Contacts of the helix formed by residues 20 - 37 (chain R) 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 R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M ALA 3.3 16.4 - - - +
38M PRO* 3.5 24.9 - - + -
16R PHE* 3.3 28.9 - - + +
17R ASP* 3.1 6.1 - - - +
19R GLY* 1.3 81.7 - - - +
21R ASP* 1.3 62.9 + - - +
22R ASN 3.1 3.4 - - - +
23R LEU* 3.1 28.3 + - + +
57R TYR* 3.2 39.3 - - + -
5X TRP* 3.6 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 21 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R ASP* 2.5 22.6 + - - +
18R THR* 3.8 11.4 + - - +
19R GLY 3.7 1.8 - - - -
20R VAL* 1.3 74.6 - - - +
22R ASN* 1.3 69.2 + - - +
24R GLN* 3.9 12.0 + - - +
25R THR* 4.0 10.4 + - - -
57R TYR* 5.0 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 22 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20R VAL* 3.1 0.6 - - - +
21R ASP* 1.3 86.5 - - - +
23R LEU* 1.3 67.4 + - - +
24R GLN 3.2 0.7 - - - -
25R THR* 3.0 10.3 + - - -
26R GLN* 2.8 35.1 + - + +
3X THR 5.5 1.2 + - - -
4X PRO* 5.3 1.8 - - - +
5X TRP* 3.8 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M PRO* 5.8 1.1 - - + -
20R VAL* 3.1 29.9 + - + +
22R ASN* 1.3 76.6 - - - +
24R GLN* 1.3 64.9 + - - +
26R GLN* 3.2 5.1 + - - +
27R VAL* 3.0 21.5 + - + +
50R LYS* 3.5 31.2 - - + +
53R GLU* 3.7 31.0 - - + +
54R TYR* 4.2 6.3 - - + +
57R TYR* 3.8 24.2 - - + -
5X TRP* 3.7 36.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 24 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42L ALA* 5.4 4.8 - - - +
20R VAL 3.7 2.4 + - - -
21R ASP* 4.2 8.2 - - - +
22R ASN 3.2 0.4 - - - -
23R LEU* 1.3 77.7 - - - +
25R THR* 1.3 56.6 + - - +
27R VAL* 3.3 7.7 - - - +
28R THR* 2.7 44.4 + - - +
54R TYR* 4.0 17.4 + - + +
57R TYR* 2.8 33.9 + - + +
58R ARG* 3.6 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 25 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21R ASP 4.0 8.5 + - - -
22R ASN* 3.0 14.5 + - - -
24R GLN* 1.3 79.6 - - - +
26R GLN* 1.3 59.7 + - + +
28R THR* 3.7 5.4 - - - -
29R GLU* 3.0 51.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 26 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22R ASN* 2.8 25.7 + - + +
23R LEU* 3.6 4.0 - - + +
25R THR* 1.3 80.0 - - + +
27R VAL* 1.3 56.9 + - - +
29R GLU* 3.4 8.8 + - - +
30R ALA* 2.9 28.9 + - - +
50R LYS* 2.9 40.2 + - + +
4X PRO* 4.4 8.7 - - - +
5X TRP* 3.0 58.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R LEU 3.0 14.4 + - - +
24R GLN 3.3 11.4 - - - +
26R GLN* 1.3 74.7 - - - +
28R THR* 1.3 66.9 + - - +
30R ALA* 4.0 5.2 - - - -
31R LEU* 3.0 21.8 + - - +
47R TYR* 3.4 29.5 - - + +
50R LYS* 3.8 13.0 - - + +
51R LEU* 3.7 36.1 - - + +
54R TYR* 3.8 29.2 - - + -
68W PHE* 6.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 28 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24R GLN* 2.7 32.5 + - - +
25R THR* 3.7 7.0 - - - -
27R VAL* 1.3 78.0 - - - +
29R GLU* 1.3 61.8 + - + +
31R LEU* 3.2 11.3 + - + +
32R ASP* 2.9 40.3 + - - +
54R TYR* 5.8 0.5 - - - -
68W PHE* 6.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25R THR* 3.0 39.2 + - + +
26R GLN* 3.8 7.8 - - - +
28R THR* 1.3 75.6 - - + +
30R ALA* 1.3 60.7 + - - +
32R ASP* 3.3 13.1 + - - +
33R LYS* 3.0 44.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26R GLN 2.9 17.6 + - - +
27R VAL* 3.7 8.3 - - - +
28R THR 3.3 0.2 - - - -
29R GLU* 1.3 77.3 - - - +
31R LEU* 1.3 56.6 + - - +
33R LYS* 3.6 7.6 + - - +
34R LEU* 2.9 30.5 + - - +
43R LEU* 4.8 5.8 - - + +
46R ALA* 4.8 5.8 - - + -
47R TYR* 3.8 33.1 - - + +
50R LYS* 4.9 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27R VAL 3.0 14.9 + - - +
28R THR* 3.4 14.4 - - + +
30R ALA* 1.3 74.9 - - - +
32R ASP* 1.3 64.1 + - - +
34R LEU* 3.7 6.0 - - + -
35R ALA* 2.8 33.9 + - + +
47R TYR* 3.6 29.8 - - + +
12W VAL* 5.1 7.6 - - + +
15W LYS* 5.0 22.4 - - + -
16W PHE* 5.3 12.3 - - + +
64W THR* 4.4 14.8 - - + +
68W PHE* 3.8 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 32 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R THR* 2.9 31.3 + - - +
29R GLU* 3.3 17.1 + - - +
31R LEU* 1.3 81.8 - - - +
33R LYS* 1.3 64.8 + - + +
35R ALA* 3.5 15.6 - - - +
36R ALA* 3.7 6.2 + - - +
15W LYS* 5.3 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R GLU* 3.0 30.6 + - - +
30R ALA* 4.0 3.6 - - - +
32R ASP* 1.3 75.5 - - + +
34R LEU* 1.3 65.6 + - - +
36R ALA* 2.9 19.5 + - - +
37R LYS 3.2 8.0 + - - -
43R LEU* 3.5 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R ALA 2.9 19.5 + - - +
31R LEU* 3.2 8.9 + - + +
33R LYS* 1.3 76.8 - - - +
35R ALA* 1.3 58.6 + - - +
37R LYS 3.0 13.4 - - - +
38R PRO* 2.8 55.5 - - + +
43R LEU* 3.5 28.9 - - + +
44R LEU* 3.6 25.4 - - + +
47R TYR* 3.3 38.1 - - + -
16W PHE* 5.4 5.8 - - + -
60W ALA* 6.2 2.5 - - + -
64W THR* 5.4 4.9 - - + -
79c PHE* 5.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R LEU* 2.8 19.9 + - + +
32R ASP* 3.5 10.1 - - - +
33R LYS 3.1 0.2 - - - -
34R LEU* 1.3 77.9 - - - +
36R ALA* 1.3 59.5 + - - +
38R PRO* 3.6 0.9 - - - +
15W LYS 3.4 26.5 - - - +
16W PHE* 3.6 25.6 - - + +
19W GLY* 3.2 22.8 - - - +
20W VAL* 3.3 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R ASP 3.7 5.5 + - - +
33R LYS* 2.9 13.5 + - - +
35R ALA* 1.3 79.8 - - - +
37R LYS* 1.3 68.1 + - + +
38R PRO* 3.6 0.4 - - - -
19W GLY* 3.5 14.5 - - - +
5c TRP* 2.7 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R LYS 3.2 2.6 + - - -
34R LEU* 3.0 12.5 + - - +
36R ALA* 1.3 89.3 - - + +
38R PRO* 1.3 67.0 - - - +
39R SER 3.0 4.3 + - - -
40R ASP* 3.1 25.9 + - + +
43R LEU* 3.7 14.8 - - + +
6c SER 3.5 23.1 - - - +
7c GLY* 4.2 1.8 - - - -
8c TYR* 4.0 25.5 - - + +
11c ASP* 2.8 22.0 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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