Contacts of the helix formed by residues 20 - 37 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D PHE* 3.3 36.8 - - + +
17D ASP* 3.1 5.8 - - - +
19D GLY* 1.3 85.8 - - - +
21D ASP* 1.3 63.3 + - - +
22D ASN 3.1 3.1 - - - +
23D LEU* 3.1 29.6 + - + +
57D TYR* 3.2 38.5 - - + -
5J TRP* 3.6 22.7 - - + +
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Residues in contact with ASP 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ASP* 2.5 23.7 + - - +
18D THR* 3.8 10.5 + - - +
19D GLY 3.7 1.6 - - - -
20D VAL* 1.3 74.1 - - - +
22D ASN* 1.3 68.0 + - - +
24D GLN* 3.9 11.3 + - - +
25D THR* 4.0 10.7 + - - -
57D TYR* 5.0 6.8 + - - -
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Residues in contact with ASN 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D VAL* 3.1 0.6 - - - +
21D ASP* 1.3 85.7 - - - +
23D LEU* 1.3 66.7 + - - +
24D GLN 3.2 0.9 - - - -
25D THR* 3.0 10.1 + - - -
26D GLN* 2.8 35.9 + - + +
3J THR 5.5 1.4 + - - -
4J PRO* 5.3 2.2 - - - +
5J TRP* 3.8 34.4 - - + +
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D VAL* 3.1 30.3 + - + +
22D ASN* 1.3 78.7 - - - +
24D GLN* 1.3 65.9 + - - +
26D GLN* 3.2 4.4 + - - +
27D VAL* 3.0 21.5 + - + +
50D LYS* 3.5 31.0 - - + +
53D GLU* 3.7 31.9 - - + +
54D TYR* 3.9 6.1 - - + +
57D TYR* 3.8 24.0 - - + -
5J TRP* 3.7 35.6 - - + -
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Residues in contact with GLN 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D VAL 3.7 2.6 + - - -
21D ASP* 4.2 7.6 - - - +
22D ASN 3.2 0.4 - - - -
23D LEU* 1.3 79.3 - - - +
25D THR* 1.3 57.0 + - - +
27D VAL* 3.3 8.1 - - - +
28D THR* 2.7 43.7 + - - +
54D TYR* 4.0 18.0 + - + +
57D TYR* 2.8 33.6 + - + +
58D ARG* 3.6 22.2 - - - +
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Residues in contact with THR 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ASP 4.0 8.2 + - - -
22D ASN* 3.0 14.8 + - - -
24D GLN* 1.3 79.1 - - - +
26D GLN* 1.3 59.3 + - + +
28D THR* 3.4 5.9 + - - -
29D GLU* 3.0 51.7 + - + +
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Residues in contact with GLN 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ASN* 2.8 23.8 + - + +
23D LEU* 3.2 5.0 + - - +
25D THR* 1.3 79.1 - - + +
27D VAL* 1.3 57.7 + - - +
29D GLU* 3.4 9.1 + - - +
30D ALA* 2.9 28.6 + - - +
50D LYS* 2.9 39.3 + - + +
4J PRO* 4.4 8.7 - - - +
5J TRP* 3.0 58.9 + - - +
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Residues in contact with VAL 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU 3.0 15.0 + - - +
24D GLN* 3.3 11.4 - - - +
26D GLN* 1.3 74.3 - - - +
28D THR* 1.3 67.9 + - - +
30D ALA* 4.0 4.5 - - - -
31D LEU* 3.0 22.0 + - - +
47D TYR* 3.4 30.5 - - + +
50D LYS* 3.8 13.9 - - + +
51D LEU* 3.7 36.1 - - + +
54D TYR* 3.8 28.7 - - + -
68I PHE* 6.1 3.1 - - + -
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Residues in contact with THR 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D GLN* 2.7 33.2 + - - +
25D THR* 3.7 6.3 - - - -
27D VAL* 1.3 78.0 - - - +
29D GLU* 1.3 61.9 + - + +
31D LEU* 3.2 11.0 + - + +
32D ASP* 2.9 40.8 + - - +
54D TYR* 5.8 0.7 - - - -
15I LYS* 6.4 0.2 - - - +
68I PHE* 6.5 0.9 - - - -
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Residues in contact with GLU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D THR* 3.0 40.0 + - + +
26D GLN* 3.8 7.6 - - - +
28D THR* 1.3 75.6 - - + +
30D ALA* 1.3 60.6 + - - +
32D ASP* 3.3 13.8 + - - +
33D LYS* 3.0 45.7 + - - +
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Residues in contact with ALA 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLN 2.9 19.0 + - - +
27D VAL* 3.7 8.7 - - - +
28D THR 3.3 0.2 - - - -
29D GLU* 1.3 77.6 - - - +
31D LEU* 1.3 55.8 + - - +
33D LYS* 3.6 7.3 + - - +
34D LEU* 2.9 30.7 + - - +
43D LEU* 4.8 5.0 - - + +
46D ALA* 4.8 6.5 - - + -
47D TYR* 3.8 32.1 - - + +
50D LYS* 4.9 4.9 - - + -
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Residues in contact with LEU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D VAL 3.0 14.9 + - - +
28D THR* 3.2 15.2 + - + +
30D ALA* 1.3 74.5 - - - +
32D ASP* 1.3 63.4 + - - +
34D LEU* 4.3 5.6 - - + -
35D ALA* 2.8 34.0 + - + +
47D TYR* 3.6 29.8 - - + +
12I VAL* 5.1 7.4 - - + +
15I LYS* 5.0 22.7 - - + -
16I PHE* 5.3 12.8 - - + +
64I THR* 4.4 14.6 - - + +
68I PHE* 3.8 31.2 - - + -
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Residues in contact with ASP 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D THR* 2.9 31.6 + - - +
29D GLU* 3.3 17.7 + - - +
31D LEU* 1.3 80.2 - - - +
33D LYS* 1.3 64.0 + - + +
35D ALA* 3.5 15.3 - - - +
36D ALA* 3.7 6.1 + - - +
15I LYS* 5.3 13.5 + - - +
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Residues in contact with LYS 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D GLU* 3.0 31.1 + - - +
30D ALA* 4.0 3.6 - - - +
32D ASP* 1.3 77.0 - - + +
34D LEU* 1.3 66.2 + - - +
36D ALA* 2.9 19.2 + - - +
37D LYS 3.2 8.1 + - - -
43D LEU* 3.5 33.1 - - + +
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Residues in contact with LEU 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ALA 2.9 19.3 + - - +
31D LEU* 3.7 8.3 - - + +
33D LYS* 1.3 75.3 - - - +
35D ALA* 1.3 57.9 + - - +
37D LYS 3.0 13.4 - - - +
38D PRO* 2.8 55.6 - - + +
43D LEU* 3.5 29.5 - - + +
44D LEU* 3.6 25.6 - - + +
47D TYR* 3.3 38.8 - - + -
16I PHE* 5.4 6.5 - - + -
60I ALA* 6.2 2.0 - - + -
64I THR* 5.4 4.7 - - + -
79O PHE* 5.6 0.9 - - + -
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Residues in contact with ALA 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LEU* 2.8 18.8 + - + +
32D ASP* 3.5 10.3 - - - +
33D LYS 3.1 0.2 - - - -
34D LEU* 1.3 78.1 - - - +
36D ALA* 1.3 60.0 + - - +
38D PRO* 3.6 1.3 - - - +
15I LYS 3.4 26.9 - - - +
16I PHE* 3.6 25.1 - - + +
19I GLY* 3.2 22.3 - - - +
20I VAL* 3.3 11.8 - - - +
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Residues in contact with ALA 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D ASP 3.7 4.8 + - - +
33D LYS* 2.9 14.3 + - - +
35D ALA* 1.3 80.5 - - - +
37D LYS* 1.3 66.7 + - + +
38D PRO* 3.6 0.2 - - - -
19I GLY* 3.5 13.8 - - - +
5O TRP* 2.7 36.5 + - + +
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Residues in contact with LYS 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LYS 3.2 3.0 + - - +
34D LEU* 3.0 11.4 + - - +
36D ALA* 1.3 89.5 - - + +
38D PRO* 1.3 67.8 - - - +
39D SER 3.0 4.1 + - - +
40D ASP* 3.1 27.1 + - + +
43D LEU* 3.7 13.7 - - + +
6O SER 3.5 23.1 - - - +
7O GLY* 4.2 1.8 - - - -
8O TYR* 4.0 25.0 - - + +
11O ASP* 2.8 22.0 + - - +
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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