Contacts of the helix formed by residues 20 - 37 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA 3.3 15.7 - - - +
38A PRO* 3.5 25.8 - - + -
16F PHE* 3.3 30.5 - - + +
17F ASP* 3.1 5.8 - - - +
19F GLY* 1.3 81.9 - - - +
21F ASP* 1.3 62.6 + - - +
22F ASN 3.1 3.8 - - - +
23F LEU* 3.1 28.0 + - + +
24F GLN 3.7 0.2 + - - -
57F TYR* 3.2 38.3 - - + -
5L TRP* 3.6 15.0 - - + +
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Residues in contact with ASP 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F ASP* 2.5 22.3 + - - +
18F THR* 3.8 11.8 + - - +
19F GLY 3.7 1.4 - - - -
20F VAL* 1.3 74.5 - - - +
22F ASN* 1.3 68.6 + - - +
24F GLN* 3.9 11.8 + - - +
25F THR* 4.0 10.7 + - - -
57F TYR* 5.0 6.5 + - - -
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Residues in contact with ASN 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F VAL* 3.1 1.2 - - - +
21F ASP* 1.3 85.3 - - - +
23F LEU* 1.3 66.9 + - - +
24F GLN 3.2 0.7 - - - -
25F THR* 3.0 10.2 + - - -
26F GLN* 2.8 34.3 + - + +
3L THR 5.5 1.2 + - - -
4L PRO* 5.3 2.4 - - - +
5L TRP* 3.8 36.5 - - + +
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Residues in contact with LEU 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PRO* 5.8 1.6 - - + -
20F VAL* 3.1 29.0 + - + +
22F ASN* 1.3 78.5 - - - +
24F GLN* 1.3 64.2 + - - +
26F GLN* 3.2 4.7 + - - +
27F VAL* 3.0 22.2 + - - +
50F LYS* 3.5 30.7 - - + +
53F GLU* 3.7 33.2 - - + +
54F TYR* 4.4 5.4 - - + -
57F TYR* 3.8 23.8 - - + -
5L TRP* 3.7 35.8 - - + -
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Residues in contact with GLN 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F VAL 3.7 2.4 + - - -
21F ASP* 4.2 7.9 - - - +
22F ASN 3.2 0.4 - - - -
23F LEU* 1.3 78.7 - - - +
25F THR* 1.3 56.5 + - - +
27F VAL* 3.3 8.4 - - - +
28F THR* 2.7 44.6 + - - +
54F TYR* 4.0 17.3 + - + +
57F TYR* 2.8 33.2 + - + +
58F ARG* 3.6 22.3 + - - +
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Residues in contact with THR 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F ASP 4.0 8.3 + - - -
22F ASN* 3.0 14.4 + - - -
24F GLN* 1.3 79.6 - - - +
26F GLN* 1.3 59.5 + - + +
28F THR* 3.4 5.3 + - - -
29F GLU* 3.0 52.4 + - + +
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Residues in contact with GLN 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F ASN* 2.8 23.9 + - + +
23F LEU* 3.6 4.3 - - - +
25F THR* 1.3 79.1 - - + +
27F VAL* 1.3 57.6 + - - +
29F GLU* 3.4 7.9 + - - +
30F ALA* 2.9 27.9 + - - +
50F LYS* 2.9 39.7 + - + +
4L PRO* 4.4 8.5 - - - +
5L TRP* 3.0 57.4 + - - +
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Residues in contact with VAL 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F LEU 3.0 15.0 + - - +
24F GLN 3.3 11.4 - - - +
26F GLN* 1.3 73.9 - - - +
28F THR* 1.3 66.8 + - - +
30F ALA* 3.7 4.7 - - - -
31F LEU* 3.0 22.0 + - - +
47F TYR* 3.4 31.1 - - + +
50F LYS* 3.8 13.0 - - + +
51F LEU* 3.7 36.6 - - + +
54F TYR* 3.8 29.2 - - + -
68K PHE* 6.1 3.8 - - + -
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Residues in contact with THR 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F GLN* 2.7 32.1 + - - +
25F THR* 3.7 6.9 - - - -
27F VAL* 1.3 79.3 - - - +
29F GLU* 1.3 62.2 + - + +
31F LEU* 3.2 11.7 + - + +
32F ASP* 2.9 40.2 + - - +
54F TYR* 5.8 0.5 - - - -
68K PHE* 6.5 0.4 - - - -
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Residues in contact with GLU 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F THR* 3.0 39.4 + - + +
26F GLN* 3.8 7.8 - - - +
28F THR* 1.3 75.7 - - + +
30F ALA* 1.3 61.0 + - - +
32F ASP* 3.3 12.6 + - - +
33F LYS* 3.0 45.4 + - - +
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Residues in contact with ALA 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F GLN 2.9 18.6 + - - +
27F VAL* 3.7 8.1 - - - +
29F GLU* 1.3 77.4 - - - +
31F LEU* 1.3 56.9 + - - +
33F LYS* 4.0 7.5 - - - +
34F LEU* 2.9 30.5 + - - +
43F LEU* 4.8 5.8 - - + +
46F ALA* 4.8 6.5 - - + -
47F TYR* 3.8 33.2 - - + +
50F LYS* 4.9 4.9 - - + -
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Residues in contact with LEU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F VAL 3.0 14.7 + - - +
28F THR* 3.2 13.4 + - + +
30F ALA* 1.3 76.0 - - - +
32F ASP* 1.3 63.3 + - - +
34F LEU* 4.3 5.8 - - + -
35F ALA* 2.8 35.1 + - + +
47F TYR* 3.6 29.3 - - + +
12K VAL* 5.1 7.2 - - + +
15K LYS* 5.0 22.9 - - + -
16K PHE* 5.3 12.1 - - + +
64K THR* 4.4 14.8 - - + +
68K PHE* 3.8 31.6 - - + -
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Residues in contact with ASP 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F THR* 2.9 30.6 + - - +
29F GLU* 3.3 17.2 + - - +
31F LEU* 1.3 81.0 - - - +
33F LYS* 1.3 62.9 + - + +
35F ALA* 3.5 15.8 - - - +
36F ALA* 3.7 6.4 + - - +
15K LYS* 5.3 13.0 + - - +
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Residues in contact with LYS 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F GLU* 3.0 30.7 + - - +
30F ALA* 4.0 3.4 - - - +
32F ASP* 1.3 76.2 - - + +
34F LEU* 1.3 65.9 + - - +
36F ALA* 2.9 19.2 + - - +
37F LYS 3.2 7.8 + - - -
43F LEU* 3.5 33.5 - - + +
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Residues in contact with LEU 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ALA 2.9 19.9 + - - +
31F LEU* 3.2 8.9 + - + +
33F LYS* 1.3 76.2 - - - +
35F ALA* 1.3 58.1 + - - +
37F LYS 3.0 13.0 - - - +
38F PRO* 2.8 56.0 - - + +
43F LEU* 3.5 29.5 - - + +
44F LEU* 3.6 24.9 - - + +
47F TYR* 3.3 38.8 - - + -
16K PHE* 5.4 6.5 - - + -
60K ALA* 6.2 2.5 - - + -
64K THR* 5.4 4.5 - - + -
79Q PHE* 5.6 1.3 - - + -
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Residues in contact with ALA 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F LEU* 2.8 19.2 + - + +
32F ASP* 3.5 10.1 - - - +
33F LYS 3.1 0.2 - - - -
34F LEU* 1.3 76.8 - - - +
36F ALA* 1.3 60.1 + - - +
38F PRO* 3.6 0.7 - - - +
15K LYS 3.4 26.2 - - - +
16K PHE* 3.6 27.1 - - + +
19K GLY* 3.2 22.2 - - - +
20K VAL* 3.3 11.8 - - - +
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Residues in contact with ALA 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F ASP 3.7 5.1 + - - +
33F LYS* 2.9 14.7 + - - +
35F ALA* 1.3 80.9 - - - +
37F LYS* 1.3 67.2 + - + +
38F PRO* 3.6 0.4 - - - -
19K GLY* 3.5 14.9 - - - +
5Q TRP* 2.7 36.1 + - + +
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Residues in contact with LYS 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F LYS 3.2 2.8 + - - -
34F LEU* 3.0 12.0 + - - +
36F ALA* 1.3 89.9 - - + +
38F PRO* 1.3 66.2 - - - +
39F SER 3.0 4.0 + - - +
40F ASP* 3.1 26.9 + - + +
43F LEU* 3.7 13.1 - - + +
6Q SER 3.5 22.9 - - - +
7Q GLY* 4.2 1.8 - - - -
8Q TYR* 4.0 26.0 - - + +
11Q ASP* 2.8 21.9 + - - +
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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