
45A PHE 2.9 19.9 + - - +
46A ARG 3.3 7.4 - - - +
47A ALA 3.2 0.2 - - - -
48A ILE* 1.3 74.8 - - - +
50A TYR* 1.3 58.0 + - - +
52A GLU* 3.4 9.3 + - - +
53A PHE 3.0 14.6 + - - -
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Residues in contact with TYR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A HIS* 4.7 2.0 - - - -
46A ARG 3.0 7.2 + - - +
47A ALA 3.0 10.3 + - - +
49A ALA* 1.3 73.8 - - - +
51A ALA* 1.3 60.5 + - - +
53A PHE* 3.2 35.5 + + + +
54A VAL* 2.9 43.9 + - + +
57A LYS* 5.8 1.0 + - - -
31B GLU* 5.1 4.7 + - - -
141B ILE* 3.7 19.5 - - + -
143B PRO* 4.0 15.6 + - + +
168B VAL* 3.8 34.1 - - + +
170B PHE* 3.5 32.5 - + + -
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Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA 3.1 8.4 + - - +
48A ILE* 3.0 11.1 + - - +
50A TYR* 1.3 76.9 - - - +
52A GLU* 1.3 57.5 + - - +
54A VAL* 3.1 7.3 + - - +
55A HIS* 3.0 32.2 + - + -
117B HIS* 3.7 21.8 - - + +
141B ILE* 3.9 15.0 - - + -
146B GLY* 3.5 23.1 - - - +
148B THR* 4.0 2.5 - - - +
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 3.4 27.2 - - - +
22A ALA* 4.3 5.8 - - + +
23A HIS* 3.9 10.3 - - + +
26A TYR* 3.4 23.1 - - + -
48A ILE* 3.0 15.4 + - - +
49A ALA* 3.6 6.1 - - - +
51A ALA* 1.3 72.6 - - - +
53A PHE* 1.3 56.0 + - - +
55A HIS* 3.3 3.8 + - - -
56A ALA* 2.8 34.8 + - - +
202A ZN 2.2 33.4 - - - -
24B MET* 4.4 2.2 - - - -
80B GLU* 3.0 7.1 - - - +
83B GLU* 5.0 0.2 - - - -
114B GLU* 3.4 0.2 - - - +
117B HIS* 3.3 4.9 + - - -
201B ZN 2.0 31.4 - - - -
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Residues in contact with PHE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A HIS* 4.0 11.0 - - + +
49A ALA 3.0 13.4 + - - +
50A TYR* 3.2 42.6 - + + +
52A GLU* 1.3 72.0 - - - +
54A VAL* 1.3 65.8 + - + +
56A ALA* 3.8 0.9 - - - +
57A LYS* 2.9 53.4 + - + +
24B MET* 3.6 29.1 - - - +
27B LEU* 3.9 29.6 - - + -
28B ILE* 3.9 22.0 - - + -
31B GLU* 3.8 26.7 - - + -
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 2.9 48.5 + - + +
51A ALA* 3.1 9.2 + - - +
53A PHE* 1.3 82.2 - - + +
55A HIS* 1.3 63.4 + - - +
57A LYS* 3.2 7.3 + - - +
58A ASN* 3.0 27.3 + - - +
142B CYS 3.9 9.9 - - - +
143B PRO 3.8 12.3 - - - +
144B ILE 3.6 22.4 - - - +
145B CYS 3.8 1.8 - - - -
146B GLY* 3.4 26.5 - - - +
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Residues in contact with HIS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 3.4 20.4 - - + +
51A ALA 3.0 12.9 + - - -
52A GLU* 3.4 6.1 + - - +
54A VAL* 1.3 76.7 - - - +
56A ALA* 1.3 61.6 + - - +
58A ASN* 3.4 9.0 + - - +
59A HIS* 3.1 30.8 + - - +
202A ZN 2.5 30.1 - - - -
106B THR 5.9 0.7 - - - -
109B TYR* 4.5 2.7 - - + -
110B ALA* 3.7 22.1 - - + -
113B ALA* 3.4 28.5 - - + +
114B GLU* 3.3 10.0 + - - -
117B HIS* 4.4 4.9 - + - -
145B CYS 3.0 31.6 + - - -
146B GLY* 3.7 4.0 - - - -
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 3.4 18.5 - - + +
19A GLU* 3.7 19.0 - - + +
52A GLU 2.8 21.0 + - - +
53A PHE 3.8 0.2 - - - +
54A VAL 3.3 0.2 - - - -
55A HIS* 1.3 71.4 - - - +
57A LYS* 1.3 57.8 + - - +
59A HIS* 3.1 5.8 + - - +
60A PHE* 2.8 30.7 + - - +
24B MET* 3.7 33.4 - - + -
28B ILE* 4.5 0.2 - - - -
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Residues in contact with LYS 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 5.8 0.8 + - - -
53A PHE* 2.9 36.1 + - + +
54A VAL* 3.6 8.3 - - - +
56A ALA* 1.3 75.6 - - - +
58A ASN* 1.3 68.8 + - - +
60A PHE* 3.1 1.4 + - - +
61A ILE* 2.9 47.9 + - + +
66A LEU* 5.9 0.4 - - + -
28B ILE* 3.8 30.9 - - + +
31B GLU* 2.6 42.5 + - - +
35B GLN* 5.8 0.4 - - - +
143B PRO 5.0 11.7 + - - -
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Residues in contact with ASN 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 3.0 24.2 + - - +
55A HIS* 3.6 10.7 - - - +
57A LYS* 1.3 83.0 - - - +
59A HIS* 1.3 55.6 - - - +
61A ILE* 4.0 6.7 - - - +
62A ALA* 3.0 30.0 + - - +
106B THR* 3.7 25.9 - - + +
109B TYR* 3.8 19.4 - - - +
144B ILE 2.9 27.8 + - - +
145B CYS* 4.4 1.8 - - - +
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Residues in contact with HIS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.1 29.4 - - + +
15A ALA* 3.7 23.3 - - + +
16A PHE* 4.0 12.1 - - + -
19A GLU* 4.1 4.2 - - + +
55A HIS 3.1 22.7 + - - -
56A ALA* 3.1 6.0 + - - +
58A ASN* 1.3 75.5 - - - +
60A PHE* 1.3 58.7 + - - +
62A ALA* 3.4 2.9 + - - +
63A LEU* 3.0 34.8 + - - +
88B TYR* 3.0 32.1 + + - -
106B THR* 3.0 44.2 + - - -
107B THR* 4.2 1.1 - - - -
110B ALA* 4.5 2.2 - - + +
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Residues in contact with PHE 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 3.4 29.6 - + + -
56A ALA 2.8 17.2 + - - +
57A LYS 3.4 4.9 - - - +
59A HIS* 1.3 77.5 - - - +
61A ILE* 1.3 58.6 + - + +
63A LEU* 3.5 6.6 + - - +
64A GLY 3.4 3.5 + - - -
65A LYS* 3.1 77.4 + - + +
66A LEU* 3.7 9.6 - - + -
75A MET* 4.2 2.9 - - - -
25B ARG* 3.4 38.8 - - + -
28B ILE* 3.8 26.5 - - + -
29B PHE* 3.8 20.9 - + - -
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Residues in contact with ILE 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A VAL* 5.0 3.1 - - - +
57A LYS* 2.9 42.8 + - + +
58A ASN* 4.0 7.2 - - - +
60A PHE* 1.3 74.6 - - + +
62A ALA* 1.3 58.7 + - - +
63A LEU 3.1 1.1 - - - -
64A GLY* 2.8 25.3 + - - -
65A LYS 4.8 1.6 - - - +
66A LEU* 3.9 36.8 - - + -
28B ILE* 5.3 0.2 - - + -
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A VAL* 3.5 6.2 - - - +
3A VAL* 2.9 30.2 + - + +
12A LEU* 4.0 16.2 - - + -
58A ASN 3.0 19.0 + - - +
59A HIS 3.7 4.9 - - - +
61A ILE* 1.3 77.0 - - - +
63A LEU* 1.3 58.6 + - - +
64A GLY 3.3 0.2 - - - -
102B GLU* 4.4 21.3 - - + +
106B THR* 4.2 13.5 - - + +
----------------------------------------------------------
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A VAL* 3.9 12.6 - - - +
3A VAL* 4.7 6.7 - - + +
9A LYS* 3.6 61.8 + - + +
12A LEU* 4.0 20.0 - - + +
13A GLU* 4.0 29.8 - - + +
16A PHE* 4.9 5.8 - - + -
59A HIS 3.0 22.7 + - - +
60A PHE* 3.8 7.4 - - - +
61A ILE 3.1 0.8 - - - -
62A ALA* 1.3 75.9 - - - +
64A GLY* 1.3 61.0 + - - +
65A LYS* 3.7 22.9 + - + +
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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