Contacts of the helix formed by residues 21 - 39 (chain A) in PDB entry 5F28
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 PHE 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A THR* 1.3 73.2 + - - +
23A LYS* 3.1 5.9 - - - +
24A ARG* 3.0 15.2 + - - +
25A LYS* 2.8 52.8 + - + +
47A ILE* 5.0 4.3 - - + -
49A ASN* 4.0 24.0 - - + -
55A PHE* 4.6 17.0 - + - -
35B LEU* 4.0 11.2 - - + -
39B CYS* 3.6 39.7 - - + -
41B CYS* 3.8 23.8 - - - -
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Residues in contact with THR 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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21A PHE* 1.3 91.1 - - - +
23A LYS* 1.3 61.9 + - - +
25A LYS* 3.5 22.9 + - - +
26A PHE* 3.2 24.3 + - + +
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Residues in contact with LYS 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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21A PHE* 3.1 3.9 - - - +
22A THR* 1.3 78.4 - - - +
24A ARG* 1.3 60.4 + - + +
26A PHE* 3.4 4.6 + - - +
27A GLY* 2.9 28.1 + - - -
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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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21A PHE* 3.0 18.6 + - - +
23A LYS* 1.3 77.5 - - + +
25A LYS* 1.3 60.7 + - - +
27A GLY 3.6 0.2 + - - -
28A LEU* 3.1 24.3 + - - +
31B LYS* 3.6 32.2 + - - +
34B GLU* 2.9 32.5 + - - +
35B LEU* 3.6 29.1 - - + +
38B LEU* 3.5 30.8 - - + +
39B CYS* 5.3 3.8 - - - -
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Residues in contact with LYS 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 PHE* 2.8 35.4 + - + +
22A THR* 3.7 27.8 - - - +
23A LYS 3.2 0.2 - - - -
24A ARG* 1.3 73.9 - - - +
26A PHE* 1.3 70.1 + - - +
28A LEU* 3.2 4.9 + - - +
29A MET* 3.1 30.5 + - + +
47A ILE* 4.2 18.7 - - + +
55A PHE* 3.6 31.1 - - + -
35B LEU* 4.3 9.6 - - + +
77B GLU* 3.3 36.5 + - - +
79B ARG* 6.0 1.1 - - - +
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Residues in contact with PHE 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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22A THR* 3.2 14.6 + - + +
23A LYS* 4.1 4.0 - - - +
25A LYS* 1.3 83.7 - - - +
27A GLY* 1.3 59.9 + - - +
29A MET* 3.3 7.3 + - + +
30A LYS* 2.7 48.5 + - + +
79B ARG* 3.9 33.2 - - - +
84B ILE* 4.1 17.3 - - + -
87B ALA* 4.7 11.0 - - + -
88B LEU* 4.0 24.9 - - + -
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Residues in contact with GLY 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 LYS 2.9 17.3 + - - -
24A ARG 4.0 1.3 - - - -
26A PHE* 1.3 81.1 - - - +
28A LEU* 1.3 55.6 + - - +
30A LYS* 3.5 10.4 + - - +
31A LYS* 3.0 30.0 + - - +
31B LYS* 3.5 13.7 - - - -
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Residues in contact with LEU 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 17.9 + - - +
25A LYS 3.2 4.7 + - - +
27A GLY* 1.3 74.6 - - - +
29A MET* 1.3 58.9 + - - +
31A LYS* 3.3 3.2 + - - +
32A ALA* 2.9 27.0 + - - +
45A LEU* 3.9 28.5 - - + -
47A ILE* 4.2 7.0 - - + -
28B LEU* 3.8 23.5 - - + +
31B LYS* 3.3 17.6 - - + +
32B ALA* 3.6 41.7 - - + +
35B LEU* 3.8 24.2 - - + -
43B ILE* 4.4 2.7 - - + -
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Residues in contact with MET 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 LYS* 3.1 29.9 + - + +
26A PHE* 3.8 9.2 - - - +
28A LEU* 1.3 73.2 - - - +
30A LYS* 1.3 61.0 + - - +
32A ALA* 3.1 7.5 + - - +
33A TYR* 2.9 30.7 + - - +
45A LEU* 4.0 9.4 - - + -
47A ILE* 4.6 7.4 - - + -
55A PHE* 4.5 2.7 - - + -
56A GLN* 3.3 36.3 - - - +
57A TYR* 3.9 20.7 - - + -
77B GLU* 3.9 20.9 - - - +
79B ARG* 4.0 25.8 - - + -
84B ILE* 4.4 15.7 - - + -
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Residues in contact with LYS 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 PHE* 2.7 46.9 + - + +
27A GLY* 3.7 8.5 - - - +
29A MET* 1.3 72.6 - - - +
31A LYS* 1.3 64.9 + - - +
33A TYR* 3.5 4.0 + - - -
34A GLU* 2.9 54.4 + - + +
84B ILE* 4.5 11.8 - - + +
88B LEU* 4.1 33.2 - - + -
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Residues in contact with LYS 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 GLY 3.0 18.7 + - - +
28A LEU* 3.7 5.8 - - - +
30A LYS* 1.3 80.2 - - - +
32A ALA* 1.3 64.9 + - - +
34A GLU* 3.1 33.1 + - + +
35A LEU* 3.2 22.2 + - - +
24B ARG* 4.7 18.9 - - + +
27B GLY 5.4 3.1 - - - +
28B LEU* 3.8 25.5 - - + +
31B LYS* 5.1 9.6 - - + -
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Residues in contact with ALA 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 LEU 2.9 17.8 + - - +
29A MET* 3.1 6.5 + - - +
31A LYS* 1.3 73.6 - - - +
33A TYR* 1.3 65.5 + - - +
35A LEU 3.5 0.7 + - - +
36A SER* 3.1 18.5 + - - -
43A ILE* 3.2 19.8 - - + +
45A LEU* 4.7 6.5 - - + -
57A TYR* 3.6 26.6 + - + -
28B LEU* 3.6 23.7 - - + +
45B LEU* 5.3 0.7 - - + -
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Residues in contact with TYR 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 MET 2.9 16.5 + - - +
30A LYS 3.7 9.2 - - - +
32A ALA* 1.3 74.5 - - - +
34A GLU* 1.3 78.5 + - + +
36A SER* 2.9 11.7 + - - -
37A VAL* 3.1 43.5 + - + +
57A TYR* 3.4 12.9 + - + +
81B ASN* 3.3 28.5 - - + +
84B ILE* 3.9 24.7 - - + -
85B VAL* 3.8 29.5 - - + +
88B LEU* 4.1 20.8 - - + +
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Residues in contact with GLU 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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30A LYS* 2.9 43.7 + - + +
31A LYS* 3.1 35.3 + - + +
32A ALA 3.3 0.6 - - - -
33A TYR* 1.3 92.0 - - + +
35A LEU* 1.3 58.9 + - - +
37A VAL* 4.3 4.7 - - - -
38A LEU* 3.0 44.0 + - + +
24B ARG* 3.3 22.3 + - - +
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Residues in contact with LEU 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 LYS 3.2 16.2 + - - +
32A ALA 3.9 4.5 - - - +
33A TYR 3.3 0.4 - - - -
34A GLU* 1.3 76.3 - - - +
36A SER* 1.3 63.0 + - - +
39A CYS* 3.2 47.8 + - + +
41A CYS* 4.1 5.1 - - - +
43A ILE* 3.9 8.5 - - + -
21B PHE* 3.9 13.5 - - + -
24B ARG* 4.0 28.6 - - + +
25B LYS* 4.0 18.2 - - + +
28B LEU* 3.9 15.3 - - + -
47B ILE* 3.9 32.8 - - + -
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Residues in contact with SER 36 (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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32A ALA 3.1 13.5 + - - -
33A TYR 2.9 10.8 + - - -
35A LEU* 1.3 77.1 - - - +
37A VAL* 1.3 59.1 - - - +
40A ASP* 3.1 9.2 + - - +
41A CYS* 2.8 45.3 + - - +
43A ILE* 3.9 5.8 - - - +
57A TYR* 3.9 3.1 - - - -
59A SER* 3.2 25.3 - - - -
60A THR* 5.9 0.3 - - - +
81B ASN* 3.2 11.5 + - - -
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Residues in contact with VAL 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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33A TYR* 3.1 52.2 + - + +
34A GLU* 3.7 7.4 - - - +
36A SER* 1.3 77.9 - - - +
38A LEU* 1.3 76.8 + - + +
39A CYS 3.3 1.0 + - - -
40A ASP* 3.9 5.8 + - - +
81B ASN* 4.4 10.8 - - - +
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Residues in contact with LEU 38 (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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34A GLU* 3.0 29.7 + - + +
37A VAL* 1.3 85.5 - - + +
39A CYS* 1.3 69.2 + - - +
40A ASP 3.7 0.2 - - - -
24B ARG* 3.6 38.4 - - - +
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Residues in contact with CYS 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 LEU* 3.2 36.7 + - + +
38A LEU* 1.3 87.4 - - - +
40A ASP* 1.3 73.6 + - - +
41A CYS* 3.3 9.5 - - - -
20B THR* 5.1 5.4 - - - -
21B PHE* 4.0 35.6 - - + -
24B ARG* 4.9 6.7 - - - -
49B ASN* 5.3 0.3 - - - +
50B SER* 4.6 5.4 + - - -
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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