Contacts of the helix formed by residues 20 - 37 (chain X) 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 X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35S ALA 3.3 15.7 - - - +
36S ALA 4.1 2.2 - - - +
38S PRO* 3.5 26.0 - - + -
16X PHE* 3.3 29.4 - - + +
17X ASP* 3.1 5.8 - - - +
19X GLY* 1.3 81.5 - - - +
21X ASP* 1.3 62.8 + - - +
22X ASN 3.1 3.6 - - - +
23X LEU* 3.1 34.3 + - + +
24X GLN 3.7 0.2 + - - -
57X TYR* 3.2 39.6 - - + -
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Residues in contact with ASP 21 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X ASP* 2.5 22.9 + - - +
18X THR* 3.8 11.6 + - - +
19X GLY 3.7 1.2 - - - -
20X VAL* 1.3 74.5 - - - +
22X ASN* 1.3 67.2 + - - +
23X LEU 3.6 0.2 + - - -
24X GLN* 3.9 11.6 + - - +
25X THR* 4.0 10.6 + - - -
57X TYR* 5.0 6.3 + - - -
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Residues in contact with ASN 22 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X VAL* 3.1 0.8 - - - +
21X ASP* 1.3 85.9 - - - +
23X LEU* 1.3 65.9 + - - +
24X GLN 3.2 0.9 - - - -
25X THR* 3.0 11.4 + - - -
26X GLN* 2.8 44.2 + - + +
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Residues in contact with LEU 23 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38S PRO* 5.8 1.6 - - + -
20X VAL* 3.1 32.5 + - + +
22X ASN* 1.3 77.4 - - - +
24X GLN* 1.3 64.0 + - - +
26X GLN* 3.2 13.2 + - - +
27X VAL* 3.0 21.9 + - + +
50X LYS* 3.5 31.4 - - + +
53X GLU* 3.7 44.4 - - + +
54X TYR* 4.4 6.1 - - + -
57X TYR* 3.8 23.6 - - + -
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Residues in contact with GLN 24 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42R ALA* 5.4 4.6 - - - +
20X VAL 3.7 2.4 + - - -
21X ASP* 4.2 8.7 - - - +
22X ASN 3.2 0.6 - - - -
23X LEU* 1.3 78.9 - - - +
25X THR* 1.3 56.1 + - - +
27X VAL* 3.3 8.4 - - - +
28X THR* 2.7 44.5 + - - +
54X TYR* 4.0 17.8 + - + +
57X TYR* 2.8 33.8 + - + +
58X ARG* 3.6 20.9 - - - +
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Residues in contact with THR 25 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X ASP 4.0 8.7 + - - -
22X ASN* 3.0 14.4 + - - -
24X GLN* 1.3 79.1 - - - +
26X GLN* 1.3 59.9 + - + +
28X THR* 3.4 5.5 + - - -
29X GLU* 3.0 51.4 + - + +
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Residues in contact with GLN 26 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22X ASN* 2.8 37.4 + - + +
23X LEU* 3.6 10.9 - - - +
25X THR* 1.3 79.6 - - + +
27X VAL* 1.3 58.6 + - - +
29X GLU* 3.4 8.5 + - - +
30X ALA* 2.9 28.1 + - - +
50X LYS* 2.9 41.4 + - + +
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Residues in contact with VAL 27 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23X LEU 3.0 13.9 + - - +
24X GLN 3.3 11.4 - - - +
26X GLN* 1.3 75.1 - - - +
28X THR* 1.3 67.0 + - - +
30X ALA* 4.0 4.7 - - - -
31X LEU* 3.0 21.8 + - - +
47X TYR* 3.4 30.5 - - + +
50X LYS* 3.8 13.0 - - + +
51X LEU* 3.7 36.6 - - + +
54X TYR* 3.8 28.5 - - + -
68c PHE* 6.1 4.0 - - + -
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Residues in contact with THR 28 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X GLN* 2.7 32.0 + - - +
25X THR* 3.7 6.3 - - - -
26X GLN 3.3 0.2 - - - -
27X VAL* 1.3 78.2 - - - +
29X GLU* 1.3 61.5 + - + +
31X LEU* 3.2 11.1 + - + +
32X ASP* 2.9 39.4 + - - +
54X TYR* 5.8 0.5 - - - -
68c PHE* 6.5 0.7 - - - -
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Residues in contact with GLU 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25X THR* 3.0 37.7 + - + +
26X GLN* 3.8 7.8 - - - +
28X THR* 1.3 75.6 - - + +
30X ALA* 1.3 61.3 + - - +
32X ASP* 3.3 13.6 + - - +
33X LYS* 3.0 46.2 + - - +
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Residues in contact with ALA 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26X GLN 2.9 18.4 + - - +
27X VAL* 3.7 8.1 - - - +
29X GLU* 1.3 78.1 - - - +
31X LEU* 1.3 55.7 + - - +
33X LYS* 4.0 6.4 - - - +
34X LEU* 2.9 31.4 + - - +
43X LEU* 4.8 6.0 - - + +
46X ALA* 4.8 5.8 - - + -
47X TYR* 3.8 33.3 - - + +
50X LYS* 4.9 5.2 - - + -
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Residues in contact with LEU 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27X VAL 3.0 15.5 + - - +
28X THR* 3.4 15.3 - - + +
30X ALA* 1.3 75.2 - - - +
32X ASP* 1.3 63.3 + - - +
34X LEU* 3.7 6.0 - - + -
35X ALA* 2.8 33.8 + - + +
47X TYR* 3.6 29.8 - - + +
12c VAL* 5.1 7.4 - - + +
15c LYS* 5.0 22.0 - - + -
16c PHE* 5.3 12.8 - - + +
64c THR* 4.4 14.4 - - + +
68c PHE* 3.8 31.6 - - + -
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Residues in contact with ASP 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28X THR* 2.9 31.0 + - - +
29X GLU* 3.3 17.8 + - - +
31X LEU* 1.3 82.9 - - - +
33X LYS* 1.3 63.9 + - + +
35X ALA* 3.5 14.9 - - - +
36X ALA* 3.7 6.2 + - - +
15c LYS* 5.3 13.3 + - - +
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Residues in contact with LYS 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29X GLU* 3.0 31.5 + - - +
30X ALA* 4.0 3.4 - - - +
32X ASP* 1.3 76.1 - - + +
34X LEU* 1.3 65.8 + - - +
36X ALA* 2.9 19.2 + - - +
37X LYS 3.2 8.1 + - - -
43X LEU* 3.5 32.2 - - + +
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Residues in contact with LEU 34 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X ALA 2.9 19.7 + - - +
31X LEU* 3.7 8.3 - - + +
33X LYS* 1.3 76.8 - - - +
35X ALA* 1.3 58.3 - - - +
37X LYS 3.0 13.2 - - - +
38X PRO* 2.8 54.9 - - + +
40X ASP 4.3 0.2 - - - +
43X LEU* 3.5 30.2 - - + +
44X LEU* 3.6 24.7 - - + +
47X TYR* 3.3 39.0 - - + -
16c PHE* 5.4 6.1 - - + -
60c ALA* 6.2 2.7 - - + -
64c THR* 5.4 4.9 - - + -
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Residues in contact with ALA 35 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X LEU* 2.8 20.3 + - + +
32X ASP* 3.5 9.9 - - - +
34X LEU* 1.3 78.0 - - - +
36X ALA* 1.3 59.6 + - - +
38X PRO* 3.6 0.9 - - - +
15c LYS 3.4 26.5 - - - +
16c PHE* 3.6 26.5 - - + +
19c GLY* 3.2 23.0 - - - +
20c VAL* 3.3 12.0 - - - +
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Residues in contact with ALA 36 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32X ASP 3.7 5.3 + - - +
33X LYS* 2.9 14.3 + - - +
35X ALA* 1.3 80.0 - - - +
37X LYS* 1.3 69.5 + - + +
38X PRO* 3.6 5.0 - - - +
19c GLY* 3.5 24.8 - - - +
20c VAL* 4.1 1.9 - - - +
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Residues in contact with LYS 37 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X LYS 3.2 3.0 + - - -
34X LEU* 3.0 11.6 + - - +
36X ALA* 1.3 89.4 - - + +
38X PRO* 1.3 67.6 - - - +
39X SER* 3.0 7.8 + - - +
40X ASP* 3.1 30.4 + - + +
43X LEU* 3.7 14.8 - - + +
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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