Contacts of the helix formed by residues 60 - 81 (chain A) in PDB entry 3CJE
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 PRO 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PHE* 4.2 16.6 - - + -
34A MSE 5.8 4.0 - - + -
40A GLU* 5.8 0.4 - - - +
42A PHE* 3.3 34.1 - - + -
58A ALA 4.6 0.4 - - - +
59A PRO* 1.3 91.5 - - + +
61A PRO* 1.3 78.3 - - + +
62A LEU* 4.4 2.9 - - + +
63A ALA* 3.0 24.1 + - + +
64A LEU* 3.4 6.2 + - - +
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Residues in contact with PRO 61 (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 PRO 4.4 1.6 - - - +
60A PRO* 1.3 88.6 - - + +
62A LEU* 1.3 66.9 + - + +
64A LEU* 3.1 15.1 + - + +
65A PHE* 3.0 19.6 + - - +
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Residues in contact with LEU 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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14A VAL* 3.9 18.8 - - + -
16A PHE* 3.7 23.0 - - + -
60A PRO* 3.2 2.6 - - + +
61A PRO* 1.3 84.0 - - + +
63A ALA* 1.3 57.4 + - - +
65A PHE* 3.5 12.5 - - + +
66A ILE* 3.0 31.0 + - - +
99A TRP* 3.7 49.9 - - + +
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Residues in contact with ALA 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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16A PHE* 3.8 7.3 - - + -
32A VAL* 3.9 25.4 - - + +
42A PHE* 4.0 8.7 - - + -
44A LEU* 3.7 7.6 - - + +
59A PRO* 3.9 11.2 - - + -
60A PRO* 3.0 30.2 + - + +
62A LEU* 1.3 76.3 - - - +
64A LEU* 1.3 64.6 + - - +
66A ILE* 3.5 2.6 + - - +
67A ALA* 3.1 25.8 + - - +
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Residues in contact with LEU 64 (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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44A LEU* 4.1 15.3 - - + -
59A PRO* 3.9 27.6 - - + +
60A PRO 3.4 8.9 + - - +
61A PRO* 3.1 13.1 + - + +
63A ALA* 1.3 79.6 - - - +
65A PHE* 1.3 56.6 + - - +
67A ALA* 3.8 2.1 - - + +
68A GLY* 2.9 26.7 + - - -
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Residues in contact with PHE 65 (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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61A PRO 3.0 13.1 + - - +
62A LEU* 3.5 14.8 - - + +
63A ALA 3.3 0.2 - - - -
64A LEU* 1.3 77.7 - - - +
66A ILE* 1.3 64.2 + - + +
68A GLY* 3.2 2.7 + - - -
69A LEU* 2.9 37.4 + - + +
97A VAL* 4.7 2.5 - - + -
99A TRP* 3.8 35.2 - + - -
115A PHE* 4.0 17.7 - + - -
143A LEU* 5.2 8.6 - - + +
147A LEU* 4.0 37.5 - - + -
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Residues in contact with ILE 66 (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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16A PHE* 3.4 42.2 - - + +
17A THR 3.8 4.5 - - - -
18A CYS* 4.0 5.8 - - + -
32A VAL* 3.6 26.9 - - + -
62A LEU 3.0 19.7 + - - +
63A ALA* 3.6 6.3 - - - +
65A PHE* 1.3 84.3 - - + +
67A ALA* 1.3 59.4 + - - +
69A LEU* 3.4 3.4 + - + +
70A THR* 2.8 35.1 + - - -
95A CYS* 3.7 31.6 - - - +
97A VAL* 3.8 20.0 - - + -
99A TRP* 5.4 1.1 - - + -
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Residues in contact with ALA 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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18A CYS* 4.3 8.3 - - - -
30A LEU* 3.4 29.3 - - + +
32A VAL* 4.0 7.4 - - + -
44A LEU* 3.7 21.5 - - + -
46A THR* 4.5 1.9 - - + +
63A ALA 3.1 19.1 + - - +
64A LEU* 3.8 4.0 - - + +
66A ILE* 1.3 78.3 - - - +
68A GLY* 1.3 57.2 + - - +
71A GLY* 2.8 26.9 + - - -
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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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46A THR* 5.1 6.9 - - - +
64A LEU 2.9 16.2 + - - -
65A PHE* 3.6 4.3 - - - -
67A ALA* 1.3 77.1 - - - +
69A LEU* 1.3 56.1 + - - +
71A GLY* 3.8 1.2 - - - -
72A CYS* 2.8 31.9 + - - +
143A LEU* 3.5 11.5 - - - +
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Residues in contact with LEU 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 PHE* 2.9 24.6 + - + +
66A ILE* 3.7 5.4 - - + +
68A GLY* 1.3 75.5 - - - +
70A THR* 1.3 64.2 + - - +
72A CYS* 3.3 0.9 + - - +
73A VAL* 3.1 28.5 + - + +
95A CYS* 4.0 22.2 - - - -
97A VAL* 4.5 2.9 - - + -
115A PHE* 4.0 26.9 - - + -
117A ILE* 4.4 13.5 - - + -
141A CYS* 4.7 0.7 - - - -
143A LEU* 3.7 20.7 - - + +
144A GLU* 4.1 23.6 - - + -
147A LEU* 4.0 23.6 - - + -
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Residues in contact with THR 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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18A CYS* 3.5 28.4 - - + +
20A GLY 4.3 0.7 - - - +
30A LEU* 3.9 10.3 - - + -
66A ILE 2.8 18.0 + - - -
67A ALA 3.9 1.6 - - - -
69A LEU* 1.3 75.8 - - - +
71A GLY* 1.3 57.8 + - - +
73A VAL* 3.4 7.1 + - - +
74A MSE 3.0 38.9 + - - +
93A VAL* 3.9 34.5 - - + +
95A CYS* 3.4 23.4 - - + +
117A ILE* 6.1 0.9 - - - -
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Residues in contact with GLY 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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28A ASN* 3.6 7.3 + - - -
30A LEU* 4.2 8.0 - - - +
46A THR* 3.9 22.0 - - - -
67A ALA 2.8 17.0 + - - -
68A GLY 3.8 1.1 - - - -
70A THR* 1.3 76.6 - - - +
72A CYS* 1.3 57.1 + - - +
74A MSE 3.4 1.3 + - - -
75A THR* 2.8 36.7 + - - -
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Residues in contact with CYS 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 2.8 19.7 + - - +
69A LEU 3.6 3.4 - - - +
70A THR 3.3 0.2 - - - -
71A GLY* 1.3 73.2 - - - +
73A VAL* 1.3 66.8 + - - +
75A THR* 3.2 5.4 + - - -
76A GLN* 3.1 40.3 + - - +
141A CYS* 3.1 30.5 - - - -
142A PHE* 3.8 21.3 - - - -
143A LEU* 4.0 17.7 - - + -
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Residues in contact with VAL 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 LEU* 3.1 14.5 + - + +
70A THR* 3.7 9.0 - - - +
72A CYS* 1.3 74.7 - - - +
74A MSE 1.3 63.7 + - - +
76A GLN* 3.2 7.0 + - - +
77A ILE* 3.1 40.2 + - + +
93A VAL* 4.5 7.6 - - + -
117A ILE* 3.9 29.6 - - + -
119A ILE* 4.6 6.1 - - + -
137A ALA* 4.4 6.4 - - + +
138A LYS* 6.3 0.2 - - - -
141A CYS* 4.1 6.3 - - + -
144A GLU* 3.3 36.3 - - + +
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Residues in contact with MSE 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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20A GLY* 3.6 30.7 - - - +
21A LYS 3.5 7.2 - - - -
22A ALA* 3.4 31.6 - - + +
28A ASN* 3.3 39.0 - - - +
30A LEU* 4.0 6.3 - - - -
70A THR* 3.0 29.5 + - - +
73A VAL* 1.3 74.5 - - - +
75A THR* 1.3 62.3 + - - +
77A ILE* 3.3 5.2 + - - +
78A ARG* 3.0 30.1 + - - +
91A LEU* 4.0 18.8 - - + +
93A VAL* 3.5 23.1 - - + +
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Residues in contact with THR 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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26A MSE 3.6 19.7 + - + +
28A ASN* 3.4 13.6 + - - +
46A THR* 4.6 3.1 + - - -
47A ASP 6.2 0.3 - - - -
48A GLU* 3.4 33.8 + - + +
71A GLY 2.8 24.8 + - - -
72A CYS* 3.6 7.1 - - - -
74A MSE 1.3 76.4 - - - +
76A GLN* 1.3 67.4 + - - +
78A ARG* 3.3 4.5 + - - +
79A ALA* 2.8 29.8 + - + +
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Residues in contact with GLN 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 CYS* 3.1 32.7 + - - +
73A VAL 3.2 2.4 + - - +
75A THR* 1.3 82.9 - - - +
77A ILE* 1.3 67.2 + - - +
79A ALA* 4.4 4.8 - - - +
80A PHE* 2.9 48.7 + - + +
137A ALA* 3.7 36.8 - - + +
140A GLY 3.4 22.8 + - - +
141A CYS* 3.7 9.2 - - + -
142A PHE* 4.7 8.3 - - - -
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Residues in contact with ILE 77 (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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73A VAL* 3.1 32.9 + - + +
74A MSE 3.6 7.0 - - - +
76A GLN* 1.3 75.7 - - - +
78A ARG* 1.3 58.8 + - - +
81A ALA* 3.0 30.8 + - - +
88A VAL* 4.5 7.4 - - + -
91A LEU* 4.1 19.3 - - + -
93A VAL* 4.4 5.8 - - + -
119A ILE* 4.1 30.3 - - + -
121A LEU* 4.0 21.8 - - + -
133A LEU* 3.8 20.7 - - + +
134A ILE* 5.1 4.5 - - + -
137A ALA* 3.8 17.9 - - + -
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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
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22A ALA* 3.4 19.7 - - - +
23A VAL 3.1 19.2 + - - -
24A GLY 3.1 10.3 + - - -
25A LYS 3.0 23.7 + - - -
26A MSE 3.4 22.2 - - - +
27A ARG 2.8 27.7 + - - -
28A ASN* 3.1 20.1 + - - +
74A MSE 3.0 20.9 + - - +
75A THR* 3.8 4.5 - - - +
77A ILE* 1.3 76.9 - - + +
79A ALA* 1.3 61.3 + - - +
80A PHE 3.5 0.2 + - - -
81A ALA* 3.8 6.5 + - - +
82A LYS 5.0 1.0 + - - -
91A LEU* 3.7 15.9 - - + -
169A GOL 3.0 37.5 + - - +
170A GOL 2.7 28.6 + - - +
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Residues in contact with ALA 79 (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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26A MSE 4.2 15.4 - - + +
75A THR* 2.8 20.1 + - + +
76A GLN* 3.9 7.2 - - - +
78A ARG* 1.3 76.9 - - - +
80A PHE* 1.3 75.7 + - + +
81A ALA 3.6 0.2 - - - -
82A LYS* 5.1 1.4 + - - +
83A ARG* 4.8 5.7 + - - +
170A GOL 5.5 0.7 - - - -
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Residues in contact with PHE 80 (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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76A GLN* 2.9 40.8 + - - +
79A ALA* 1.3 88.0 - - + +
81A ALA* 1.3 66.6 + - - +
82A LYS 3.4 1.3 - - - -
83A ARG* 3.2 13.6 + - + +
84A LEU* 3.0 29.9 + - + +
133A LEU* 3.6 13.9 - - + -
136A ALA* 3.4 43.5 - - + -
137A ALA* 3.9 5.6 - - - -
140A GLY* 4.2 10.3 - - - -
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Residues in contact with ALA 81 (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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77A ILE 3.0 19.4 + - - +
78A ARG* 3.8 7.2 + - - +
79A ALA 3.6 1.8 - - - -
80A PHE* 1.3 77.8 - - - +
82A LYS* 1.3 64.3 + - - +
84A LEU 3.1 1.4 + - - -
85A LYS 3.0 4.3 + - - -
86A VAL* 2.9 38.6 + - - +
88A VAL* 3.9 16.4 - - + -
133A LEU* 3.7 12.8 - - + -
174A GOL 3.7 15.7 - - - -
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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