Contacts of the helix formed by residues 19 - 33 (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 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LYS* 1.3 75.7 - - - +
20A ALA* 1.3 69.7 + - - +
21A GLU* 3.7 14.1 + - + +
22A GLN* 2.7 58.7 + - + +
23A LEU* 2.9 13.0 + - - +
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Residues in contact with ALA 20 (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 4.1 0.8 + - - -
19A THR* 1.3 73.9 + - - +
21A GLU* 1.3 56.8 + - - +
23A LEU* 4.0 9.1 - - - +
24A ARG* 2.9 33.8 + - - +
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Residues in contact with GLU 21 (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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19A THR* 2.8 15.6 + - + +
20A ALA* 1.3 81.5 - - - +
22A GLN* 1.3 63.0 + - + +
24A ARG* 3.8 6.6 - - - +
25A VAL* 3.2 26.4 + - + +
47A GLN 5.1 6.8 - - - +
49A LYS* 6.2 0.5 - - - +
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Residues in contact with GLN 22 (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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17A GLU 5.1 1.2 + - - -
18A LYS* 4.5 8.7 - - + +
19A THR* 2.7 42.0 + - + +
21A GLU* 1.3 71.5 - - + +
23A LEU* 1.3 64.2 + - - +
25A VAL* 3.0 14.8 + - - +
26A LEU* 3.1 23.0 + - + +
47A GLN 5.3 1.1 - - - +
48A THR* 3.3 35.8 - - - +
49A LYS* 6.1 0.2 - - + -
50A LEU* 3.2 39.6 - - - +
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Residues in contact with LEU 23 (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* 3.8 34.8 - - + +
19A THR 2.9 13.9 + - - +
20A ALA* 4.0 7.2 - - - +
22A GLN* 1.3 71.9 - - - +
24A ARG* 1.3 55.1 + - - +
25A VAL 2.5 16.8 + - - -
26A LEU* 2.9 4.5 + - + -
27A GLN* 2.8 30.5 + - + +
58A TRP* 3.8 38.1 - - + +
62A LYS* 6.0 0.4 - - - +
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Residues in contact with ARG 24 (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 ALA 2.9 24.1 + - - +
21A GLU* 3.8 8.3 - - - +
23A LEU* 1.3 71.6 - - - +
25A VAL* 1.3 58.3 + - + +
27A GLN* 4.5 3.9 - - - +
28A ALA* 3.1 25.1 + - - +
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Residues in contact with VAL 25 (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 GLU* 3.2 19.7 - - + +
22A GLN* 3.0 8.5 + - - +
23A LEU 2.5 4.9 + - - -
24A ARG* 1.3 76.0 - - + +
26A LEU* 1.3 59.3 + - - +
27A GLN 3.1 1.1 - - - -
28A ALA* 2.7 25.9 + - - +
29A SER* 2.9 11.7 + - - -
44A LEU* 3.5 25.8 - - + -
47A GLN* 3.8 37.7 - - + +
48A THR* 4.0 6.3 - - + -
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Residues in contact with LEU 26 (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* 4.0 33.4 - - + -
22A GLN* 3.1 15.5 + - + +
23A LEU* 2.9 8.3 + - + +
25A VAL* 1.3 77.2 - - - +
27A GLN* 1.3 56.1 + - - +
29A SER* 3.1 3.4 + - - -
30A PHE* 2.7 37.8 + - - +
44A LEU* 4.2 4.3 - - + -
48A THR* 3.4 26.5 - - + -
50A LEU* 4.7 4.0 - - + -
55A ILE* 3.5 40.2 - - + -
58A TRP* 3.5 21.7 - - + -
59A PHE* 3.7 11.1 - - + -
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Residues in contact with GLN 27 (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* 2.8 24.7 + - + +
24A ARG* 4.5 4.0 - - - +
26A LEU* 1.3 74.5 - - - +
28A ALA* 1.3 61.3 + - - +
29A SER 3.3 0.5 + - - -
30A PHE* 4.6 1.9 - - + +
31A LEU* 3.1 66.7 + - - +
58A TRP* 3.7 12.0 - - + -
62A LYS* 4.3 26.3 - - - +
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Residues in contact with ALA 28 (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 ARG* 3.1 20.4 + - + +
25A VAL* 2.7 12.4 + - - +
27A GLN* 1.3 78.4 + - - +
29A SER* 1.3 58.3 + - - +
31A LEU* 4.3 8.1 - - - +
32A ASN* 4.3 10.9 + - - +
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Residues in contact with SER 29 (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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25A VAL* 2.9 9.3 + - - -
26A LEU 3.6 4.9 - - - -
28A ALA* 1.3 76.9 - - - +
30A PHE* 1.3 68.7 + - - +
31A LEU 2.7 4.0 + - - -
32A ASN* 2.7 17.9 + - - +
33A SER 3.1 8.7 + - - -
40A GLU* 2.5 44.7 + - - +
44A LEU* 3.8 17.8 - - - +
59A PHE* 3.9 5.8 - - - -
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Residues in contact with PHE 30 (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 2.7 21.3 + - - +
27A GLN* 4.6 2.0 - - - +
29A SER* 1.3 71.9 - - - +
31A LEU* 1.3 70.6 + - + +
33A SER 3.7 0.9 - - - -
34A SER* 2.9 69.7 + - - -
58A TRP* 3.4 15.3 - + + -
59A PHE* 2.9 51.4 - + + -
62A LYS* 3.0 37.0 - - + -
63A LYS* 3.5 20.0 - - + -
66A LYS* 4.3 19.7 + - + -
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Residues in contact with LEU 31 (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 GLN* 3.1 53.5 + - - +
28A ALA* 4.3 8.7 - - - +
29A SER 2.7 4.2 + - - +
30A PHE* 1.3 89.9 - - + +
32A ASN* 1.3 64.4 + - - +
34A SER* 4.2 3.1 + - - -
66A LYS* 5.7 5.4 + - + +
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Residues in contact with ASN 32 (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 ALA 4.3 8.0 + - - +
29A SER* 2.7 14.4 + - - +
31A LEU* 1.3 77.6 - - - +
33A SER* 1.3 64.1 + - - +
34A SER 4.3 0.3 + - - -
40A GLU* 5.4 4.2 + - - +
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Residues in contact with SER 33 (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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29A SER 3.1 5.1 + - - -
30A PHE* 3.0 14.1 - - - +
32A ASN* 1.3 83.9 + - - +
34A SER* 1.3 67.6 + - - +
35A VAL* 2.9 23.9 + - - +
37A THR* 6.1 1.6 - - - -
40A GLU* 4.7 14.8 - - - -
59A PHE* 3.8 5.2 - - - -
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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