Contacts of the helix formed by residues 20 - 37 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G ALA 3.3 16.4 - - - +
38G PRO* 3.5 25.4 - - + -
16L PHE* 3.3 28.9 - - + +
17L ASP* 3.1 6.1 - - - +
19L GLY* 1.3 81.5 - - - +
21L ASP* 1.3 63.2 + - - +
22L ASN 3.1 3.8 - - - +
23L LEU* 3.1 27.4 + - + +
57L TYR* 3.2 38.8 - - + -
5R TRP* 3.6 15.3 - - + +
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Residues in contact with ASP 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L ASP* 2.5 22.7 + - - +
18L THR* 3.8 11.4 + - - +
19L GLY 3.7 1.8 - - - -
20L VAL* 1.3 74.1 - - - +
22L ASN* 1.3 68.6 + - - +
24L GLN* 3.9 11.6 + - - +
25L THR* 4.0 10.9 + - - -
57L TYR* 5.0 6.3 + - - -
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Residues in contact with ASN 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L VAL* 3.1 0.8 - - - +
21L ASP* 1.3 85.1 - - - +
23L LEU* 1.3 66.7 + - - +
24L GLN 3.2 0.9 - - - -
25L THR* 3.0 10.8 + - - -
26L GLN* 2.8 34.6 + - + +
3R THR 5.5 1.2 + - - -
4R PRO* 5.3 2.0 - - - +
5R TRP* 3.8 35.9 - - + +
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Residues in contact with LEU 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G PRO* 5.8 1.3 - - + -
20L VAL* 3.1 28.3 + - + +
22L ASN* 1.3 78.3 - - - +
24L GLN* 1.3 64.5 + - - +
26L GLN* 3.2 4.7 + - - +
27L VAL* 3.0 21.9 + - + +
50L LYS* 3.5 31.0 - - + +
53L GLU* 3.7 31.2 - - + +
54L TYR* 4.4 5.4 - - + -
57L TYR* 3.8 24.5 - - + -
5R TRP* 3.7 36.7 - - + -
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Residues in contact with GLN 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F ALA* 5.4 4.8 - - - +
20L VAL 3.7 2.4 + - - -
21L ASP* 4.2 7.7 - - - +
22L ASN 3.2 0.2 - - - -
23L LEU* 1.3 78.5 - - - +
25L THR* 1.3 56.5 + - - +
27L VAL* 3.3 8.4 - - - +
28L THR* 2.7 44.2 + - - +
54L TYR* 4.0 16.9 + - + +
57L TYR* 2.8 32.8 + - + +
58L ARG* 3.6 22.1 + - - +
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Residues in contact with THR 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L ASP 4.0 8.5 + - - -
22L ASN* 3.0 14.3 + - - -
24L GLN* 1.3 80.2 - - - +
26L GLN* 1.3 59.8 + - + +
28L THR* 3.7 5.3 - - - -
29L GLU* 3.0 51.8 + - + +
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Residues in contact with GLN 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L ASN* 2.8 24.2 + - + +
23L LEU* 3.6 4.2 - - - +
25L THR* 1.3 80.3 - - + +
27L VAL* 1.3 57.4 + - - +
29L GLU* 3.4 8.2 + - - +
30L ALA* 2.9 28.9 + - - +
50L LYS* 2.9 41.6 + - + +
4R PRO* 4.4 9.1 - - - +
5R TRP* 3.0 57.9 + - - +
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Residues in contact with VAL 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L LEU 3.0 14.8 + - - +
24L GLN 3.3 11.2 - - - +
26L GLN* 1.3 74.3 - - - +
28L THR* 1.3 67.1 + - - +
30L ALA* 4.0 4.7 - - - -
31L LEU* 3.0 21.7 + - - +
47L TYR* 3.4 30.1 - - + +
50L LYS* 3.8 13.7 - - + +
51L LEU* 3.7 35.4 - - + +
54L TYR* 3.8 28.7 - - + -
68Q PHE* 6.1 3.5 - - + -
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Residues in contact with THR 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L GLN* 2.7 32.9 + - - +
25L THR* 3.7 6.9 - - - -
27L VAL* 1.3 78.6 - - - +
29L GLU* 1.3 61.9 + - + +
31L LEU* 3.2 11.6 + - + +
32L ASP* 2.9 40.3 + - - +
54L TYR* 5.8 0.5 - - - -
68Q PHE* 6.5 0.4 - - - -
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Residues in contact with GLU 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L THR* 3.0 39.6 + - + +
26L GLN* 3.8 7.4 - - - +
28L THR* 1.3 74.5 - - + +
30L ALA* 1.3 60.8 + - - +
32L ASP* 3.3 14.0 + - - +
33L LYS* 3.0 45.1 + - - +
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Residues in contact with ALA 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L GLN 2.9 18.6 + - - +
27L VAL* 3.7 8.3 - - - +
28L THR 3.3 0.2 - - - -
29L GLU* 1.3 77.5 - - - +
31L LEU* 1.3 57.0 + - - +
33L LYS* 4.0 7.7 - - - +
34L LEU* 2.9 30.1 + - - +
43L LEU* 4.8 6.6 - - + +
46L ALA* 4.8 5.8 - - + -
47L TYR* 3.8 32.2 - - + +
50L LYS* 4.9 5.2 - - + -
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Residues in contact with LEU 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L VAL 3.0 15.1 + - - +
28L THR* 3.2 13.4 + - + +
30L ALA* 1.3 74.3 - - - +
32L ASP* 1.3 64.2 + - - +
34L LEU* 3.7 6.0 - - + -
35L ALA* 2.8 34.3 + - + +
47L TYR* 3.6 30.4 - - + +
12Q VAL* 5.1 7.6 - - + +
15Q LYS* 5.0 22.7 - - + -
16Q PHE* 5.3 12.3 - - + +
64Q THR* 4.4 14.6 - - + +
68Q PHE* 3.8 31.6 - - + -
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Residues in contact with ASP 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L THR* 2.9 31.2 + - - +
29L GLU* 3.3 17.5 + - - +
31L LEU* 1.3 81.3 - - - +
33L LYS* 1.3 63.0 + - + +
35L ALA* 3.5 15.3 - - - +
36L ALA* 3.7 6.1 + - - +
15Q LYS* 5.3 13.3 + - - +
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Residues in contact with LYS 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L GLU* 3.0 31.4 + - - +
30L ALA* 4.0 3.1 - - - +
32L ASP* 1.3 75.7 - - + +
34L LEU* 1.3 65.6 + - - +
36L ALA* 2.9 19.5 + - - +
37L LYS 3.2 7.8 + - - -
43L LEU* 3.5 33.3 - - + +
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Residues in contact with LEU 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L ALA 2.9 20.0 + - - +
31L LEU* 3.7 7.4 - - + +
33L LYS* 1.3 76.3 - - - +
35L ALA* 1.3 58.4 + - - +
37L LYS 3.0 13.4 - - - +
38L PRO* 2.8 55.2 - - + +
43L LEU* 3.5 29.7 - - + +
44L LEU* 3.6 25.4 - - + +
47L TYR* 3.3 39.5 - - + -
16Q PHE* 5.4 6.7 - - + -
60Q ALA* 6.2 2.2 - - + -
64Q THR* 5.4 4.7 - - + -
79W PHE* 5.6 1.1 - - + -
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Residues in contact with ALA 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L LEU* 2.8 19.2 + - + +
32L ASP* 3.5 10.5 - - - +
33L LYS 3.1 0.2 - - - -
34L LEU* 1.3 76.3 - - - +
36L ALA* 1.3 60.5 + - - +
38L PRO* 3.6 0.9 - - - +
15Q LYS 3.4 26.2 - - - +
16Q PHE* 3.6 26.2 - - + +
19Q GLY* 3.2 22.6 - - - +
20Q VAL* 3.3 11.6 - - - +
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Residues in contact with ALA 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L ASP 3.7 5.0 + - - +
33L LYS* 2.9 13.9 + - - +
35L ALA* 1.3 79.9 - - - +
37L LYS* 1.3 67.8 + - + +
38L PRO* 3.6 0.4 - - - -
19Q GLY* 3.5 14.0 - - - +
5W TRP* 2.7 36.6 + - + +
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Residues in contact with LYS 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L LYS 3.2 2.8 + - - -
34L LEU* 3.0 11.8 + - - +
36L ALA* 1.3 89.7 - - + +
38L PRO* 1.3 66.7 - - - +
39L SER 3.0 3.9 + - - +
40L ASP* 3.1 26.1 + - + +
43L LEU* 3.7 13.5 - - + +
6W SER 3.5 22.9 - - - +
7W GLY* 4.2 1.8 - - - -
8W TYR* 4.0 24.8 - - + +
11W ASP* 2.8 21.5 + - - +
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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
------------------------------------------------------------
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