Contacts of the helix formed by residues 51 - 68 (chain A) in PDB entry 2ECB
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 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ARG* 4.8 0.9 - - - -
50A LEU* 1.3 79.6 - - + +
52A ARG* 1.3 68.8 + - - +
53A ARG* 4.1 16.1 - - - +
54A GLU* 3.2 31.9 + - - +
55A ILE* 3.1 26.2 + - - +
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Residues in contact with ARG 52 (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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41A LEU* 3.5 38.1 - - + +
45A ARG* 2.7 52.8 - - - +
50A LEU 4.1 0.6 + - - -
51A THR* 1.3 74.0 - - - +
53A ARG* 1.3 80.1 + - + +
55A ILE* 3.6 2.1 + - - +
56A ASP* 3.1 27.0 + - - +
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Residues in contact with ARG 53 (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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10A PHE* 6.2 3.8 - - - -
15A PHE* 4.6 11.5 - - + -
51A THR* 3.2 15.2 - - - +
52A ARG* 1.3 91.7 - - + +
54A GLU* 1.3 59.3 + - - +
56A ASP* 3.9 4.0 - - - +
57A ALA* 2.9 32.8 + - - +
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Residues in contact with GLU 54 (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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15A PHE* 3.6 55.3 - - + +
17A GLU 5.1 3.5 - - - +
18A LYS* 4.2 7.4 + - - -
50A LEU* 3.1 43.1 - - + +
51A THR* 3.2 28.7 + - - +
53A ARG* 1.3 80.0 - - - +
55A ILE* 1.3 64.2 + - - +
57A ALA* 3.5 2.1 - - - +
58A TRP* 2.9 24.2 + - - +
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Residues in contact with ILE 55 (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 LYS* 6.1 0.2 - - - +
26A LEU* 3.5 27.4 - - + -
36A LEU* 3.4 20.4 - - + -
41A LEU* 4.0 8.7 - - + +
44A LEU* 3.8 14.1 - - + -
45A ARG* 3.5 39.3 - - + +
48A THR* 3.8 15.7 - - - +
50A LEU* 4.2 7.8 - - + +
51A THR 3.1 18.7 + - - +
52A ARG 3.9 2.9 - - - +
54A GLU* 1.3 74.1 - - - +
56A ASP* 1.3 65.2 + - - +
58A TRP* 2.9 16.1 + - - +
59A PHE* 3.0 23.3 + - + -
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Residues in contact with ASP 56 (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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36A LEU* 3.5 36.0 - - + +
41A LEU* 4.5 7.7 - - + +
52A ARG 3.1 16.9 + - - +
53A ARG* 3.9 3.8 - - - +
55A ILE* 1.3 80.2 - - - +
57A ALA* 1.3 65.3 + - - +
58A TRP 3.1 0.5 + - - -
59A PHE* 3.1 12.4 + - - +
60A THR* 3.1 20.3 + - - -
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Residues in contact with ALA 57 (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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15A PHE* 4.2 20.0 - - + -
53A ARG 2.9 19.9 + - - +
54A GLU 3.5 4.3 - - - +
56A ASP* 1.3 76.8 + - - +
58A TRP* 1.3 63.9 + - - +
60A THR* 3.3 8.4 + - - -
61A GLU* 3.3 20.3 + - - +
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Residues in contact with TRP 58 (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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15A PHE* 6.0 0.2 - - - -
18A LYS* 3.5 32.5 - - - +
23A LEU* 3.8 29.9 - - + +
26A LEU* 3.5 18.6 - - + -
27A GLN* 3.7 23.6 - - + -
30A PHE* 3.4 28.9 - + + -
54A GLU 2.9 12.0 + - - +
55A ILE* 2.9 13.9 + - - +
57A ALA* 1.3 73.2 - - - +
59A PHE* 1.3 90.7 + + - +
60A THR 2.9 1.4 + - - -
61A GLU* 3.2 32.5 + - - +
62A LYS* 3.0 62.3 + - + +
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Residues in contact with PHE 59 (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 LEU* 3.7 13.5 - - + -
29A SER* 3.9 3.6 - - - -
30A PHE* 2.9 68.9 - + + -
33A SER 3.8 7.9 - - - -
34A SER 3.5 21.5 - - - +
36A LEU* 3.1 38.6 - - + +
40A GLU* 5.0 1.1 - - + -
44A LEU* 3.3 25.6 - - + -
55A ILE* 3.0 27.8 + - + -
56A ASP 3.1 8.7 + - - +
58A TRP* 1.3 90.8 - + - +
60A THR* 1.3 64.1 + - - +
62A LYS* 3.3 3.0 - - - +
63A LYS* 3.4 3.0 + - - +
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Residues in contact with THR 60 (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 ASP* 3.1 21.4 + - - -
57A ALA* 3.4 10.5 - - - -
58A TRP 2.9 1.0 + - - -
59A PHE* 1.3 73.4 - - - +
61A GLU* 1.3 70.7 + - - +
63A LYS* 2.8 38.2 + - + +
64A LYS* 3.8 8.9 + - - +
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Residues in contact with GLU 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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15A PHE 5.7 0.7 - - - +
16A LYS* 5.8 2.4 + - - -
18A LYS* 5.2 0.3 + - - -
57A ALA 3.3 6.6 + - - +
58A TRP* 3.2 42.1 + - + +
60A THR* 1.3 79.5 - - - +
62A LYS* 1.3 82.9 + - + +
64A LYS* 2.8 37.2 + - + +
65A SER* 3.5 2.0 + - - -
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Residues in contact with LYS 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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23A LEU* 6.0 0.2 - - - +
27A GLN* 4.3 20.2 - - - +
30A PHE* 3.0 41.7 - - + -
58A TRP* 3.0 45.7 + - + +
59A PHE* 3.3 8.3 - - - +
60A THR 3.0 0.2 + - - -
61A GLU* 1.3 84.2 - - + +
63A LYS* 1.3 55.1 + - - +
65A SER* 2.6 47.6 + - - -
66A LYS* 3.4 4.0 + - + +
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Residues in contact with LYS 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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30A PHE* 3.5 13.4 - - + -
34A SER* 3.7 31.6 - - - -
35A VAL* 3.6 23.3 - - - +
59A PHE 3.7 7.9 - - - +
60A THR* 2.8 31.1 + - + +
62A LYS* 1.3 72.9 - - - +
64A LYS* 1.3 65.7 + - + +
66A LYS* 2.8 29.7 + - - +
67A ALA* 3.3 3.5 + - - +
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Residues in contact with LYS 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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60A THR* 4.9 8.3 - - - +
61A GLU* 2.8 29.4 + - + +
63A LYS* 1.3 74.3 - - + +
65A SER* 1.3 62.8 + - - +
67A ALA* 2.8 29.4 + - + +
68A LEU* 3.8 4.3 + - - +
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Residues in contact with SER 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 GLU 3.5 1.8 + - - -
62A LYS* 2.6 35.2 + - - -
64A LYS* 1.3 73.9 - - - +
66A LYS* 1.3 60.4 + - - -
68A LEU* 3.3 34.0 + - - +
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Residues in contact with LYS 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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30A PHE* 4.3 23.1 + - + -
31A LEU* 5.7 5.3 + - + +
34A SER* 3.9 24.8 + - - -
62A LYS* 4.4 5.2 - - + +
63A LYS* 2.8 16.6 + - - +
65A SER* 1.3 72.1 - - - +
67A ALA* 1.3 58.7 + - - +
68A LEU 2.6 27.9 - - - +
70A GLU* 5.4 3.9 - - - +
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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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63A LYS 3.3 3.2 + - - +
64A LYS* 2.8 27.9 + - + +
66A LYS* 1.3 73.5 - - - +
68A LEU* 1.3 61.7 + - + +
69A LYS* 3.5 5.4 + - - +
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Residues in contact with LEU 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 LYS 4.4 3.8 - - - +
65A SER* 3.4 28.8 - - - +
66A LYS* 2.6 21.9 + - - +
67A ALA* 1.3 73.6 - - + +
69A LYS* 1.3 55.5 + - - +
70A GLU* 2.6 21.2 + - - +
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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