Contacts of the helix formed by residues 20 - 37 (chain Z) in PDB entry 2LPZ
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 VAL 20 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35U ALA 3.3 15.9 - - - +
36U ALA 4.1 2.9 - - - +
38U PRO* 3.5 25.1 - - + -
16Z PHE* 3.3 29.4 - - + +
17Z ASP* 3.1 5.6 - - - +
19Z GLY* 1.3 80.7 - - - +
21Z ASP* 1.3 62.7 + - - +
22Z ASN 3.1 3.1 - - - +
23Z LEU* 3.1 34.9 + - + +
57Z TYR* 3.2 39.9 - - + -
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Residues in contact with ASP 21 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Z ASP* 2.5 23.4 + - - +
18Z THR* 3.8 11.8 + - - +
19Z GLY 3.7 1.8 - - - -
20Z VAL* 1.3 74.2 - - - +
22Z ASN* 1.3 69.0 + - - +
24Z GLN* 3.9 12.0 + - - +
25Z THR* 4.0 10.9 + - - -
57Z TYR* 5.0 6.8 + - - -
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Residues in contact with ASN 22 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20Z VAL* 3.1 0.8 - - - +
21Z ASP* 1.3 85.8 - - - +
23Z LEU* 1.3 68.4 + - - +
24Z GLN 3.2 0.4 - - - -
25Z THR* 3.0 11.1 + - - -
26Z GLN* 2.8 42.4 + - + +
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Residues in contact with LEU 23 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38U PRO* 5.8 1.6 - - + -
20Z VAL* 3.1 33.8 + - + +
22Z ASN* 1.3 78.7 - - - +
24Z GLN* 1.3 64.5 + - - +
26Z GLN* 3.2 12.1 + - - +
27Z VAL* 3.0 21.5 + - + +
50Z LYS* 3.5 31.4 - - + +
53Z GLU* 3.7 44.0 - - + +
54Z TYR* 4.4 6.1 - - + -
57Z TYR* 3.8 24.0 - - + +
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Residues in contact with GLN 24 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42T ALA* 5.4 4.8 - - - +
20Z VAL 3.7 2.2 + - - -
21Z ASP* 4.2 7.4 - - - +
22Z ASN 3.2 0.6 - - - -
23Z LEU* 1.3 78.1 - - - +
25Z THR* 1.3 57.1 + - - +
27Z VAL* 3.3 8.1 - - - +
28Z THR* 2.7 44.9 + - - +
54Z TYR* 4.0 16.0 + - + +
57Z TYR* 2.8 34.3 + - + +
58Z ARG* 3.6 20.8 + - - +
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Residues in contact with THR 25 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Z ASP 4.0 8.3 + - - -
22Z ASN* 3.0 15.4 + - - -
24Z GLN* 1.3 79.3 - - - +
26Z GLN* 1.3 59.9 + - + +
28Z THR* 3.4 5.6 + - - -
29Z GLU* 3.0 51.2 + - + +
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Residues in contact with GLN 26 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22Z ASN* 2.8 36.4 + - + +
23Z LEU* 3.6 11.8 - - - +
25Z THR* 1.3 80.6 - - + +
27Z VAL* 1.3 56.6 + - - +
29Z GLU* 3.4 8.4 + - - +
30Z ALA* 2.9 28.4 + - - +
50Z LYS* 2.9 41.9 + - + +
53Z GLU* 5.8 0.2 - - - +
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Residues in contact with VAL 27 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Z LEU 3.0 14.0 + - - +
24Z GLN 3.3 11.9 - - - +
26Z GLN* 1.3 73.8 - - - +
28Z THR* 1.3 67.2 + - - +
30Z ALA* 3.7 4.9 - - - -
31Z LEU* 3.0 22.0 + - - +
47Z TYR* 3.4 29.9 - - + +
50Z LYS* 3.8 13.4 - - + +
51Z LEU* 3.7 35.9 - - + +
54Z TYR* 3.8 27.8 - - + -
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Residues in contact with THR 28 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Z GLN* 2.7 31.9 + - - +
25Z THR* 3.7 7.0 - - - -
27Z VAL* 1.3 79.3 - - - +
29Z GLU* 1.3 61.0 + - + +
31Z LEU* 3.2 10.6 + - + +
32Z ASP* 2.9 40.4 + - - +
54Z TYR* 6.0 0.5 - - - -
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Residues in contact with GLU 29 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Z THR* 3.0 39.7 + - + +
26Z GLN* 3.8 8.2 - - - +
28Z THR* 1.3 76.4 - - + +
30Z ALA* 1.3 60.0 + - - +
32Z ASP* 3.3 13.2 + - - +
33Z LYS* 3.0 44.8 + - - +
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Residues in contact with ALA 30 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26Z GLN 2.9 19.1 + - - +
27Z VAL* 3.7 8.5 - - - +
29Z GLU* 1.3 77.4 - - - +
31Z LEU* 1.3 56.8 + - - +
33Z LYS* 4.0 7.0 - - - +
34Z LEU* 2.9 30.5 + - - +
43Z LEU* 4.8 6.2 - - + +
46Z ALA* 4.8 5.6 - - + -
47Z TYR* 3.8 31.6 - - + +
50Z LYS* 4.9 5.2 - - + -
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Residues in contact with LEU 31 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27Z VAL 3.0 15.2 + - - +
28Z THR* 3.2 14.3 + - + +
30Z ALA* 1.3 73.7 - - - +
32Z ASP* 1.3 63.3 + - - +
34Z LEU* 4.3 6.1 - - + -
35Z ALA* 2.8 36.7 + - + +
47Z TYR* 3.6 37.1 - - + +
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Residues in contact with ASP 32 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Z THR* 2.9 31.1 + - - +
29Z GLU* 3.5 17.6 - - - +
31Z LEU* 1.3 83.0 - - - +
33Z LYS* 1.3 62.7 + - + +
35Z ALA* 3.5 15.2 - - - +
36Z ALA* 3.7 6.4 + - - +
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Residues in contact with LYS 33 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Z GLU* 3.0 31.5 + - - +
30Z ALA* 4.0 3.4 - - - +
32Z ASP* 1.3 75.5 - - + +
34Z LEU* 1.3 65.3 + - - +
36Z ALA* 2.9 19.5 + - - +
37Z LYS 3.2 8.5 + - - -
43Z LEU* 3.5 31.7 - - + +
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Residues in contact with LEU 34 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Z ALA 2.9 19.5 + - - +
31Z LEU* 3.2 8.0 + - + +
33Z LYS* 1.3 76.4 - - - +
35Z ALA* 1.3 58.0 + - - +
37Z LYS 3.0 13.6 - - - +
38Z PRO* 2.8 55.6 - - + +
43Z LEU* 3.5 29.6 - - + +
44Z LEU* 3.6 25.6 - - + +
47Z TYR* 3.3 38.8 - - + -
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Residues in contact with ALA 35 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Z LEU* 2.8 23.0 + - + +
32Z ASP* 3.5 10.3 - - - +
34Z LEU* 1.3 77.6 - - - +
36Z ALA* 1.3 60.0 + - - +
38Z PRO* 3.6 13.1 - - - +
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Residues in contact with ALA 36 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Z ASP 3.7 4.4 + - - +
33Z LYS* 2.9 14.5 + - - +
35Z ALA* 1.3 82.7 - - - +
37Z LYS* 1.3 70.9 + - + +
38Z PRO* 3.6 4.2 - - - +
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Residues in contact with LYS 37 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Z LYS 3.2 2.6 + - - -
34Z LEU* 3.0 11.8 + - - +
36Z ALA* 1.3 90.1 - - + +
38Z PRO* 1.3 67.4 - - - +
39Z SER* 3.0 7.5 + - - +
40Z ASP* 3.1 30.0 + - + +
43Z LEU* 3.7 13.6 - - + +
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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