Contacts of the helix formed by residues 15 - 26 (chain H) in PDB entry 5L08
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 15 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32F GLN* 4.2 17.8 + - + -
33F ARG* 4.3 2.7 - - - -
36F GLU* 4.9 11.6 - - - +
144F ILE* 5.8 0.2 - - - +
145F GLU* 4.9 0.3 - - - +
148F LYS* 3.0 27.9 + - - +
14H LEU* 1.3 72.5 - - - +
16H SER* 1.3 77.1 + - - +
17H GLU* 2.9 27.1 + - - +
18H ASP* 2.7 44.2 + - - +
19H LEU* 3.0 12.3 + - - +
71H ARG* 3.3 7.0 - - - +
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Residues in contact with SER 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F ARG* 3.7 21.3 - - - +
36F GLU* 4.0 18.3 - - - +
14H LEU 3.5 4.0 + - - -
15H ASP* 1.3 77.9 + - - +
17H GLU* 1.3 72.2 + - - +
19H LEU* 3.5 30.1 - - - +
20H ALA* 4.1 3.3 + - - +
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Residues in contact with GLU 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F GLU* 5.2 9.3 - - - +
15H ASP* 2.9 18.7 + - - +
16H SER* 1.3 87.0 + - - +
18H ASP* 1.3 65.9 + - - +
19H LEU 3.3 0.4 + - - -
20H ALA* 3.7 16.3 + - - +
21H SER* 4.4 1.7 + - - -
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Residues in contact with ASP 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F LYS* 3.0 32.5 + - - +
14H LEU* 6.0 0.4 - - + -
15H ASP* 2.7 21.5 + - + +
17H GLU* 1.3 78.8 - - - +
19H LEU* 1.3 64.9 + - + +
20H ALA 3.1 2.5 - - - -
21H SER* 2.5 31.0 + - - +
22H LEU* 3.2 9.4 + - - +
69H ILE* 4.3 25.1 - - + +
71H ARG* 4.4 7.3 - - - -
106H TYR* 5.5 2.3 + - - -
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Residues in contact with LEU 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F ARG* 4.6 10.8 - - - +
14H LEU* 3.9 15.9 - - + -
15H ASP 3.0 14.9 + - - +
16H SER* 3.5 24.7 - - - +
17H GLU 3.3 0.4 - - - -
18H ASP* 1.3 78.4 - - - +
20H ALA* 1.3 60.8 + - - +
22H LEU* 3.2 21.8 + - + +
23H LYS* 3.1 29.3 + - - +
39H LYS 4.4 5.6 - - - +
40H ASP* 3.9 30.3 - - + -
41H ALA* 3.6 29.2 - - + +
44H LEU* 5.6 0.6 - - + +
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Residues in contact with ALA 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H SER 4.1 3.6 + - - +
17H GLU* 3.7 13.1 + - - +
18H ASP 3.1 0.4 - - - -
19H LEU* 1.3 79.8 - - - +
21H SER* 1.3 60.4 + - - +
23H LYS* 3.3 15.3 + - - +
24H PHE* 3.2 18.9 + - - +
138H ASN* 6.1 3.4 - - - +
140H LEU* 5.2 2.6 - - + +
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Residues in contact with SER 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H GLU 4.4 1.5 + - - -
18H ASP* 2.5 26.3 + - - +
20H ALA* 1.3 78.6 - - - +
22H LEU* 1.3 58.6 + - - +
24H PHE* 3.1 4.4 + - - +
25H LEU* 2.9 32.8 + - - +
69H ILE* 3.3 16.5 - - - +
106H TYR* 3.6 29.6 - - - -
140H LEU* 4.1 17.7 - - - +
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Residues in contact with LEU 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H LEU* 4.2 12.3 - - + -
18H ASP 3.8 7.2 - - - +
19H LEU* 3.2 36.5 + - + +
21H SER* 1.3 80.0 + - - +
23H LYS* 1.3 58.6 + - - +
25H LEU* 3.2 7.6 + - + +
26H SER* 2.9 29.6 + - - -
41H ALA* 4.9 3.8 - - + -
44H LEU* 4.2 19.2 - - + +
45H PHE* 5.6 3.4 - - + -
62H LEU* 6.1 2.5 - - + -
65H LEU* 3.8 38.7 - - + +
66H LEU* 5.9 1.6 - - + -
69H ILE* 3.6 38.4 - - + -
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Residues in contact with LYS 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H LEU* 3.1 17.5 + - - +
20H ALA* 3.4 14.4 - - - +
22H LEU* 1.3 73.2 - - - +
24H PHE* 1.3 66.4 + - - +
26H SER* 2.7 13.7 + - - -
27H LEU* 3.2 2.0 + - - +
35H GLN* 2.7 63.8 + - + +
36H GLU* 4.4 6.8 + - - +
38H ILE* 2.9 42.6 + - + +
39H LYS 6.0 0.4 - - - -
44H LEU* 4.8 8.7 - - + +
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Residues in contact with PHE 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H ALA 3.2 9.0 + - - +
21H SER* 3.1 14.8 + - - +
23H LYS* 1.3 79.1 - - - +
25H LEU* 1.3 68.9 + - + +
27H LEU* 2.9 48.8 + - + +
102H ARG* 3.6 45.1 - - - -
105H LEU* 3.7 30.7 - - + -
106H TYR* 4.3 2.7 - + + -
140H LEU* 3.6 57.2 - - + -
143H PHE* 4.0 9.9 - + + -
144H ILE* 4.0 9.2 - - + +
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Residues in contact with LEU 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H SER* 2.9 18.6 + - - +
22H LEU* 3.5 9.6 - - + +
23H LYS 3.2 0.2 - - - -
24H PHE* 1.3 83.2 - - + +
26H SER* 1.3 58.2 + - - +
27H LEU 3.2 1.3 + - - -
28H ASP* 4.5 4.5 + - - +
29H TYR* 4.8 2.3 - - - -
65H LEU* 3.8 25.1 - - + +
68H ARG* 3.4 34.3 - - + -
69H ILE* 4.0 18.4 - - + -
98H ILE* 3.5 42.4 - - + +
102H ARG* 4.3 27.1 - - + +
106H TYR* 4.7 11.0 - - + -
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Residues in contact with SER 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H LEU 2.9 14.1 + - - -
23H LYS* 2.7 22.1 + - - -
25H LEU* 1.3 74.4 - - - +
27H LEU* 1.3 57.4 + - - +
28H ASP 3.1 3.4 - - - -
29H TYR* 2.9 11.8 + - - +
30H ILE* 2.8 39.8 + - - +
35H GLN* 2.7 14.3 + - - +
44H LEU* 4.2 22.2 - - - +
48H LEU* 5.3 6.3 - - - -
61H PHE* 5.3 6.5 - - - -
65H LEU* 5.6 2.7 - - - -
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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