Contacts of the helix formed by residues 20 - 37 (chain U) 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 U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35P ALA 3.3 15.9 - - - +
38P PRO* 3.5 25.6 - - + -
16U PHE* 3.3 29.4 - - + +
17U ASP* 3.1 5.6 - - - +
19U GLY* 1.3 81.3 - - - +
21U ASP* 1.3 62.9 + - - +
22U ASN 3.1 3.4 - - - +
23U LEU* 3.1 28.8 + - + +
24U GLN 3.7 0.2 + - - -
57U TYR* 3.2 39.8 - - + -
5a TRP* 3.6 15.0 - - + +
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Residues in contact with ASP 21 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17U ASP* 2.5 23.0 + - - +
18U THR* 3.8 11.4 + - - +
19U GLY 3.7 1.2 - - - -
20U VAL* 1.3 75.0 - - - +
22U ASN* 1.3 67.7 - - - +
23U LEU 3.6 0.2 + - - -
24U GLN* 3.9 11.6 + - - +
25U THR* 4.0 10.6 + - - -
57U TYR* 5.0 6.7 + - - -
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Residues in contact with ASN 22 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20U VAL* 3.1 0.6 - - - +
21U ASP* 1.3 85.9 - - - +
23U LEU* 1.3 66.3 + - - +
24U GLN 3.2 0.9 - - - -
25U THR* 3.0 11.1 + - - -
26U GLN* 2.8 34.8 + - + +
4a PRO* 5.3 1.8 - - - +
5a TRP* 3.8 35.9 - - + +
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Residues in contact with LEU 23 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P PRO* 5.8 1.3 - - + -
20U VAL* 3.1 30.0 + - + +
22U ASN* 1.3 77.3 - - - +
24U GLN* 1.3 63.8 + - - +
26U GLN* 3.2 3.8 + - - +
27U VAL* 3.0 22.2 + - + +
50U LYS* 3.5 31.2 - - + +
53U GLU* 3.7 32.1 - - + +
54U TYR* 4.2 5.6 - - + +
57U TYR* 3.8 23.6 - - + -
5a TRP* 3.7 36.9 - - + -
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Residues in contact with GLN 24 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42O ALA* 5.4 4.4 - - - +
20U VAL 3.7 2.8 + - - -
21U ASP* 4.2 8.2 - - - +
22U ASN 3.2 0.6 - - - -
23U LEU* 1.3 78.7 - - - +
25U THR* 1.3 57.0 + - - +
27U VAL* 3.3 8.1 - - - +
28U THR* 2.7 44.2 + - - +
54U TYR* 4.0 17.6 + - + +
57U TYR* 2.8 33.8 + - + +
58U ARG* 3.6 22.2 - - - +
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Residues in contact with THR 25 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21U ASP 4.0 8.5 + - - -
22U ASN* 3.0 14.1 + - - -
24U GLN* 1.3 80.2 - - - +
26U GLN* 1.3 58.6 + - + +
28U THR* 3.4 5.0 + - - -
29U GLU* 3.0 51.8 + - + +
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Residues in contact with GLN 26 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22U ASN* 2.8 24.8 + - + +
23U LEU* 3.6 4.0 - - + +
25U THR* 1.3 79.4 - - + +
27U VAL* 1.3 57.7 + - - +
29U GLU* 3.8 8.1 - - - +
30U ALA* 2.9 28.9 + - - +
50U LYS* 2.9 39.7 + - + +
4a PRO* 4.4 8.9 - - - +
5a TRP* 3.0 59.3 + - - +
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Residues in contact with VAL 27 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23U LEU 3.0 14.1 + - - +
24U GLN 3.3 11.4 - - - +
26U GLN* 1.3 75.4 - - - +
28U THR* 1.3 67.5 + - - +
30U ALA* 4.0 4.5 - - - -
31U LEU* 3.0 22.2 + - - +
47U TYR* 3.4 29.5 - - + +
50U LYS* 3.8 13.4 - - + +
51U LEU* 3.7 36.8 - - + +
54U TYR* 3.8 29.2 - - + -
68Z PHE* 6.1 3.5 - - + -
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Residues in contact with THR 28 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24U GLN* 2.7 32.3 + - - +
25U THR* 3.7 6.5 - - - -
27U VAL* 1.3 78.1 - - - +
29U GLU* 1.3 60.4 + - + +
31U LEU* 3.2 10.7 + - + +
32U ASP* 2.9 40.8 + - - +
54U TYR* 5.8 0.5 - - - -
68Z PHE* 6.5 0.9 - - - -
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Residues in contact with GLU 29 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25U THR* 3.0 38.0 + - + +
26U GLN* 3.8 7.6 - - - +
28U THR* 1.3 75.0 - - + +
30U ALA* 1.3 61.6 + - - +
32U ASP* 3.3 13.6 + - - +
33U LYS* 3.0 45.2 + - - +
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Residues in contact with ALA 30 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26U GLN 2.9 18.8 + - - +
27U VAL* 3.7 8.1 - - - +
29U GLU* 1.3 78.2 - - - +
31U LEU* 1.3 56.4 + - - +
33U LYS* 3.6 7.4 + - - +
34U LEU* 2.9 31.0 + - - +
43U LEU* 4.8 5.6 - - + +
46U ALA* 4.8 6.1 - - + -
47U TYR* 3.8 32.6 - - + +
50U LYS* 4.9 4.7 - - + -
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Residues in contact with LEU 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27U VAL 3.0 16.2 + - - +
28U THR* 3.4 14.6 - - + +
30U ALA* 1.3 75.2 - - - +
32U ASP* 1.3 62.8 + - - +
34U LEU* 3.7 6.0 - - + -
35U ALA* 2.8 34.1 + - + +
47U TYR* 3.6 29.5 - - + +
12Z VAL* 5.1 7.4 - - + +
15Z LYS* 5.0 22.2 - - + -
16Z PHE* 5.3 12.3 - - + +
64Z THR* 4.4 14.6 - - + +
68Z PHE* 3.8 31.2 - - + -
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Residues in contact with ASP 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28U THR* 2.9 31.9 + - - +
29U GLU* 3.3 17.3 + - - +
31U LEU* 1.3 82.2 - - - +
33U LYS* 1.3 64.1 + - + +
35U ALA* 3.5 15.2 - - - +
36U ALA* 3.7 6.1 + - - +
15Z LYS* 5.3 13.3 + - - +
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Residues in contact with LYS 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29U GLU* 3.0 31.3 + - - +
30U ALA* 4.0 3.8 - - - +
32U ASP* 1.3 75.9 - - + +
34U LEU* 1.3 65.3 + - - +
36U ALA* 2.9 18.7 + - - +
37U LYS 3.2 8.5 + - - -
43U LEU* 3.5 33.1 - - + +
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Residues in contact with LEU 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30U ALA 2.9 18.4 + - - +
31U LEU* 3.7 8.3 - - + +
33U LYS* 1.3 76.7 - - - +
35U ALA* 1.3 58.3 - - - +
37U LYS 3.0 13.4 - - - +
38U PRO* 2.8 55.7 - - + +
40U ASP 4.3 0.2 - - - +
43U LEU* 3.5 29.3 - - + +
44U LEU* 3.6 24.9 - - + +
47U TYR* 3.3 38.8 - - + -
16Z PHE* 5.4 6.1 - - + -
60Z ALA* 6.2 2.7 - - + -
64Z THR* 5.4 4.7 - - + -
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Residues in contact with ALA 35 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31U LEU* 2.8 20.3 + - + +
32U ASP* 3.5 10.1 - - - +
33U LYS 3.1 0.2 - - - -
34U LEU* 1.3 78.8 - - - +
36U ALA* 1.3 59.0 + - - +
38U PRO* 3.6 0.9 - - - +
15Z LYS 3.4 26.0 - - - +
16Z PHE* 3.6 25.3 - - + +
19Z GLY* 3.2 22.4 - - - +
20Z VAL* 3.3 12.3 - - - +
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Residues in contact with ALA 36 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32U ASP 3.7 5.3 + - - +
33U LYS* 2.9 13.9 + - - +
35U ALA* 1.3 80.2 - - - +
37U LYS* 1.3 68.6 + - + +
38U PRO* 3.6 4.7 - - - +
19Z GLY* 3.5 24.5 - - - +
20Z VAL* 4.1 2.1 - - - +
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Residues in contact with LYS 37 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33U LYS 3.2 2.8 + - - -
34U LEU* 3.0 11.8 + - - +
36U ALA* 1.3 89.2 - - + +
38U PRO* 1.3 67.4 - - - +
39U SER* 3.0 7.7 + - - +
40U ASP* 3.1 29.2 + - + +
43U 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
------------------------------------------------------------
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