Contacts of the helix formed by residues 26 - 41 (chain A) in PDB entry 5M72
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 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A TYR* 2.8 27.0 + - + +
24A ASN* 3.2 7.6 - - + +
25A GLY* 1.3 73.2 - - - +
27A PHE* 1.3 56.8 + - - +
28A THR* 3.6 9.0 + - - -
29A ARG* 2.8 59.9 + - - +
30A ALA* 2.9 27.1 + - - +
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Residues in contact with PHE 27 (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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22A GLY* 4.2 19.5 - - - -
25A GLY* 3.2 25.6 + - - -
26A ASP* 1.3 71.8 - - - +
28A THR* 1.3 60.3 + - - +
30A ALA* 4.0 3.4 - - - -
31A LEU* 2.9 30.1 + - - +
53A VAL* 4.1 5.8 - - + -
54A CYS* 3.5 23.1 - - - +
57A GLN* 3.6 51.4 - - + -
58A ASN* 4.1 9.8 + - - +
598B VAL 5.3 1.6 - - - -
599B ALA* 5.9 1.6 - - - -
600B PHE* 3.9 39.0 - + - -
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Residues in contact with THR 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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26A ASP* 3.2 7.6 - - - -
27A PHE* 1.3 79.9 - - - +
29A ARG* 1.3 66.3 + - + +
31A LEU* 3.4 6.9 + - - +
32A LYS* 3.4 17.2 + - - +
58A ASN* 3.0 26.3 + - - +
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Residues in contact with ARG 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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21A TYR* 3.6 36.5 - - + -
26A ASP* 2.8 51.3 + - - +
28A THR* 1.3 77.1 - - + +
30A ALA* 1.3 66.2 + - - +
32A LYS* 3.2 12.1 + - + +
33A THR* 3.1 25.3 + - - -
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Residues in contact with ALA 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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18A VAL* 4.3 5.8 - - + +
21A TYR* 3.7 20.5 - - + -
22A GLY 4.5 0.9 - - - +
26A ASP 2.9 17.8 + - - +
27A PHE* 3.8 2.9 - - - +
28A THR 3.4 0.2 - - - -
29A ARG* 1.3 77.2 - - - +
31A LEU* 1.3 56.9 - - - +
33A THR* 3.2 4.0 + - - -
34A VAL* 2.8 34.1 + - - +
54A CYS* 3.7 18.4 - - - -
600B PHE* 3.9 20.4 - - + -
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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 PHE 2.9 18.5 + - - +
28A THR* 3.6 7.0 - - + +
30A ALA* 1.3 77.2 - - - +
32A LYS* 1.3 63.0 + - - +
34A VAL* 3.3 2.4 + - + +
35A ASN* 2.9 40.8 + - - +
51A LYS* 3.7 37.0 - - + +
54A CYS* 3.6 18.8 - - + -
55A LEU* 3.9 23.3 - - + +
58A ASN* 5.4 8.1 - - - +
63A GLU* 5.7 0.7 - - - +
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Residues in contact with LYS 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 THR 3.4 8.6 + - - +
29A ARG* 3.2 14.9 + - + +
31A LEU* 1.3 79.0 - - - +
33A THR* 1.3 63.0 + - - +
35A ASN* 3.4 8.8 + - - +
36A LYS* 3.2 48.1 + - + +
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Residues in contact with THR 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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14A LEU* 3.5 40.4 - - + +
17A GLU* 2.9 33.2 + - + +
18A VAL* 3.6 11.0 - - + -
21A TYR* 3.6 7.2 - - - -
29A ARG 3.1 13.1 + - - -
30A ALA* 3.7 7.6 - - - -
32A LYS* 1.3 74.2 - - - +
34A VAL* 1.3 67.2 + - - +
36A LYS* 3.0 20.4 + - + +
37A ILE* 3.0 12.5 + - - +
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Residues in contact with VAL 34 (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 TRP* 5.2 3.8 - - + -
18A VAL* 3.7 22.9 - - + -
30A ALA 2.8 25.1 + - - +
31A LEU* 3.7 7.4 - - - +
33A THR* 1.3 72.2 - - - +
35A ASN* 1.3 58.9 + - - +
37A ILE* 3.1 8.2 + - - +
38A LEU* 2.8 32.9 + - + +
47A ALA* 3.2 28.5 - - - +
50A CYS* 3.8 24.5 - - + -
51A LYS* 3.8 20.6 - - + +
54A CYS* 4.9 1.3 - - - -
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Residues in contact with ASN 35 (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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31A LEU* 2.9 40.0 + - - +
32A LYS* 3.6 7.4 - - - +
33A THR 3.2 0.2 - - - -
34A VAL* 1.3 76.7 - - - +
36A LYS* 1.3 57.1 + - + +
38A LEU* 3.4 9.5 + - - +
39A GLN* 3.1 31.7 + - - +
51A LYS* 2.9 38.0 + - - +
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Residues in contact with LYS 36 (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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14A LEU* 4.6 22.0 - - + -
17A GLU* 5.7 3.6 + - - +
32A LYS* 3.2 41.7 + - - +
33A THR* 3.0 14.8 + - + +
35A ASN* 1.3 74.1 - - - +
37A ILE* 1.3 66.1 + - - +
39A GLN* 3.2 21.9 + - - +
40A ILE* 3.5 13.6 + - + +
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Residues in contact with ILE 37 (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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11A VAL* 5.2 4.5 - - + +
14A LEU* 3.6 33.9 - - + -
15A TRP* 3.6 46.4 - - + +
18A VAL* 3.8 24.2 - - + -
33A THR 3.0 9.8 + - - +
34A VAL* 3.1 9.4 + - - +
36A LYS* 1.3 76.5 - - - +
38A LEU* 1.3 57.2 + - - +
40A ILE* 2.9 9.8 + - - +
41A ASN* 2.8 37.1 + - - +
44A ASP* 5.0 4.7 - - + -
47A ALA* 4.0 17.5 - - + -
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Residues in contact with LEU 38 (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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34A VAL* 2.8 27.3 + - + +
35A ASN* 3.8 11.4 - - - +
36A LYS 3.3 0.2 - - - -
37A ILE* 1.3 76.0 - - - +
39A GLN* 1.3 61.6 + - - +
40A ILE 3.2 0.2 - - - -
41A ASN 3.7 14.4 - - - +
42A LYS* 3.4 33.3 - - - +
44A ASP 4.1 1.8 - - - +
47A ALA* 3.6 25.6 - - + +
48A LEU* 3.9 31.2 - - + -
51A LYS* 3.8 31.2 - - + +
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Residues in contact with GLN 39 (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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35A ASN 3.1 20.9 + - - +
36A LYS* 3.4 12.1 - - - +
37A ILE 3.1 0.8 - - - -
38A LEU* 1.3 78.4 - - - +
40A ILE* 1.3 63.9 + - + +
42A LYS* 5.3 1.0 + - - +
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Residues in contact with ILE 40 (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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11A VAL* 3.6 34.1 - - + -
14A LEU* 3.9 15.3 - - + -
36A LYS* 3.6 15.3 - - + +
37A ILE* 2.9 7.7 + - - +
39A GLN* 1.3 82.7 - - + +
41A ASN* 1.3 73.1 + - - +
42A LYS 3.8 2.0 + - - -
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Residues in contact with ASN 41 (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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11A VAL* 4.6 18.4 - - - +
15A TRP* 5.7 1.6 - - - +
37A ILE* 2.8 18.6 + - + +
38A LEU* 3.7 13.6 - - - +
40A ILE* 1.3 90.1 - - - +
42A LYS* 1.3 64.7 + - - +
43A ASP 3.1 4.1 + - - -
44A ASP* 3.2 36.9 + - + +
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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