Contacts of the helix formed by residues 44 - 59 (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 ASP 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A LYS* 1.3 76.5 - - - +
45A ASN* 1.3 57.4 + - - +
46A ARG* 3.6 12.6 + - + +
47A ALA* 2.8 56.0 + - - +
48A ILE* 3.0 14.6 + - - +
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Residues in contact with ASN 45 (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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33A ARG* 5.2 10.0 + - - -
44A ASP* 1.3 72.5 - - - +
46A ARG* 1.3 68.1 + - - +
47A ALA 3.0 1.2 + - - -
48A ILE* 3.0 23.5 + - - +
49A SER* 3.1 25.0 + - - -
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Residues in contact with ARG 46 (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 ASP* 3.2 12.9 - - + +
45A ASN* 1.3 84.9 - - - +
47A ALA* 1.3 57.9 + - - +
49A SER* 3.9 6.3 + - - -
50A VAL* 3.0 32.5 + - + +
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Residues in contact with ALA 47 (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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43A LYS* 4.0 20.6 - - + +
44A ASP* 2.8 31.8 + - - +
46A ARG* 1.3 75.6 - - - +
48A ILE* 1.3 65.3 + - - +
49A SER 3.1 2.4 + - - -
50A VAL* 3.1 7.9 + - - +
51A ILE* 3.0 30.9 + - + +
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Residues in contact with ILE 48 (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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33A ARG* 4.1 16.6 - - + +
36A TYR* 3.5 49.1 - - + +
37A THR* 4.4 8.1 - - - +
40A TYR* 3.9 23.3 - - + +
43A LYS* 4.5 7.0 - - + +
44A ASP 3.0 16.0 + - - +
45A ASN* 3.0 16.5 + - - +
47A ALA* 1.3 74.9 - - - +
49A SER* 1.3 61.2 + - - +
51A ILE* 4.0 6.6 - - + +
52A LEU* 3.2 33.1 + - + +
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Residues in contact with SER 49 (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 PHE* 4.9 4.9 - - - -
29A ALA* 6.1 0.9 - - - -
45A ASN* 3.1 25.1 + - - -
46A ARG* 4.1 6.0 + - - -
47A ALA 3.1 0.8 - - - -
48A ILE* 1.3 76.4 - - - +
50A VAL* 1.3 67.8 + - - +
52A LEU* 3.0 22.5 + - - +
53A GLY* 3.1 11.1 + - - -
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Residues in contact with VAL 50 (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 ARG* 3.0 24.0 - - + +
47A ALA* 3.1 9.1 + - - +
49A SER* 1.3 77.9 - - - +
51A ILE* 1.3 66.1 + - + +
53A GLY* 3.6 2.1 + - - -
54A ASP* 3.4 17.0 + - - +
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Residues in contact with ILE 51 (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 TYR* 3.6 29.2 - - + -
40A TYR* 4.8 13.2 - - + +
43A LYS* 3.5 37.9 - - + -
47A ALA* 3.0 19.1 + - + +
48A ILE* 4.0 7.2 - - + +
50A VAL* 1.3 75.3 - - + +
52A LEU* 1.3 66.9 + - - +
54A ASP* 3.1 20.7 + - + +
55A ARG* 3.2 19.6 - - - +
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Residues in contact with LEU 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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25A PHE* 4.5 1.6 - - + -
28A PHE* 3.0 46.0 - - + -
29A ALA* 3.3 37.9 - - + +
32A TYR* 3.4 33.7 - - + +
33A ARG* 4.6 1.6 - - + -
36A TYR* 4.2 11.9 - - + -
48A ILE* 3.2 34.2 + - + +
49A SER* 3.0 12.5 + - - +
51A ILE* 1.3 79.5 - - - +
53A GLY* 1.3 64.3 + - - +
55A ARG* 3.0 15.2 + - - +
56A TRP 3.3 1.4 + - - -
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Residues in contact with GLY 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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25A PHE* 3.7 23.6 - - - -
49A SER 3.1 8.4 + - - -
50A VAL* 3.6 3.5 + - - -
51A ILE 3.3 0.2 - - - -
52A LEU* 1.3 78.5 - - - +
54A ASP* 1.3 62.8 + - - +
56A TRP* 2.9 15.2 + - - +
57A LYS* 3.0 22.0 + - - +
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Residues in contact with ASP 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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50A VAL 3.4 11.9 + - - +
51A ILE* 3.1 16.4 + - + +
53A GLY* 1.3 73.7 - - - +
55A ARG* 1.3 77.2 + - - +
57A LYS* 3.1 19.5 + - - +
58A LYS* 2.9 37.6 + - - +
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Residues in contact with ARG 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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28A PHE* 3.5 16.2 - - + -
32A TYR* 6.4 0.2 - - + -
36A TYR* 3.2 30.3 + - - +
51A ILE* 3.2 32.6 + - - +
52A LEU* 3.0 9.2 + - - +
54A ASP* 1.3 95.6 + - - +
56A TRP* 1.3 54.2 + - - +
58A LYS* 3.9 26.7 - - - +
59A MET* 2.7 44.2 + - + +
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Residues in contact with TRP 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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24A ALA* 3.6 28.3 - - + -
25A PHE* 4.1 34.9 - + + +
28A PHE* 4.2 16.0 - - + -
52A LEU 3.3 4.1 + - - +
53A GLY* 2.9 13.5 + - - +
55A ARG* 1.3 79.0 - - - +
57A LYS* 1.3 65.6 + - + +
59A MET* 3.6 27.0 + - + -
64A ARG* 3.1 68.6 + - + +
67A TYR* 3.6 24.2 - + + -
68A THR* 4.6 2.0 - - - -
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Residues in contact with LYS 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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53A GLY* 3.0 23.6 + - - +
54A ASP* 3.1 18.1 + - - +
56A TRP* 1.3 86.6 - - + +
58A LYS* 1.3 60.1 + - - +
59A MET 4.1 3.7 - - - +
64A ARG* 4.6 8.5 + - - +
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Residues in contact with LYS 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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54A ASP* 2.9 23.3 + - - +
55A ARG* 3.9 27.6 - - - +
57A LYS* 1.3 77.1 - - - +
59A MET* 1.3 70.2 + - - +
60A LYS* 4.9 8.3 - - - -
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Residues in contact with MET 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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28A PHE* 3.8 21.8 - - + -
32A TYR* 6.0 0.9 - - - -
55A ARG* 2.7 18.2 + - + +
56A TRP* 3.6 47.8 - - + +
57A LYS 3.5 2.7 - - - +
58A LYS* 1.3 87.0 - - - +
60A LYS* 1.3 67.9 + - - +
63A GLU* 3.6 34.5 - - + +
64A ARG* 3.6 21.2 + - + -
66A MET* 5.5 1.1 - - - +
67A TYR* 4.0 9.6 - - + -
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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