Contacts of the helix formed by residues 60 - 82 (chain A) in PDB entry 2E6O
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 LYS 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A LYS 4.9 7.9 - - - -
59A MET* 1.3 76.7 - - - +
61A ASN* 1.3 69.4 + - - +
62A GLU* 3.4 7.0 - - + +
63A GLU* 3.6 24.5 - - + +
64A ARG* 2.8 32.9 + - - +
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Residues in contact with ASN 61 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A LYS* 1.3 79.4 - - - +
62A GLU* 1.3 66.7 + - + +
64A ARG* 3.7 20.0 + - - +
65A ARG* 3.3 19.9 + - - +
68A THR* 5.3 0.2 + - - -
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Residues in contact with GLU 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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60A LYS* 4.2 3.7 - - + +
61A ASN* 1.3 78.0 - - + +
63A GLU* 1.3 70.2 + - + +
64A ARG 3.1 2.5 - - - -
65A ARG* 3.1 34.7 + - + +
66A MET* 3.8 9.0 + - - +
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Residues in contact with GLU 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 MET* 3.6 23.3 - - + +
60A LYS* 3.6 40.4 - - + +
61A ASN 3.4 0.4 - - - -
62A GLU* 1.3 80.7 - - + +
64A ARG* 1.3 57.4 + - - +
66A MET* 3.1 39.8 - - + +
67A TYR* 3.4 6.4 - - - -
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Residues in contact with ARG 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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56A TRP* 3.1 71.7 + - + +
57A LYS* 4.6 8.2 + - - +
59A MET* 3.6 32.1 + - + -
60A LYS* 2.8 19.2 + - - +
61A ASN* 3.8 23.1 + - - +
62A GLU 3.1 0.6 - - - -
63A GLU* 1.3 75.1 - - - +
65A ARG* 1.3 57.8 + - - +
66A MET 3.1 2.5 - - - -
67A TYR* 2.8 27.3 + - - +
68A THR* 2.7 21.6 + - - +
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Residues in contact with ARG 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 ASN 3.3 12.9 + - - +
62A GLU* 3.1 28.1 + - - +
64A ARG* 1.3 78.1 - - - +
66A MET* 1.3 63.1 + - - +
67A TYR 3.0 0.9 + - - -
68A THR* 3.0 19.8 + - - +
69A LEU* 3.0 50.1 + - + +
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Residues in contact with MET 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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27A LEU* 4.4 1.4 - - - +
32A TYR* 5.1 2.0 - - - -
59A MET* 5.5 1.1 - - - +
62A GLU 3.8 6.6 + - - +
63A GLU* 3.1 47.1 - - + +
65A ARG* 1.3 78.7 - - - +
67A TYR* 1.3 94.3 + - + +
69A LEU* 5.4 0.4 - - - +
70A GLU* 2.9 25.7 + - - +
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Residues in contact with TYR 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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24A ALA* 3.6 21.8 - - - +
27A LEU* 3.7 26.0 - - + -
28A PHE* 3.9 29.7 - + + -
31A LYS* 4.1 23.3 - - + +
32A TYR* 2.9 35.9 + + - -
56A TRP* 3.6 18.6 - + + -
59A MET* 4.0 7.8 - - + -
63A GLU 3.4 11.2 - - - -
64A ARG 2.8 11.2 + - - +
66A MET* 1.3 112.9 - - + +
68A THR* 1.3 59.5 + - - +
71A ALA* 2.7 38.0 + - - +
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Residues in contact with THR 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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24A ALA* 3.9 12.9 - - + +
56A TRP* 4.6 4.2 - - + -
64A ARG* 2.7 22.7 + - - +
65A ARG* 3.0 17.1 + - - -
67A TYR* 1.3 76.9 - - - +
69A LEU* 1.3 65.5 + - + +
71A ALA* 3.9 1.7 - - - +
72A LYS* 3.0 37.3 + - - +
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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 ARG* 3.0 54.2 + - + +
68A THR* 1.3 78.5 - - + +
70A GLU* 1.3 69.0 + - - +
72A LYS* 3.0 34.2 + - + +
73A ALA* 3.2 7.6 + - - +
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Residues in contact with GLU 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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27A LEU* 3.5 26.7 - - + -
31A LYS* 5.8 1.9 + - - -
66A MET 2.9 24.8 + - - +
68A THR 3.4 0.2 - - - -
69A LEU* 1.3 81.3 - - - +
71A ALA* 1.3 63.1 + - - +
72A LYS 3.2 0.2 + - - -
73A ALA* 3.2 15.4 + - - +
74A LEU* 3.4 26.5 + - + +
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Residues in contact with ALA 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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22A MET* 3.1 24.6 - - - +
23A ASN* 3.5 4.5 - - - +
24A ALA* 3.5 20.6 - - - +
27A LEU* 4.4 6.9 - - + +
67A TYR 2.7 24.0 + - - +
68A THR 3.9 2.0 - - - +
70A GLU* 1.3 75.3 - - - +
72A LYS* 1.3 56.8 + - - +
74A LEU* 3.0 12.4 + - - +
75A ALA* 2.8 28.6 + - - +
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Residues in contact with LYS 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 THR* 3.0 31.0 + - - +
69A LEU* 3.0 26.2 + - + +
71A ALA* 1.3 76.2 - - - +
73A ALA* 1.3 56.5 + - - +
75A ALA* 2.8 27.2 + - + +
76A GLU* 3.0 34.6 + - + +
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Residues in contact with ALA 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 3.2 6.4 + - - +
70A GLU* 3.2 15.2 + - - +
72A LYS* 1.3 78.3 - - - +
74A LEU* 1.3 62.7 + - + +
76A GLU* 3.4 6.4 + - - +
77A GLU* 2.8 33.7 + - - +
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Residues in contact with LEU 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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22A MET* 4.1 36.6 - - + -
27A LEU* 4.7 14.1 - - + -
70A GLU* 3.5 25.4 - - + +
71A ALA* 3.0 12.9 + - - +
73A ALA* 1.3 81.4 - - + +
75A ALA* 1.3 59.6 + - - +
77A GLU* 4.4 12.6 - - - +
78A GLN* 3.1 44.8 + - + +
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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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21A PRO* 4.6 23.1 - - + +
22A MET 5.2 4.0 + - - +
23A ASN* 6.1 2.0 - - - +
71A ALA 2.8 11.8 + - - +
72A LYS* 2.8 16.0 + - + +
74A LEU* 1.3 77.1 - - - +
76A GLU* 1.3 60.9 + - + +
78A GLN* 4.4 2.1 - - - +
79A LYS* 3.1 26.7 + - - +
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Residues in contact with GLU 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 LYS* 3.0 34.3 + - + +
73A ALA* 4.0 5.6 - - - +
75A ALA* 1.3 81.4 - - + +
77A GLU* 1.3 64.8 + - - +
78A GLN 3.3 0.4 - - - -
79A LYS* 3.1 26.2 + - + +
80A ARG* 3.4 12.7 + - + +
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Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ALA* 2.8 20.0 + - + +
74A LEU* 4.4 13.4 - - - +
76A GLU* 1.3 75.3 - - - +
78A GLN* 1.3 57.6 + - + +
80A ARG* 2.8 34.2 + - + +
81A LEU* 3.0 30.2 + - + +
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Residues in contact with GLN 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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20A ARG 4.2 6.5 + - - +
21A PRO* 4.0 18.2 - - + +
22A MET* 4.1 32.7 - - - +
74A LEU* 3.1 31.2 + - + +
75A ALA* 4.6 4.0 - - - +
77A GLU* 1.3 77.6 - - + +
79A LYS* 1.3 61.0 + - + +
81A LEU* 3.6 10.8 + - + +
82A ASN* 3.2 36.4 + - - +
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Residues in contact with LYS 79 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A GLY 4.3 15.8 + - - +
2A SER* 4.3 23.9 + - - -
75A ALA 3.1 24.5 - - - +
76A GLU* 3.3 14.6 - - + +
77A GLU 3.0 0.6 + - - -
78A GLN* 1.3 77.6 - - + +
80A ARG* 1.3 64.5 + - + +
82A ASN* 3.2 22.4 - - - +
83A PRO* 3.7 3.8 - - - +
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Residues in contact with ARG 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 GLU* 3.5 15.9 - - - +
77A GLU* 2.8 16.4 + - + +
79A LYS* 1.3 77.1 - - + +
81A LEU* 1.3 62.7 + - + +
82A ASN 3.4 0.3 + - - -
83A PRO* 3.5 14.8 - - - +
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Residues in contact with LEU 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 GLU* 3.0 34.8 + - + +
78A GLN* 4.0 10.3 - - + +
80A ARG* 1.3 77.1 - - + +
82A ASN* 1.3 66.0 + - - +
83A PRO* 2.9 10.5 - - - +
84A ASP* 5.1 0.3 - - - +
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Residues in contact with ASN 82 (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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1A GLY 3.5 14.0 - - - +
19A LYS* 5.7 8.2 - - - +
78A GLN* 3.2 29.7 + - - +
79A LYS* 3.2 11.6 - - - +
80A ARG 3.2 0.6 - - - -
81A LEU* 1.3 85.8 - - - +
83A PRO* 1.3 63.2 - - - +
84A ASP* 3.2 12.7 + - - +
85A CYS* 3.9 14.0 - - + +
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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