Contacts of the helix formed by residues 56 - 77 (chain F) in PDB entry 2IAN
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 ALA 56 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34F VAL* 4.3 12.6 - - + -
39F LYS 5.0 9.2 - - - +
41F THR* 4.6 8.1 - - - +
54F PHE* 3.6 21.6 + - + +
55F GLU* 1.3 69.5 - - - +
57F GLN* 1.3 61.5 + - - +
58F GLY 3.3 2.7 - - - -
59F ALA* 2.7 26.5 + - - +
60F LEU* 3.1 28.9 + - + +
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Residues in contact with GLN 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F GLU* 3.0 40.2 + - - +
56F ALA* 1.3 80.3 + - - +
58F GLY* 1.3 63.2 + - - +
59F ALA 3.1 0.2 + - - -
60F LEU* 3.3 10.2 + - + +
61F ALA 3.1 19.4 + - - -
93I ALA* 3.8 5.4 - - - +
48J TYR* 3.8 16.8 + - - +
50J VAL* 3.4 31.5 - - + +
54J ILE* 5.0 5.4 - - + -
56J ASP* 3.3 40.3 + - - +
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Residues in contact with GLY 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F GLN* 1.3 79.3 - - - +
59F ALA* 1.3 55.8 + - - +
61F ALA* 3.8 7.3 - - - +
62F ASN* 2.8 32.4 + - - +
28H THR* 4.2 9.6 - - - +
30H ASN* 5.3 0.3 - - - +
92I GLY 3.2 21.0 + - - -
94I GLN* 3.8 20.7 - - - +
31J TYR* 4.6 3.0 + - - -
50J VAL* 5.0 0.4 - - - -
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Residues in contact with ALA 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F PHE* 3.8 47.0 - - + -
34F VAL* 4.6 2.2 - - + -
54F PHE* 3.9 13.7 - - + -
56F ALA* 2.7 18.0 + - - +
58F GLY* 1.3 71.9 - - - +
60F LEU* 1.3 69.6 + - + +
61F ALA 3.3 0.2 - - - -
62F ASN* 3.3 5.5 + - - +
63F ILE* 3.2 26.2 + - - +
28H THR* 4.8 1.2 + - - +
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Residues in contact with LEU 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F VAL* 3.8 29.2 - - + -
36F MET* 4.4 15.3 - - + -
39F LYS* 3.9 39.3 - - + +
56F ALA* 3.1 21.8 + - + +
57F GLN* 4.0 10.3 - - + +
59F ALA* 1.3 77.5 - - + +
61F ALA* 1.3 63.7 + - - +
63F ILE* 3.3 9.9 + - - +
64F ALA* 3.3 19.9 + - - +
54J ILE* 4.1 23.1 - - + +
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Residues in contact with ALA 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F GLN 3.1 17.3 + - - +
58F GLY 3.8 6.5 - - - +
60F LEU* 1.3 77.3 - - - +
62F ASN* 1.3 63.2 + - - +
64F ALA* 3.2 7.6 + - - +
65F VAL* 3.1 25.4 + - - +
30J ASN* 4.1 6.6 + - - +
31J TYR* 4.3 8.5 - - + +
50J VAL* 3.7 33.4 - - + +
51J GLY* 5.7 0.4 - - - -
54J ILE* 3.9 9.5 - - - +
95J TYR* 5.9 0.9 - - + -
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Residues in contact with ASN 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F GLN* 3.5 2.0 - - - +
11F GLU* 2.8 38.3 + - - +
58F GLY 2.8 19.6 + - - +
59F ALA* 3.3 10.8 + - - +
61F ALA* 1.3 74.1 - - - +
63F ILE* 1.3 55.5 + - - +
65F VAL* 3.1 3.6 + - - +
66F ASP* 2.6 41.5 + - - +
13G PHE* 4.6 0.6 - - - -
28H THR* 4.0 4.4 - - - +
29H LEU 3.1 23.2 + - - -
30H ASN* 3.6 9.1 - - - +
31H ALA* 3.2 30.2 + - + +
95J TYR* 4.5 2.1 + - - -
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Residues in contact with ILE 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F GLU* 4.4 3.4 - - + +
12F PHE 4.1 4.3 - - - +
13F TYR* 3.9 26.1 - - + -
20F GLY* 4.3 5.8 - - - -
21F GLU 3.6 35.7 - - - +
22F PHE* 4.3 6.1 - - + -
36F MET* 4.0 27.4 - - + -
59F ALA 3.2 15.1 + - - +
60F LEU* 3.6 8.5 - - - +
61F ALA 3.2 0.4 - - - -
62F ASN* 1.3 78.6 - - - +
64F ALA* 1.3 64.2 + - - +
66F ASP* 3.1 19.0 + - + +
67F LYS* 2.9 22.2 + - - +
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Residues in contact with ALA 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F LEU 3.3 8.3 + - - +
61F ALA* 3.2 12.0 + - - +
63F ILE* 1.3 79.3 - - - +
65F VAL* 1.3 63.7 + - + +
67F LYS* 3.1 10.0 + - - +
68F ALA* 3.1 21.1 + - - +
30J ASN* 5.7 3.4 - - - +
51J GLY* 6.3 1.6 - - - -
52J ALA 5.6 6.7 - - - +
54J ILE* 5.6 5.4 - - + -
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Residues in contact with VAL 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F ALA 3.1 15.5 + - - +
62F ASN* 3.1 7.2 + - - +
64F ALA* 1.3 73.0 - - + +
66F ASP* 1.3 66.1 + - - +
68F ALA* 3.4 6.1 + - + +
69F ASN* 2.9 51.0 + - - +
31H ALA* 3.9 18.4 - - + +
32H ALA 3.9 12.6 - - - +
33H LYS* 4.2 17.3 - - + +
30J ASN* 4.5 16.8 - - - +
95J TYR* 3.9 18.4 - - + +
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Residues in contact with ASP 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F GLU* 2.6 42.1 - - - +
12F PHE 4.7 1.7 + - - -
13F TYR* 4.1 17.1 - - + +
62F ASN 2.6 27.3 + - - +
63F ILE* 3.1 12.4 + - - +
65F VAL* 1.3 72.6 - - - +
67F LYS* 1.3 56.9 + - - +
69F ASN* 3.5 2.0 + - - -
70F LEU* 3.0 27.2 + - - +
9G TRP* 3.5 28.0 + - + +
11G LEU* 3.8 19.8 - - - +
31H ALA* 3.8 5.9 - - - +
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Residues in contact with LYS 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F TYR* 3.2 51.5 + - + +
15F ASN* 4.7 1.7 + - - +
18F GLN* 4.4 15.8 - - - +
63F ILE 2.9 11.5 + - - +
64F ALA* 3.3 12.8 - - - +
65F VAL 3.1 0.2 - - - -
66F ASP* 1.3 72.7 - - - +
68F ALA* 1.3 67.8 + - - +
69F ASN 3.0 1.8 + - - -
70F LEU* 3.1 3.5 + - - +
71F GLU* 3.0 55.3 + - - +
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Residues in contact with ALA 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F ALA 3.1 9.5 + - - +
65F VAL* 3.9 8.7 - - + +
67F LYS* 1.3 77.7 - - - +
69F ASN* 1.3 66.9 + - - +
71F GLU* 3.2 9.6 + - - +
72F ILE* 3.0 37.7 + - + +
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Residues in contact with ASN 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F VAL* 2.9 28.6 + - - +
66F ASP* 3.6 6.9 + - - +
68F ALA* 1.3 77.8 - - - +
70F LEU* 1.3 67.2 + - - +
72F ILE* 3.4 1.7 + - - +
73F MET* 2.8 28.4 + - - +
9G TRP* 3.9 27.3 - - + +
61G TRP* 5.2 0.2 - - - -
31H ALA* 5.3 1.0 - - - +
32H ALA 3.0 25.3 + - - -
33H LYS* 4.0 4.9 - - - +
34H VAL* 3.3 38.9 + - + +
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Residues in contact with LEU 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F TYR* 3.4 25.4 - - + +
15F ASN* 3.6 30.1 - - - +
66F ASP 3.0 14.8 + - - +
67F LYS* 3.5 8.5 - - - +
69F ASN* 1.3 75.0 - - - +
71F GLU* 1.3 52.5 + - - +
73F MET* 2.9 5.5 + - - +
74F THR* 2.6 51.3 + - - +
7G PHE* 3.2 36.6 - - + +
8G LEU 3.8 9.0 - - - -
9G TRP* 3.7 11.9 - - + -
32G TYR* 3.8 15.7 - - + -
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Residues in contact with GLU 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ASN* 2.9 29.3 + - - +
67F LYS* 3.0 45.8 + - - +
68F ALA* 3.6 11.2 - - - +
70F LEU* 1.3 76.8 - - - +
72F ILE* 1.3 64.1 + - + +
74F THR* 3.4 8.8 + - - +
75F LYS* 3.2 22.0 + - - +
79F TYR* 5.9 0.2 - - - -
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Residues in contact with ILE 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F ALA* 3.0 27.3 + - + +
69F ASN 3.9 2.7 - - - +
71F GLU* 1.3 77.6 - - + +
73F MET* 1.3 58.9 + - - +
75F LYS* 3.1 7.3 + - - +
76F ARG* 3.0 42.4 + - + +
34H VAL* 3.5 29.8 - - + +
35H PRO 4.2 13.9 - - - +
36H ALA* 4.7 9.2 - - + -
37H ASP* 3.4 30.5 - - - +
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Residues in contact with MET 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F ASN 2.8 15.5 + - - +
70F LEU 3.5 2.5 - - - +
72F ILE* 1.3 75.6 - - - +
74F THR* 1.3 67.2 + - - +
76F ARG* 3.3 24.1 + - - +
77F SER* 2.9 25.5 + - - -
9G TRP* 3.6 29.6 - - + -
32G TYR* 3.7 26.0 - - + -
37G SER* 5.3 1.6 - - - -
53G LEU* 2.9 36.6 - - + -
57G ASP* 3.6 22.0 - - - +
34H VAL* 3.8 20.4 - - + -
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Residues in contact with THR 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ASN* 5.1 2.1 + - - -
70F LEU* 2.6 46.1 + - - +
71F GLU* 3.6 8.7 + - - -
73F MET* 1.3 72.9 - - - +
75F LYS* 1.3 59.7 + - - +
77F SER* 2.7 19.6 + - - -
79F TYR* 3.0 35.2 + - + -
7G PHE* 3.4 44.3 - - + +
32G TYR* 3.5 9.8 + - - -
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Residues in contact with LYS 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F GLU 3.2 8.8 + - - +
72F ILE* 3.1 10.6 + - - +
74F THR* 1.3 80.8 - - - +
76F ARG* 1.3 56.9 + - - +
78F ASN* 3.0 24.3 + - - -
79F TYR* 3.3 35.6 + - + +
37H ASP* 3.4 27.5 + - - +
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Residues in contact with ARG 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F ILE* 3.0 27.1 + - + +
73F MET* 3.7 21.4 - - - +
75F LYS* 1.3 76.0 - - - +
77F SER* 1.3 59.9 + - - +
78F ASN* 3.1 9.6 + - - +
53G LEU* 2.7 51.1 + - + +
56G PRO* 3.7 26.8 - - - +
57G ASP* 3.0 35.4 + - - -
34H VAL* 4.4 8.7 - - - +
35H PRO* 4.6 7.9 + - - +
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Residues in contact with SER 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F MET 2.9 14.1 + - - -
74F THR 2.7 17.0 + - - -
76F ARG* 1.3 75.9 - - - +
78F ASN* 1.3 64.0 + - - +
80F THR* 2.9 42.7 + - - -
32G TYR* 3.2 28.7 + - - -
53G LEU* 5.0 10.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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