Contacts of the helix formed by residues 20 - 37 (chain b) 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 b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35W ALA 3.3 15.5 - - - +
36W ALA 4.1 2.5 - - - +
38W PRO* 3.5 25.4 - - + -
16b PHE* 3.3 28.9 - - + +
17b ASP* 3.1 6.1 - - - +
19b GLY* 1.3 81.5 - - - +
21b ASP* 1.3 62.9 + - - +
22b ASN 3.1 3.1 - - - +
23b LEU* 3.1 34.2 + - + +
24b GLN 3.7 0.2 + - - -
57b TYR* 3.2 39.3 - - + -
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Residues in contact with ASP 21 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17b ASP* 2.5 23.3 + - - +
18b THR* 3.8 11.2 + - - +
19b GLY 3.7 1.2 - - - -
20b VAL* 1.3 75.4 - - - +
22b ASN* 1.3 68.5 + - - +
24b GLN* 3.9 11.6 + - - +
25b THR* 4.0 10.6 + - - -
57b TYR* 5.0 6.9 + - - -
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Residues in contact with ASN 22 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20b VAL* 3.1 0.6 - - - +
21b ASP* 1.3 86.6 - - - +
23b LEU* 1.3 66.2 + - - +
24b GLN 3.2 0.9 - - - -
25b THR* 3.0 11.3 + - - -
26b GLN* 2.8 43.6 + - + +
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Residues in contact with LEU 23 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38W PRO* 5.8 2.2 - - + -
20b VAL* 3.1 32.2 + - + +
22b ASN* 1.3 77.5 - - - +
24b GLN* 1.3 63.6 + - - +
26b GLN* 3.2 13.0 + - - +
27b VAL* 3.0 22.6 + - + +
50b LYS* 3.5 31.9 - - + +
53b GLU* 3.7 43.7 - - + +
54b TYR* 4.2 6.1 - - + +
57b TYR* 3.8 24.2 - - + -
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Residues in contact with GLN 24 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42V ALA* 5.4 4.2 - - - +
20b VAL 3.7 2.8 + - - -
21b ASP* 4.2 7.8 - - - +
22b ASN 3.2 0.6 - - - -
23b LEU* 1.3 79.1 - - - +
25b THR* 1.3 56.6 + - - +
27b VAL* 3.3 8.2 - - - +
28b THR* 2.7 44.4 + - - +
54b TYR* 4.0 17.6 + - + +
57b TYR* 2.8 34.5 + - + +
58b ARG* 3.6 21.5 - - - +
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Residues in contact with THR 25 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21b ASP 4.0 8.5 + - - -
22b ASN* 3.0 13.9 + - - -
24b GLN* 1.3 78.9 - - - +
26b GLN* 1.3 59.2 + - + +
28b THR* 3.7 5.1 - - - -
29b GLU* 3.0 51.4 + - + +
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Residues in contact with GLN 26 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22b ASN* 2.8 38.9 + - + +
23b LEU* 3.6 10.7 - - + +
25b THR* 1.3 80.2 - - + +
27b VAL* 1.3 57.4 + - - +
29b GLU* 3.8 8.3 - - - +
30b ALA* 2.9 28.6 + - - +
50b LYS* 2.9 41.0 + - + +
53b GLU* 5.8 0.2 - - - +
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Residues in contact with VAL 27 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23b LEU 3.0 14.1 + - - +
24b GLN 3.3 11.4 - - - +
26b GLN* 1.3 74.5 - - - +
28b THR* 1.3 68.0 + - - +
30b ALA* 4.0 4.5 - - - -
31b LEU* 3.0 22.0 + - - +
47b TYR* 3.4 30.3 - - + +
50b LYS* 3.8 12.8 - - + +
51b LEU* 3.7 36.3 - - + +
54b TYR* 3.8 29.4 - - + -
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Residues in contact with THR 28 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24b GLN* 2.7 32.3 + - - +
25b THR* 3.7 6.3 - - - -
26b GLN 3.3 0.2 - - - -
27b VAL* 1.3 77.6 - - - +
29b GLU* 1.3 61.2 + - + +
31b LEU* 3.2 11.5 + - + +
32b ASP* 2.9 39.8 + - - +
54b TYR* 5.8 0.5 - - - -
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Residues in contact with GLU 29 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25b THR* 3.0 38.6 + - + +
26b GLN* 3.8 7.9 - - - +
28b THR* 1.3 76.2 - - + +
30b ALA* 1.3 61.2 + - - +
32b ASP* 3.3 13.1 + - - +
33b LYS* 3.0 44.8 + - - +
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Residues in contact with ALA 30 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26b GLN 2.9 18.6 + - - +
27b VAL* 3.7 8.5 - - - +
29b GLU* 1.3 77.4 - - - +
31b LEU* 1.3 56.1 + - - +
33b LYS* 3.6 7.2 + - - +
34b LEU* 2.9 30.8 + - - +
43b LEU* 4.8 5.7 - - + +
46b ALA* 4.8 6.1 - - + -
47b TYR* 3.8 32.6 - - + +
50b LYS* 4.9 5.2 - - + -
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Residues in contact with LEU 31 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27b VAL 3.0 15.6 + - - +
28b THR* 3.4 14.8 - - + +
30b ALA* 1.3 75.3 - - - +
32b ASP* 1.3 63.0 + - - +
34b LEU* 4.3 6.1 - - + -
35b ALA* 2.8 35.5 + - + +
47b TYR* 3.6 36.3 - - + +
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Residues in contact with ASP 32 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28b THR* 2.9 32.0 + - - +
29b GLU* 3.3 17.5 + - - +
31b LEU* 1.3 82.7 - - - +
33b LYS* 1.3 64.0 + - + +
35b ALA* 3.5 15.2 - - - +
36b ALA* 3.7 5.9 + - - +
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Residues in contact with LYS 33 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29b GLU* 3.0 30.3 + - - +
30b ALA* 4.0 3.8 - - - +
32b ASP* 1.3 76.3 - - + +
34b LEU* 1.3 65.8 + - - +
36b ALA* 2.9 18.7 + - - +
37b LYS 3.2 8.0 + - - -
43b LEU* 3.5 32.4 - - + +
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Residues in contact with LEU 34 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30b ALA 2.9 18.9 + - - +
31b LEU* 3.7 8.3 - - + +
33b LYS* 1.3 77.2 - - - +
35b ALA* 1.3 58.6 - - - +
37b LYS 3.0 13.6 - - - +
38b PRO* 2.8 55.9 - - + +
40b ASP 4.3 0.2 - - - +
43b LEU* 3.5 29.8 - - + +
44b LEU* 3.6 24.9 - - + +
47b TYR* 3.3 38.6 - - + -
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Residues in contact with ALA 35 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31b LEU* 2.8 24.5 + - + +
32b ASP* 3.5 10.1 - - - +
34b LEU* 1.3 78.4 - - - +
36b ALA* 1.3 59.9 + - - +
38b PRO* 3.6 13.0 - - - +
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Residues in contact with ALA 36 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32b ASP 3.7 5.5 + - - +
33b LYS* 2.9 13.4 + - - +
35b ALA* 1.3 81.6 - - - +
37b LYS* 1.3 68.7 + - + +
38b PRO* 3.6 5.0 - - - +
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Residues in contact with LYS 37 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33b LYS 3.2 3.0 + - - -
34b LEU* 3.0 12.0 + - - +
36b ALA* 1.3 89.0 - - + +
38b PRO* 1.3 67.6 - - - +
39b SER* 3.0 8.0 + - - +
40b ASP* 3.1 30.0 + - + +
43b LEU* 3.7 15.3 - - + +
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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