Contacts of the helix formed by residues 29 - 51 (chain O) in PDB entry 5IY8
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 29 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32N ASP* 4.2 14.4 + - - +
23O ILE* 4.7 1.1 - - - -
28O ILE* 1.3 85.4 - - - +
30O PRO* 1.3 68.6 - - + +
31O GLN* 4.1 6.6 + - - +
32O LEU* 3.1 25.3 + - - +
33O ALA* 3.0 27.0 + - - +
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Residues in contact with PRO 30 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23O ILE* 4.2 30.7 - - + -
28O ILE 4.4 2.7 - - - +
29O THR* 1.3 88.1 - - + +
31O GLN* 1.3 56.4 + - - +
33O ALA* 3.5 3.8 + - + +
34O LEU* 3.0 26.0 + - - +
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Residues in contact with GLN 31 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O THR* 3.3 6.8 + - - +
30O PRO* 1.3 79.7 - - - +
32O LEU* 1.3 58.2 + - - +
34O LEU* 3.3 25.9 + - - +
35O GLN* 2.9 46.4 + - + +
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Residues in contact with LEU 32 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N ILE* 4.0 24.2 - - + +
29N PHE* 4.2 19.1 - - + -
32N ASP* 3.3 42.0 - - + +
34N VAL* 4.8 2.7 - - + -
28O ILE* 4.4 20.0 - - + -
29O THR* 3.1 22.5 + - - +
31O GLN* 1.3 77.7 - - - +
33O ALA* 1.3 61.0 + - - +
35O GLN* 3.2 8.6 + - - +
36O VAL* 2.8 46.8 + - + +
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Residues in contact with ALA 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19O LEU* 3.7 38.5 - - + +
23O ILE* 4.5 7.9 - - + -
28O ILE* 4.2 7.8 - - + +
29O THR 3.0 12.4 + - - +
30O PRO* 3.6 12.1 - - + +
32O LEU* 1.3 78.2 - - - +
34O LEU* 1.3 56.1 - - - +
36O VAL* 3.1 5.2 + - - +
37O LEU* 2.8 35.0 + - + +
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Residues in contact with LEU 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7O ARG* 3.4 30.3 + - - +
30O PRO 3.0 14.3 + - - +
31O GLN* 3.4 29.8 - - - +
32O LEU 3.3 0.2 - - - -
33O ALA* 1.3 76.2 - - - +
35O GLN* 1.3 59.9 + - - +
37O LEU* 3.2 10.6 + - + +
38O LEU* 2.8 32.7 + - + +
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Residues in contact with GLN 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N ILE* 4.1 23.7 - - + +
31O GLN* 2.9 34.9 + - + +
32O LEU* 3.4 12.1 - - - +
34O LEU* 1.3 78.8 - - - +
36O VAL* 1.3 57.2 + - - +
38O LEU* 3.7 24.6 + - - +
39O GLN* 3.1 26.0 + - - +
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Residues in contact with VAL 36 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21N VAL* 4.9 5.8 - - + -
25N VAL* 3.8 36.7 - - + +
28N ILE* 4.6 5.2 - - + -
29N PHE* 4.2 9.4 - - + -
42N LEU* 5.3 4.7 - - + -
15O LEU* 4.8 12.1 - - + -
19O LEU* 4.4 19.7 - - + -
32O LEU* 2.8 35.6 + - + +
33O ALA* 3.1 10.3 + - - +
35O GLN* 1.3 74.6 - - - +
37O LEU* 1.3 62.7 + - - +
39O GLN* 3.3 1.6 + - - +
40O PHE* 2.9 27.4 + - - +
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Residues in contact with LEU 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7O ARG* 3.4 37.7 - - + +
12O GLY* 4.8 1.1 - - - +
15O LEU* 3.6 26.0 - - + -
16O GLN* 3.7 38.1 - - + +
19O LEU* 3.7 14.6 - - + -
33O ALA* 2.8 22.8 + - + +
34O LEU* 3.2 13.7 + - + +
36O VAL* 1.3 74.1 - - - +
38O LEU* 1.3 57.0 + - - +
40O PHE* 3.5 5.1 - - + +
41O ASP* 3.0 34.1 + - - +
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Residues in contact with LEU 38 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1O MET* 5.9 11.2 - - + -
7O ARG* 3.3 12.5 - - - +
34O LEU* 2.8 22.2 + - + +
35O GLN* 3.8 26.2 - - - +
37O LEU* 1.3 71.1 - - - +
39O GLN* 1.3 63.9 + - - +
41O ASP* 3.4 8.1 + - + +
42O LYS* 3.2 49.0 + - + +
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Residues in contact with GLN 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21N VAL* 5.2 1.6 - - - +
24N ASP* 2.6 53.7 + - + +
25N VAL* 3.8 17.5 - - + -
28N ILE* 4.6 6.4 - - + +
35O GLN 3.1 18.9 + - - +
36O VAL 3.3 4.5 + - - +
38O LEU* 1.3 73.8 - - - +
40O PHE* 1.3 61.7 + - - +
42O LYS* 3.1 37.8 + - - +
43O ALA* 2.9 34.4 + - + +
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Residues in contact with PHE 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17N VAL* 3.9 22.2 - - + -
21N VAL* 3.4 33.3 - - + +
46N TRP* 5.1 7.9 - + - -
6O TYR* 4.8 10.5 - - + -
7O ARG* 5.4 2.2 - - + -
9O THR* 5.7 0.4 - - - -
11O LEU* 4.0 20.9 - - + -
12O GLY* 4.3 17.5 - - - -
15O LEU* 3.5 32.1 - - + -
36O VAL 2.9 17.5 + - - +
37O LEU* 3.5 7.2 - - + +
38O LEU 3.3 0.2 - - - -
39O GLN* 1.3 78.0 - - - +
41O ASP* 1.3 69.0 - - - +
43O ALA* 3.9 0.2 - - - +
44O ILE* 2.9 57.2 + - + +
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Residues in contact with ASP 41 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2O ALA* 4.1 16.6 - - + +
3O TYR 4.1 16.8 - - - +
4O GLN* 4.3 8.1 + - - -
6O TYR* 5.1 4.3 - - + +
7O ARG* 3.1 41.4 + - - +
37O LEU 3.0 18.3 + - - +
38O LEU* 3.4 10.0 - - + +
40O PHE* 1.3 84.3 - - - +
42O LYS* 1.3 58.1 + - - +
44O ILE* 3.2 6.6 - - - +
45O ASN* 2.4 41.8 + - - +
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Residues in contact with LYS 42 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2O ALA* 4.8 11.9 - - + -
38O LEU* 3.2 33.9 + - + +
39O GLN* 3.1 38.4 + - - +
41O ASP* 1.3 78.3 - - - +
43O ALA* 1.3 56.9 + - - +
45O ASN* 3.3 7.2 + - - +
46O ALA* 2.8 30.8 + - - +
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Residues in contact with ALA 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17N VAL* 5.9 1.7 - - - -
20N ASP* 4.2 28.0 - - + +
21N VAL* 4.1 21.1 - - + +
24N ASP* 5.1 8.5 - - - +
39O GLN* 2.9 19.8 + - + +
40O PHE 3.9 2.9 - - - +
42O LYS* 1.3 77.2 - - - +
44O ILE* 1.3 58.9 + - - +
46O ALA* 3.4 8.1 + - - +
47O ALA* 2.9 27.4 + - - +
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Residues in contact with ILE 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17N VAL* 4.4 19.2 - - + +
357N ILE* 4.6 15.9 - - + -
6O TYR* 4.2 19.5 - - + -
9O THR* 6.2 0.2 - - - +
11O LEU* 3.7 19.3 - - + -
40O PHE* 2.9 49.0 + - + +
41O ASP* 3.2 18.6 - - - +
43O ALA* 1.3 73.0 - - - +
45O ASN* 1.3 70.2 + - - +
47O ALA* 3.6 5.6 - - + +
48O LEU* 2.9 40.6 + - + +
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Residues in contact with ASN 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338N GLN* 4.8 6.8 + - - -
2O ALA* 3.7 22.2 - - + +
3O TYR* 5.0 2.6 + - - +
6O TYR* 4.0 29.2 + - - -
41O ASP* 2.4 36.8 + - - +
42O LYS* 3.4 7.0 - - - +
44O ILE* 1.3 80.1 - - - +
46O ALA* 1.3 56.4 + - - +
48O LEU* 3.2 10.9 + - - +
49O ALA* 2.8 29.5 + - - +
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Residues in contact with ALA 46 (chain O).
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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20N ASP* 5.2 4.9 - - - +
42O LYS 2.8 20.0 + - - +
43O ALA* 3.5 9.2 - - - +
45O ASN* 1.3 70.7 - - - +
47O ALA* 1.3 58.2 + - - +
49O ALA* 3.2 6.9 + - - +
50O GLN* 2.8 41.9 + - + +
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Residues in contact with ALA 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13N LEU* 5.0 4.5 - - + -
16N SER* 6.1 1.1 - - - -
17N VAL* 4.2 22.4 - - + +
20N ASP* 5.3 5.8 + - - +
43O ALA 2.9 17.4 + - - +
44O ILE* 3.6 10.8 - - + +
45O ASN 3.3 0.2 - - - -
46O ALA* 1.3 72.5 - - - +
48O LEU* 1.3 60.3 + - - +
50O GLN* 5.1 0.2 - - - -
51O ARG* 3.0 44.8 + - - +
52O VAL* 3.3 10.9 + - - +
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Residues in contact with LEU 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338N GLN* 5.7 0.7 - - - +
355N ASP* 4.1 23.0 - - + +
356N GLY 4.7 15.7 - - - +
357N ILE* 4.7 22.0 - - + -
366N ILE* 5.5 2.0 - - + -
367N PHE 5.0 1.3 - - - +
368N SER* 5.4 1.4 + - - -
6O TYR* 4.2 30.7 - - + +
44O ILE* 2.9 27.7 + - + +
45O ASN* 3.3 15.5 - - - +
47O ALA* 1.3 77.0 - - + +
49O ALA* 1.3 62.5 + - - +
52O VAL* 3.2 53.1 + - + +
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Residues in contact with ALA 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355N ASP* 5.0 2.9 + - - -
45O ASN 2.8 16.2 + - - +
46O ALA* 3.6 8.1 - - - +
48O LEU* 1.3 78.9 - - - +
50O GLN* 1.3 73.6 + - - +
52O VAL 4.5 3.5 - - - +
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Residues in contact with GLN 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46O ALA* 2.8 27.8 + - + +
47O ALA* 5.1 0.2 - - - -
49O ALA* 1.3 86.5 + - - +
51O ARG* 1.3 69.0 + - + +
52O VAL 5.1 0.2 - - - -
53O ARG* 6.0 0.2 - - - +
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Residues in contact with ARG 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13N LEU* 3.6 29.4 - - + -
16N SER* 3.9 27.8 + - - -
20N ASP* 6.0 0.2 + - - -
47O ALA* 3.0 21.0 + - - +
50O GLN* 1.3 85.2 - - + +
52O VAL* 1.3 65.0 + - - +
53O ARG* 3.2 16.6 + - - +
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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