Contacts of the helix formed by residues 20 - 37 (chain W) 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 W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35R ALA 3.3 15.7 - - - +
38R PRO* 3.5 25.8 - - + -
16W PHE* 3.3 29.2 - - + +
17W ASP* 3.1 5.4 - - - +
19W GLY* 1.3 80.5 - - - +
21W ASP* 1.3 62.4 + - - +
22W ASN 3.1 3.4 - - - +
23W LEU* 3.1 28.4 + - + +
24W GLN 3.7 0.2 + - - -
57W TYR* 3.2 39.5 - - + -
5c TRP* 3.6 15.3 - - + +
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Residues in contact with ASP 21 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17W ASP* 2.5 23.4 + - - +
18W THR* 3.8 11.4 + - - +
19W GLY 3.7 1.8 - - - -
20W VAL* 1.3 73.5 - - - +
22W ASN* 1.3 69.2 + - - +
24W GLN* 3.9 11.6 + - - +
25W THR* 4.0 10.7 + - - -
57W TYR* 5.0 6.3 + - - -
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Residues in contact with ASN 22 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19W GLY 5.5 0.2 - - - -
20W VAL* 3.1 1.0 - - - +
21W ASP* 1.3 86.3 - - - +
23W LEU* 1.3 66.7 + - - +
24W GLN 3.2 0.7 - - - -
25W THR* 3.0 10.7 + - - -
26W GLN* 2.8 33.7 + - + +
3c THR 5.5 1.2 + - - -
4c PRO* 5.3 2.2 - - - +
5c TRP* 3.8 35.9 - - + +
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Residues in contact with LEU 23 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38R PRO* 5.8 1.3 - - + -
20W VAL* 3.1 29.2 + - + +
22W ASN* 1.3 78.5 - - - +
24W GLN* 1.3 64.9 + - - +
26W GLN* 3.2 4.3 + - - +
27W VAL* 3.0 21.2 + - + +
50W LYS* 3.5 31.2 - - + +
53W GLU* 3.7 31.6 - - + +
54W TYR* 4.4 5.6 - - + -
57W TYR* 3.8 24.5 - - + +
5c TRP* 3.7 38.0 - - + -
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Residues in contact with GLN 24 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42Q ALA* 5.4 4.8 - - - +
20W VAL 3.7 2.2 + - - -
21W ASP* 4.2 7.9 - - - +
22W ASN 3.2 0.6 - - - -
23W LEU* 1.3 78.1 - - - +
25W THR* 1.3 55.6 + - - +
27W VAL* 3.3 8.3 - - - +
28W THR* 2.7 44.9 + - - +
54W TYR* 4.0 17.4 + - + +
57W TYR* 2.8 33.5 + - + +
58W ARG* 3.6 21.7 + - - +
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Residues in contact with THR 25 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21W ASP 4.0 8.5 + - - -
22W ASN* 3.0 14.6 + - - -
24W GLN* 1.3 78.9 - - - +
26W GLN* 1.3 59.6 + - + +
28W THR* 3.4 5.3 + - - -
29W GLU* 3.0 51.8 + - + +
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Residues in contact with GLN 26 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22W ASN* 2.8 24.2 + - + +
23W LEU* 3.6 4.0 - - - +
25W THR* 1.3 80.4 - - + +
27W VAL* 1.3 56.7 + - - +
29W GLU* 3.4 9.0 + - - +
30W ALA* 2.9 28.1 + - - +
50W LYS* 2.9 39.4 + - + +
4c PRO* 4.4 8.3 - - - +
5c TRP* 3.0 58.2 + - - +
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Residues in contact with VAL 27 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23W LEU 3.0 15.2 + - - +
24W GLN 3.3 11.9 - - - +
26W GLN* 1.3 75.3 - - - +
28W THR* 1.3 66.9 + - - +
30W ALA* 4.0 4.7 - - - -
31W LEU* 3.0 22.0 + - - +
47W TYR* 3.4 30.3 - - + +
50W LYS* 3.8 13.2 - - + +
51W LEU* 3.7 35.7 - - + +
54W TYR* 3.8 28.5 - - + -
68b PHE* 6.1 4.2 - - + -
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Residues in contact with THR 28 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24W GLN* 2.7 32.5 + - - +
25W THR* 3.7 6.5 - - - -
27W VAL* 1.3 78.4 - - - +
29W GLU* 1.3 60.8 + - + +
31W LEU* 3.2 10.7 + - + +
32W ASP* 2.9 40.8 + - - +
54W TYR* 5.8 0.5 - - - -
68b PHE* 6.5 0.7 - - - -
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Residues in contact with GLU 29 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25W THR* 3.0 39.5 + - + +
26W GLN* 3.8 7.8 - - - +
28W THR* 1.3 75.0 - - + +
30W ALA* 1.3 60.9 + - - +
32W ASP* 3.3 13.6 + - - +
33W LYS* 3.0 45.2 + - - +
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Residues in contact with ALA 30 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26W GLN 2.9 19.2 + - - +
27W VAL* 3.7 8.7 - - - +
29W GLU* 1.3 77.6 - - - +
31W LEU* 1.3 56.8 + - - +
33W LYS* 4.0 7.3 - - - +
34W LEU* 2.9 30.8 + - - +
43W LEU* 4.8 6.3 - - + +
46W ALA* 4.8 5.6 - - + -
47W TYR* 3.8 32.0 - - + +
50W LYS* 4.9 4.7 - - + -
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Residues in contact with LEU 31 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27W VAL 3.0 14.9 + - - +
28W THR* 3.2 14.1 + - + +
30W ALA* 1.3 73.9 - - - +
32W ASP* 1.3 63.1 + - - +
34W LEU* 4.3 6.1 - - + -
35W ALA* 2.8 35.2 + - + +
47W TYR* 3.6 30.0 - - + +
12b VAL* 5.1 7.4 - - + +
15b LYS* 5.0 22.0 - - + -
16b PHE* 5.3 12.8 - - + +
64b THR* 4.4 14.4 - - + +
68b PHE* 3.8 32.3 - - + -
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Residues in contact with ASP 32 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28W THR* 2.9 31.2 + - - +
29W GLU* 3.3 18.2 + - - +
31W LEU* 1.3 82.1 - - - +
33W LYS* 1.3 62.6 + - + +
35W ALA* 3.5 15.3 - - - +
36W ALA* 3.7 6.6 + - - +
15b LYS* 5.3 13.7 + - - +
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Residues in contact with LYS 33 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29W GLU* 3.0 30.4 + - - +
30W ALA* 4.0 3.4 - - - +
32W ASP* 1.3 76.2 - - + +
34W LEU* 1.3 65.1 + - - +
36W ALA* 2.9 19.2 + - - +
37W LYS 3.2 8.3 + - - -
43W LEU* 3.5 33.2 - - + +
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Residues in contact with LEU 34 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30W ALA 2.9 19.7 + - - +
31W LEU* 3.7 6.7 - - + +
33W LYS* 1.3 76.6 - - - +
35W ALA* 1.3 59.2 + - - +
37W LYS 3.0 13.6 - - - +
38W PRO* 2.8 54.5 - - + +
43W LEU* 3.5 30.0 - - + +
44W LEU* 3.6 25.4 - - + +
47W TYR* 3.3 39.0 - - + -
16b PHE* 5.4 6.1 - - + -
60b ALA* 6.2 2.5 - - + -
64b THR* 5.4 4.7 - - + -
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Residues in contact with ALA 35 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31W LEU* 2.8 19.8 + - + +
32W ASP* 3.5 10.3 - - - +
34W LEU* 1.3 77.1 - - - +
36W ALA* 1.3 60.4 + - - +
38W PRO* 3.6 0.9 - - - +
15b LYS 3.4 25.8 - - - +
16b PHE* 3.6 26.7 - - + +
19b GLY* 3.2 23.0 - - - +
20b VAL* 3.3 11.6 - - - +
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Residues in contact with ALA 36 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32W ASP 3.7 5.1 + - - +
33W LYS* 2.9 14.5 + - - +
35W ALA* 1.3 81.0 - - - +
37W LYS* 1.3 70.1 + - + +
38W PRO* 3.6 4.6 - - - +
19b GLY* 3.5 25.5 - - - +
20b VAL* 4.1 1.7 - - - +
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Residues in contact with LYS 37 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33W LYS 3.2 3.0 + - - -
34W LEU* 3.0 12.2 + - - +
36W ALA* 1.3 89.5 - - + +
38W PRO* 1.3 67.3 - - - +
39W SER* 3.0 7.8 + - - +
40W ASP* 3.1 30.0 + - + +
43W LEU* 3.7 13.2 - - + +
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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
------------------------------------------------------------
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