Contacts of the helix formed by residues 54 - 78 (chain A) in PDB entry 3N1Z
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 THR 54 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ARG* 4.0 12.0 - - + +
9A TRP* 3.8 30.0 - - + -
10A TYR* 3.6 31.0 - - + -
13A THR* 5.0 4.3 - - + -
53A ILE* 1.3 73.7 - - - +
55A TYR* 1.3 67.4 + - - +
56A PRO* 3.8 11.6 - - - +
57A GLU* 2.9 30.4 + - - +
58A TYR* 3.0 18.7 + - - +
129A PHE* 3.9 6.5 - - - -
167B THR* 4.8 1.6 - - - -
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Residues in contact with TYR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 1.3 71.1 - - - +
56A PRO* 1.3 70.3 - - + +
58A TYR* 3.0 12.0 + + - +
59A VAL* 3.0 35.3 + - + +
129A PHE* 3.5 27.2 - + + -
86B TYR* 2.7 26.5 + + - -
90B GLN* 3.3 23.5 + - + +
94B GLU* 3.8 20.4 - - + -
160B ALA* 3.3 29.4 - - + -
163B LEU* 4.7 5.2 - - + -
164B ARG* 3.6 38.8 - - + -
167B THR* 3.9 21.5 + - - +
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Residues in contact with PRO 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TRP* 5.1 4.5 - - + -
54A THR* 3.5 13.9 - - - +
55A TYR* 1.3 94.3 - - + +
57A GLU* 1.3 64.5 + - + +
58A TYR 3.1 0.9 + - - -
59A VAL* 3.2 11.6 - - + +
60A SER* 3.1 24.9 + - - -
94B GLU* 3.5 26.2 - - + +
98B GLN* 4.0 28.0 - - + +
167B THR* 4.1 13.5 - - + -
168B HIS* 6.2 0.2 - - - +
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 3.0 42.8 + - - +
53A ILE* 3.7 9.4 - - + +
54A THR* 2.9 38.6 + - - +
56A PRO* 1.3 78.8 - - + +
58A TYR* 1.3 57.5 + - - +
60A SER* 3.8 3.9 - - - -
61A ILE* 2.9 47.8 + - + +
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Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 4.1 12.5 - - + +
54A THR 3.0 11.3 + - - +
55A TYR* 3.0 11.8 + + - +
57A GLU* 1.3 72.9 - - - +
59A VAL* 1.3 75.5 + - + +
60A SER 2.9 2.0 + - - -
61A ILE* 3.2 1.4 + - - -
62A GLN* 2.8 41.8 + - + +
129A PHE* 3.4 36.1 - + + -
132A MET* 3.2 34.2 - - + +
133A ASP* 2.8 26.8 + - - -
233A ARG* 3.8 21.1 - - - -
83B TYR* 2.7 31.6 + + - -
86B TYR* 6.3 0.2 - + - -
87B ASN* 4.2 11.4 - - - -
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TYR* 3.0 48.4 + - + +
56A PRO* 3.2 17.5 - - + +
58A TYR* 1.3 79.4 - - + +
60A SER* 1.3 59.6 + - - +
63A ARG* 3.1 27.5 + - - +
86B TYR* 4.5 2.2 - - + -
87B ASN* 3.3 30.5 - - - +
90B GLN* 4.1 6.7 - - + -
91B ASP* 3.9 29.4 - - - +
94B GLU* 4.1 7.9 - - + -
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Residues in contact with SER 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO 3.1 18.4 + - - -
57A GLU* 3.8 4.9 - - - -
58A TYR 2.9 2.4 + - - -
59A VAL* 1.3 77.7 - - - +
61A ILE* 1.3 66.0 + - - +
63A ARG* 3.2 5.9 + - - +
64A GLU* 3.2 24.9 + - - +
91B ASP* 3.2 20.8 + - - -
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Residues in contact with ILE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 4.6 10.1 - - + -
57A GLU* 2.9 37.8 + - + +
58A TYR* 4.0 2.5 - - - +
60A SER* 1.3 74.1 + - - +
62A GLN* 1.3 64.8 + - - +
64A GLU* 3.1 10.9 + - - +
65A LYS* 3.0 50.6 + - + +
233A ARG* 4.5 3.8 - - - +
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Residues in contact with GLN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TYR* 2.8 40.7 + - + +
61A ILE* 1.3 72.4 - - + +
63A ARG* 1.3 65.4 + - - +
65A LYS* 3.1 21.0 + - - +
66A ASP* 3.1 27.5 + - - +
133A ASP* 4.6 0.2 + - - -
136A ARG* 4.1 7.9 - - - +
230A ASP* 2.9 29.9 + - - +
233A ARG* 2.6 33.2 + - - +
83B TYR* 3.1 29.9 + - - +
87B ASN* 3.9 10.8 - - - +
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Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A VAL 3.1 23.1 + - - +
60A SER 3.3 4.0 - - - +
61A ILE 3.2 0.6 - - - -
62A GLN* 1.3 77.2 - - - +
64A GLU* 1.3 80.0 + - - +
66A ASP* 3.5 4.4 + - - +
67A SER* 3.1 29.2 + - - +
84B ARG 5.9 0.7 - - - -
87B ASN* 4.2 15.2 - - + +
88B LEU* 3.5 39.6 + - + +
91B ASP* 2.8 44.1 + - - +
92B GLY* 5.1 3.4 - - - +
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A SER* 3.2 12.8 + - - +
61A ILE* 3.1 10.6 + - - +
63A ARG* 1.3 98.8 + - - +
65A LYS* 1.3 66.9 + - - +
67A SER* 3.2 13.2 + - - -
68A GLY* 3.1 19.4 + - - -
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE* 3.0 32.3 + - + +
62A GLN* 3.1 31.6 + - - +
64A GLU* 1.3 76.9 - - + +
66A ASP* 1.3 62.4 + - - +
68A GLY* 3.4 1.6 + - - -
69A ALA* 3.2 21.5 + - - +
136A ARG* 3.5 19.4 + - - +
226A SER* 4.1 7.2 + - - +
229A THR* 2.7 38.7 + - - +
230A ASP* 2.7 23.9 + - - +
233A ARG* 3.4 9.3 - - - +
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Residues in contact with ASP 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN 3.1 14.9 + - - +
63A ARG* 4.1 3.6 - - - +
65A LYS* 1.3 74.6 - - - +
67A SER* 1.3 68.1 + - - +
69A ALA* 4.5 0.9 - - - -
70A TYR* 2.8 55.8 + - + +
136A ARG* 2.9 29.2 + - - +
140A ILE* 3.7 3.5 - - - +
83B TYR* 3.2 31.0 - - - -
84B ARG* 3.7 22.7 - - + +
87B ASN* 5.1 0.5 - - - +
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Residues in contact with SER 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ARG* 3.1 26.6 + - - +
64A GLU* 3.2 20.3 + - - -
66A ASP* 1.3 74.6 - - - +
68A GLY* 1.3 58.0 + - - +
70A TYR* 3.8 2.5 - - - +
71A SER* 2.8 38.7 + - - -
88B LEU* 5.5 3.3 - - - +
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Residues in contact with GLY 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLU 3.1 10.3 + - - -
65A LYS 3.8 2.9 - - - -
67A SER* 1.3 79.6 - - - +
69A ALA* 1.3 55.7 + - - +
71A SER* 3.2 5.7 + - - -
72A ILE* 2.9 42.8 + - - +
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS 3.2 16.4 + - - +
66A ASP* 3.9 3.1 - - - +
68A GLY* 1.3 75.4 - - - +
70A TYR* 1.3 65.2 + - + +
72A ILE* 3.3 8.9 + - - +
73A LYS* 3.0 23.9 + - - +
140A ILE* 4.1 24.9 - - + -
144A PHE* 3.9 11.3 - - + -
222A SER* 5.1 5.3 - - - +
223A LEU* 5.2 4.9 - - - -
226A SER* 4.4 16.6 - - - +
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Residues in contact with TYR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ASP* 2.8 60.8 + - + +
67A SER* 4.2 2.5 - - - +
69A ALA* 1.3 75.9 - - - +
71A SER* 1.3 62.4 + - - +
73A LYS* 3.6 6.2 + - - +
74A ALA* 3.2 23.2 + - - +
139A GLN* 4.8 2.9 + - - +
140A ILE* 3.4 40.8 + - + +
143A TYR* 3.3 41.6 - + - +
144A PHE* 4.7 4.3 - + - -
27B GLU* 4.2 7.2 + - - -
31B VAL* 5.9 0.5 - - - +
84B ARG* 3.8 32.0 - - + +
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Residues in contact with SER 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A SER* 2.8 25.5 + - - -
68A GLY* 3.4 6.5 - - - -
70A TYR* 1.3 73.8 - - - +
72A ILE* 1.3 67.4 + - - +
74A ALA* 3.2 7.8 + - - +
75A ALA* 3.1 22.2 + - - +
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLY* 2.9 27.4 + - - +
69A ALA* 3.7 3.6 - - - +
71A SER* 1.3 76.0 - - - +
73A LYS* 1.3 64.0 + - - +
75A ALA* 3.1 16.6 + - - +
76A LEU* 3.1 33.8 + - + +
218A HIS* 4.4 2.0 - - + +
219A THR* 4.3 7.4 - - - -
222A SER* 3.2 39.7 - - - +
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Residues in contact with LYS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ALA 3.0 16.9 + - - +
70A TYR* 3.9 6.3 - - - +
71A SER 3.3 0.2 - - - -
72A ILE* 1.3 76.8 - - - +
74A ALA* 1.3 58.9 + - - +
76A LEU* 3.8 0.7 - - - +
77A GLU* 2.9 60.6 + - - +
143A TYR* 3.5 45.4 + - + -
144A PHE* 3.6 42.2 - - + +
147A ALA* 3.9 10.7 - - + +
219A THR* 3.8 20.1 + - + +
500A GOL 5.7 0.2 - - - +
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A TYR 3.2 10.7 + - - +
71A SER* 3.2 11.0 + - - +
73A LYS* 1.3 80.8 - - - +
75A ALA* 1.3 64.2 + - - +
77A GLU* 3.3 20.1 + - - +
78A ARG* 4.6 2.4 + - - +
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A SER 3.1 10.0 + - - +
72A ILE* 3.1 11.4 + - - +
74A ALA* 1.3 81.3 - - - +
76A LEU* 1.3 68.2 + - + +
78A ARG* 5.0 2.9 + - - +
79A ASP* 5.3 1.6 + - - +
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ILE* 3.1 22.9 + - + +
73A LYS 3.8 0.4 - - - +
75A ALA* 1.3 85.4 - - + +
77A GLU* 1.3 67.2 + - - +
78A ARG 3.5 1.6 - - - -
79A ASP* 3.1 28.0 - - + +
80A GLY 3.9 1.6 + - - -
81A PHE* 5.0 3.3 + - + +
218A HIS* 3.7 35.4 - - + +
219A THR* 3.5 27.9 + - - +
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Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LYS* 2.9 38.8 + - - +
74A ALA* 3.3 14.7 + - - +
76A LEU* 1.3 76.8 - - - +
78A ARG* 1.3 65.6 + - + +
79A ASP 3.0 5.5 + - - -
80A GLY* 3.0 16.3 + - - -
147A ALA* 3.5 26.2 - - - +
151A ARG* 5.2 2.6 + - - -
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Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA 4.6 2.3 + - - +
75A ALA 5.0 2.6 + - - +
76A LEU 3.5 0.4 - - - -
77A GLU* 1.3 79.8 - - + +
79A ASP* 1.3 59.2 + - - +
80A GLY* 3.0 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) + - + + + + + -
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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