Contacts of the helix formed by residues 20 - 37 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O ALA 3.3 15.9 - - - +
38O PRO* 3.5 25.6 - - + -
16T PHE* 3.3 29.8 - - + +
17T ASP* 3.1 5.8 - - - +
19T GLY* 1.3 81.3 - - - +
21T ASP* 1.3 63.0 + - - +
22T ASN 3.1 3.6 - - - +
23T LEU* 3.1 27.9 + - + +
24T GLN 3.7 0.2 + - - -
57T TYR* 3.2 39.9 - - + -
5Z TRP* 3.6 15.0 - - + +
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Residues in contact with ASP 21 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17T ASP* 2.5 23.0 + - - +
18T THR* 3.8 11.8 + - - +
19T GLY 3.7 1.4 - - - -
20T VAL* 1.3 73.9 - - - +
22T ASN* 1.3 69.0 + - - +
24T GLN* 3.9 11.4 + - - +
25T THR* 4.0 10.7 + - - -
57T TYR* 5.0 6.4 + - - -
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Residues in contact with ASN 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20T VAL* 3.1 1.2 - - - +
21T ASP* 1.3 85.3 - - - +
23T LEU* 1.3 65.2 + - - +
24T GLN 3.2 0.7 - - - -
25T THR* 3.0 11.0 + - - -
26T GLN* 2.8 35.1 + - + +
3Z THR 5.5 1.2 + - - -
4Z PRO* 5.3 2.0 - - - +
5Z TRP* 3.8 36.3 - - + +
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Residues in contact with LEU 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38O PRO* 5.8 1.3 - - + -
20T VAL* 3.1 29.2 + - + +
22T ASN* 1.3 77.9 - - - +
24T GLN* 1.3 64.8 + - - +
26T GLN* 3.2 4.5 + - - +
27T VAL* 3.0 21.5 + - - +
50T LYS* 3.5 30.7 - - + +
53T GLU* 3.7 32.1 - - + +
54T TYR* 4.4 5.8 - - + -
57T TYR* 3.8 23.6 - - + +
5Z TRP* 3.7 36.3 - - + -
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Residues in contact with GLN 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42N ALA* 5.4 4.8 - - - +
20T VAL 3.7 2.6 + - - -
21T ASP* 4.2 7.9 - - - +
22T ASN 3.2 0.6 - - - -
23T LEU* 1.3 79.1 - - - +
25T THR* 1.3 55.5 + - - +
27T VAL* 3.3 8.1 - - - +
28T THR* 2.7 44.3 + - - +
54T TYR* 4.0 17.6 + - + +
57T TYR* 2.8 34.0 + - + +
58T ARG* 3.6 21.9 + - - +
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Residues in contact with THR 25 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21T ASP 4.0 8.7 + - - -
22T ASN* 3.0 14.6 + - - -
24T GLN* 1.3 78.9 - - - +
26T GLN* 1.3 60.5 + - + +
28T THR* 3.4 5.3 + - - -
29T GLU* 3.0 51.9 + - + +
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Residues in contact with GLN 26 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22T ASN* 2.8 25.7 + - + +
23T LEU* 3.6 3.8 - - - +
25T THR* 1.3 79.7 - - + +
27T VAL* 1.3 56.3 + - - +
29T GLU* 3.4 9.0 + - - +
30T ALA* 2.9 28.2 + - - +
50T LYS* 2.9 39.6 + - + +
4Z PRO* 4.4 8.9 - - - +
5Z TRP* 3.0 58.4 + - - +
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Residues in contact with VAL 27 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23T LEU 3.0 15.0 + - - +
24T GLN 3.3 11.4 - - - +
26T GLN* 1.3 74.3 - - - +
28T THR* 1.3 67.4 + - - +
30T ALA* 3.7 4.3 - - - -
31T LEU* 3.0 21.8 + - - +
47T TYR* 3.4 30.0 - - + +
50T LYS* 3.8 13.2 - - + +
51T LEU* 3.7 36.6 - - + +
54T TYR* 3.8 28.5 - - + -
68Y PHE* 6.1 4.2 - - + -
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Residues in contact with THR 28 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24T GLN* 2.7 32.6 + - - +
25T THR* 3.7 6.7 - - - -
26T GLN 3.3 0.2 - - - -
27T VAL* 1.3 77.3 - - - +
29T GLU* 1.3 60.9 + - + +
31T LEU* 3.2 10.9 + - + +
32T ASP* 2.9 40.4 + - - +
54T TYR* 5.8 0.5 - - - -
68Y PHE* 6.5 0.7 - - - -
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Residues in contact with GLU 29 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25T THR* 3.0 37.8 + - + +
26T GLN* 3.8 7.9 - - - +
28T THR* 1.3 75.2 - - + +
30T ALA* 1.3 60.5 + - - +
32T ASP* 3.3 13.4 + - - +
33T LYS* 3.0 45.3 + - - +
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Residues in contact with ALA 30 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26T GLN 2.9 18.2 + - - +
27T VAL* 3.7 8.3 - - - +
29T GLU* 1.3 77.8 - - - +
31T LEU* 1.3 56.7 + - - +
33T LYS* 4.0 7.3 - - - +
34T LEU* 2.9 30.8 + - - +
43T LEU* 4.8 5.7 - - + +
46T ALA* 4.8 5.8 - - + -
47T TYR* 3.8 32.8 - - + +
50T LYS* 4.9 4.9 - - + -
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Residues in contact with LEU 31 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27T VAL 3.0 14.7 + - - +
28T THR* 3.2 14.3 + - + +
30T ALA* 1.3 75.4 - - - +
32T ASP* 1.3 63.5 + - - +
34T LEU* 4.3 5.8 - - + -
35T ALA* 2.8 35.1 + - + +
47T TYR* 3.6 29.3 - - + +
12Y VAL* 5.1 7.0 - - + +
15Y LYS* 5.0 22.9 - - + -
16Y PHE* 5.3 13.2 - - + +
64Y THR* 4.4 14.1 - - + +
68Y PHE* 3.8 31.6 - - + -
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Residues in contact with ASP 32 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28T THR* 2.9 31.7 + - - +
29T GLU* 3.3 17.8 + - - +
31T LEU* 1.3 81.4 - - - +
33T LYS* 1.3 63.5 + - + +
35T ALA* 3.5 14.9 - - - +
36T ALA* 3.7 6.8 + - - +
15Y LYS* 5.3 12.8 + - - +
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Residues in contact with LYS 33 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29T GLU* 3.0 30.6 + - - +
30T ALA* 4.0 3.1 - - - +
32T ASP* 1.3 75.7 - - + +
34T LEU* 1.3 65.6 + - - +
36T ALA* 2.9 19.0 + - - +
37T LYS 3.2 8.1 + - - -
43T LEU* 3.5 32.3 - - + +
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Residues in contact with LEU 34 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30T ALA 2.9 19.3 + - - +
31T LEU* 3.7 7.6 - - + +
33T LYS* 1.3 75.7 - - - +
35T ALA* 1.3 58.3 + - - +
37T LYS 3.0 13.6 - - - +
38T PRO* 2.8 54.9 - - + +
43T LEU* 3.5 30.4 - - + +
44T LEU* 3.6 25.1 - - + +
47T TYR* 3.3 39.0 - - + -
16Y PHE* 5.4 6.1 - - + -
60Y ALA* 6.2 2.0 - - + -
64Y THR* 5.4 4.7 - - + -
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Residues in contact with ALA 35 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31T LEU* 2.8 19.9 + - + +
32T ASP* 3.5 10.3 - - - +
33T LYS 3.1 0.2 - - - -
34T LEU* 1.3 77.4 - - - +
36T ALA* 1.3 60.2 + - - +
38T PRO* 3.6 0.9 - - - +
15Y LYS 3.4 26.0 - - - +
16Y PHE* 3.6 27.5 - - + +
19Y GLY* 3.2 22.7 - - - +
20Y VAL* 3.3 11.6 - - - +
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Residues in contact with ALA 36 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32T ASP 3.7 5.1 + - - +
33T LYS* 2.9 14.7 + - - +
35T ALA* 1.3 80.4 - - - +
37T LYS* 1.3 69.5 + - + +
38T PRO* 3.6 4.6 - - - +
19Y GLY* 3.5 25.1 - - - +
20Y VAL* 4.1 1.9 - - - +
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Residues in contact with LYS 37 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33T LYS 3.2 3.0 + - - -
34T LEU* 3.0 11.9 + - - +
36T ALA* 1.3 89.7 - - + +
38T PRO* 1.3 66.4 - - - +
39T SER* 3.0 8.7 + - - +
40T ASP* 3.1 29.8 + - + +
43T LEU* 3.7 13.4 - - + +
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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