Contacts of the helix formed by residues 20 - 37 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35T ALA 3.3 15.9 - - - +
36T ALA 4.1 2.7 - - - +
38T PRO* 3.5 25.1 - - + -
16Y PHE* 3.3 28.7 - - + +
17Y ASP* 3.1 5.8 - - - +
19Y GLY* 1.3 81.4 - - - +
21Y ASP* 1.3 63.1 + - - +
22Y ASN* 3.1 3.6 - - - +
23Y LEU* 3.1 34.0 + - + +
24Y GLN 3.7 0.2 + - - -
57Y TYR* 3.2 39.1 - - + -
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Residues in contact with ASP 21 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Y ASP* 2.5 22.8 + - - +
18Y THR* 3.8 11.2 + - - +
19Y GLY 3.7 1.4 - - - -
20Y VAL* 1.3 75.0 - - - +
22Y ASN* 1.3 69.1 + - - +
23Y LEU 3.6 0.2 + - - -
24Y GLN* 3.9 11.6 + - - +
25Y THR* 4.0 10.6 + - - -
57Y TYR* 5.0 6.3 + - - -
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Residues in contact with ASN 22 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20Y VAL* 3.1 0.6 - - - +
21Y ASP* 1.3 86.3 - - - +
23Y LEU* 1.3 66.7 + - - +
24Y GLN 3.2 0.9 - - - -
25Y THR* 3.0 10.4 + - - -
26Y GLN* 2.8 43.6 + - + +
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Residues in contact with LEU 23 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38T PRO* 5.8 1.8 - - + -
20Y VAL* 3.1 32.7 + - + +
22Y ASN* 1.3 77.5 - - - +
24Y GLN* 1.3 64.2 + - - +
26Y GLN* 3.2 12.9 + - - +
27Y VAL* 3.0 22.1 + - + +
50Y LYS* 3.5 30.7 - - + +
53Y GLU* 3.7 43.3 - - + +
54Y TYR* 4.2 6.1 - - + +
57Y TYR* 3.8 24.7 - - + -
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Residues in contact with GLN 24 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42S ALA* 5.4 4.8 - - - +
20Y VAL 3.7 2.6 + - - -
21Y ASP* 4.2 7.6 - - - +
22Y ASN 3.2 0.6 - - - -
23Y LEU* 1.3 78.9 - - - +
25Y THR* 1.3 56.3 + - - +
27Y VAL* 3.3 8.0 - - - +
28Y THR* 2.7 44.8 + - - +
54Y TYR* 4.0 16.9 + - + +
57Y TYR* 2.8 34.2 + - + +
58Y ARG* 3.6 21.3 - - - +
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Residues in contact with THR 25 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Y ASP 4.0 8.9 + - - -
22Y ASN* 3.0 14.3 + - - -
24Y GLN* 1.3 79.4 - - - +
26Y GLN* 1.3 59.5 + - + +
28Y THR* 3.7 5.0 - - - -
29Y GLU* 3.0 51.1 + - + +
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Residues in contact with GLN 26 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22Y ASN* 2.8 38.5 + - + +
23Y LEU* 3.6 11.6 - - + +
25Y THR* 1.3 79.3 - - + +
27Y VAL* 1.3 57.3 + - - +
29Y GLU* 3.4 8.7 + - - +
30Y ALA* 2.9 28.4 + - - +
50Y LYS* 2.9 40.4 + - + +
53Y GLU* 5.8 0.2 - - - +
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Residues in contact with VAL 27 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Y LEU 3.0 13.9 + - - +
24Y GLN 3.3 11.2 - - - +
26Y GLN* 1.3 74.9 - - - +
28Y THR* 1.3 68.0 + - - +
30Y ALA* 3.7 4.5 - - - -
31Y LEU* 3.0 21.8 + - - +
47Y TYR* 3.4 30.4 - - + +
50Y LYS* 3.8 14.1 - - + +
51Y LEU* 3.7 35.9 - - + +
54Y TYR* 3.8 29.4 - - + -
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Residues in contact with THR 28 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Y GLN* 2.7 32.0 + - - +
25Y THR* 3.7 7.0 - - - -
27Y VAL* 1.3 78.9 - - - +
29Y GLU* 1.3 61.3 + - + +
31Y LEU* 3.2 11.3 + - + +
32Y ASP* 2.9 39.9 + - - +
54Y TYR* 6.0 0.3 - - - -
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Residues in contact with GLU 29 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Y THR* 3.0 39.2 + - + +
26Y GLN* 3.8 8.0 - - - +
28Y THR* 1.3 75.1 - - + +
30Y ALA* 1.3 61.2 + - - +
32Y ASP* 3.3 13.7 + - - +
33Y LYS* 3.0 44.2 + - - +
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Residues in contact with ALA 30 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26Y GLN 2.9 17.9 + - - +
27Y VAL* 3.7 8.5 - - - +
28Y THR 3.3 0.2 - - - -
29Y GLU* 1.3 77.8 - - - +
31Y LEU* 1.3 56.3 + - - +
33Y LYS* 3.6 8.0 + - - +
34Y LEU* 2.9 30.3 + - - +
43Y LEU* 4.8 6.1 - - + +
46Y ALA* 4.8 5.8 - - + -
47Y TYR* 3.8 32.6 - - + +
50Y LYS* 4.9 5.2 - - + -
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Residues in contact with LEU 31 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27Y VAL 3.0 15.2 + - - +
28Y THR* 3.4 14.6 - - + +
30Y ALA* 1.3 74.1 - - - +
32Y ASP* 1.3 63.2 + - - +
34Y LEU* 4.3 7.2 - - + -
35Y ALA* 2.8 36.0 + - + +
47Y TYR* 3.6 36.5 - - + +
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Residues in contact with ASP 32 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Y THR* 2.9 30.9 + - - +
29Y GLU* 3.3 17.4 + - - +
31Y LEU* 1.3 82.7 - - - +
33Y LYS* 1.3 63.3 + - + +
35Y ALA* 3.5 15.4 - - - +
36Y ALA* 3.7 6.4 + - - +
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Residues in contact with LYS 33 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Y GLU* 3.0 29.8 + - - +
30Y ALA* 4.0 3.6 - - - +
32Y ASP* 1.3 75.7 - - + +
34Y LEU* 1.3 65.3 + - - +
36Y ALA* 2.9 19.7 + - - +
37Y LYS 3.2 7.8 + - - -
43Y LEU* 3.5 33.1 - - + +
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Residues in contact with LEU 34 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Y ALA 2.9 19.1 + - - +
31Y LEU* 3.2 8.5 + - + +
33Y LYS* 1.3 76.3 - - - +
35Y ALA* 1.3 58.6 + - - +
37Y LYS 3.0 13.2 - - - +
38Y PRO* 2.8 55.5 - - + +
43Y LEU* 3.5 29.1 - - + +
44Y LEU* 3.6 25.6 - - + +
47Y TYR* 3.3 38.8 - - + -
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Residues in contact with ALA 35 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Y LEU* 2.8 23.8 + - + +
32Y ASP* 3.5 10.3 - - - +
33Y LYS 3.1 0.2 - - - -
34Y LEU* 1.3 78.4 - - - +
36Y ALA* 1.3 59.0 - - - +
38Y PRO* 3.6 13.4 - - - +
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Residues in contact with ALA 36 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Y ASP 3.7 5.5 + - - +
33Y LYS* 2.9 13.2 + - - +
35Y ALA* 1.3 81.8 - - - +
37Y LYS* 1.3 69.1 + - + +
38Y PRO* 3.6 4.3 - - - +
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Residues in contact with LYS 37 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Y LYS 3.2 2.8 + - - -
34Y LEU* 3.0 12.1 + - - +
36Y ALA* 1.3 89.5 - - + +
38Y PRO* 1.3 66.5 - - - +
39Y SER* 3.0 8.0 + - - +
40Y ASP* 3.1 29.6 + - + +
43Y LEU* 3.7 14.1 - - + +
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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