Contacts of the helix formed by residues 20 - 37 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C PHE* 3.3 37.9 - - + +
17C ASP* 2.9 6.0 + - - +
19C GLY* 1.3 84.9 - - - +
21C ASP* 1.3 62.9 + - - +
22C ASN 3.1 3.4 - - - +
23C LEU* 3.1 29.0 + - + +
57C TYR* 3.2 38.8 - - + -
5I TRP* 3.6 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ASP* 2.5 22.5 + - - +
18C THR* 3.8 12.1 + - - +
19C GLY 3.7 1.6 - - - -
20C VAL* 1.3 74.5 - - - +
22C ASN* 1.3 68.4 + - - +
23C LEU 3.6 0.2 + - - -
24C GLN* 3.9 11.8 + - - +
25C THR* 4.0 10.7 + - - -
57C TYR* 5.0 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C VAL* 3.1 0.8 - - - +
21C ASP* 1.3 85.6 - - - +
23C LEU* 1.3 66.6 + - - +
24C GLN 3.2 0.9 - - - -
25C THR* 3.0 10.1 + - - -
26C GLN* 2.8 35.5 + - + +
3I THR 5.5 1.2 + - - -
4I PRO* 5.3 2.2 - - - +
5I TRP* 3.8 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C VAL* 3.1 29.0 + - + +
22C ASN* 1.3 78.7 - - - +
24C GLN* 1.3 65.4 + - - +
26C GLN* 3.2 4.7 + - - +
27C VAL* 3.0 22.1 + - + +
50C LYS* 3.5 30.3 - - + +
53C GLU* 3.7 32.3 - - + +
54C TYR* 4.4 5.8 - - + -
57C TYR* 3.8 23.8 - - + -
5I TRP* 3.7 36.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C VAL 3.7 2.4 + - - -
21C ASP* 4.2 7.7 - - - +
22C ASN 3.2 0.4 - - - -
23C LEU* 1.3 79.3 - - - +
25C THR* 1.3 56.7 + - - +
27C VAL* 3.3 8.1 - - - +
28C THR* 2.7 44.5 + - - +
54C TYR* 4.0 17.6 + - + +
57C TYR* 2.8 33.6 + - + +
58C ARG* 3.6 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ASP 4.0 8.5 + - - -
22C ASN* 3.0 14.5 + - - -
24C GLN* 1.3 78.9 - - - +
26C GLN* 1.3 59.4 + - + +
28C THR* 3.4 5.1 + - - -
29C GLU* 3.0 52.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ASN* 2.8 24.3 + - + +
23C LEU* 3.6 4.5 - - - +
25C THR* 1.3 79.7 - - + +
27C VAL* 1.3 56.9 + - - +
29C GLU* 3.4 8.5 + - - +
30C ALA* 2.9 28.2 + - - +
50C LYS* 2.9 40.5 + - + +
4I PRO* 4.4 8.7 - - - +
5I TRP* 3.0 57.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU 3.0 14.6 + - - +
24C GLN 3.3 11.4 - - - +
26C GLN* 1.3 74.3 - - - +
28C THR* 1.3 67.6 + - - +
30C ALA* 4.0 4.3 - - - -
31C LEU* 3.0 21.7 + - - +
47C TYR* 3.4 30.4 - - + +
50C LYS* 3.8 13.4 - - + +
51C LEU* 3.7 36.6 - - + +
54C TYR* 3.8 29.8 - - + -
68H PHE* 6.1 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN* 2.7 33.0 + - - +
25C THR* 3.7 7.2 - - - -
27C VAL* 1.3 79.1 - - - +
29C GLU* 1.3 62.8 + - + +
31C LEU* 3.2 11.4 + - + +
32C ASP* 2.9 40.4 + - - +
54C TYR* 5.8 0.5 - - - -
68H PHE* 6.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C THR* 3.0 39.2 + - + +
26C GLN* 3.8 7.2 - - - +
28C THR* 1.3 75.6 - - + +
30C ALA* 1.3 60.2 + - - +
32C ASP* 3.3 13.4 + - - +
33C LYS* 3.0 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLN 2.9 19.4 + - - +
27C VAL* 3.7 7.6 - - - +
29C GLU* 1.3 77.0 - - - +
31C LEU* 1.3 57.3 + - - +
33C LYS* 3.9 6.4 - - - +
34C LEU* 2.9 30.8 + - - +
43C LEU* 4.8 6.0 - - + +
46C ALA* 4.8 6.5 - - + -
47C TYR* 3.8 32.7 - - + +
50C LYS* 4.9 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C VAL 3.0 14.5 + - - +
28C THR* 3.2 14.1 + - + +
30C ALA* 1.3 75.0 - - - +
32C ASP* 1.3 63.1 + - - +
34C LEU* 3.2 5.8 + - + -
35C ALA* 2.8 34.6 + - + +
47C TYR* 3.6 30.0 - - + +
12H VAL* 5.1 6.7 - - + +
15H LYS* 5.0 22.4 - - + -
16H PHE* 5.3 12.6 - - + +
64H THR* 4.4 14.6 - - + +
68H PHE* 3.8 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C THR* 2.9 30.9 + - - +
29C GLU* 3.3 17.8 + - - +
31C LEU* 1.3 80.9 - - - +
33C LYS* 1.3 64.2 + - + +
35C ALA* 3.5 16.1 - - - +
36C ALA* 3.7 6.2 + - - +
15H LYS* 5.3 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLU* 3.0 29.6 + - - +
30C ALA* 4.0 3.6 - - - +
32C ASP* 1.3 77.0 - - + +
34C LEU* 1.3 65.6 + - - +
36C ALA* 2.9 19.4 + - - +
37C LYS 3.2 7.8 + - - -
43C LEU* 3.5 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ALA 2.9 20.1 + - - +
31C LEU* 3.7 8.1 - - + +
33C LYS* 1.3 76.2 - - - +
35C ALA* 1.3 57.8 - - - +
37C LYS 3.0 13.6 - - - +
38C PRO* 2.8 56.2 - - + +
43C LEU* 3.5 30.0 - - + +
44C LEU* 3.6 25.6 - - + +
47C TYR* 3.3 39.3 - - + -
16H PHE* 5.4 6.1 - - + -
60H ALA* 6.2 2.0 - - + -
64H THR* 5.4 4.7 - - + -
79N PHE* 5.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 2.8 19.3 + - + +
32C ASP* 3.5 9.9 - - - +
33C LYS 3.1 0.4 - - - -
34C LEU* 1.3 77.5 - - - +
36C ALA* 1.3 60.2 + - - +
38C PRO* 3.6 0.7 - - - +
15H LYS 3.4 26.2 - - - +
16H PHE* 3.6 26.9 - - + +
19H GLY* 3.2 22.6 - - - +
20H VAL* 3.3 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ASP 3.7 4.6 + - - +
33C LYS* 2.9 14.5 + - - +
35C ALA* 1.3 79.8 - - - +
37C LYS* 1.3 67.3 + - + +
38C PRO* 3.6 0.4 - - - -
19H GLY* 3.5 15.3 - - - +
5N TRP* 2.7 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LYS 3.2 3.0 + - - -
34C LEU* 3.0 11.4 + - - +
36C ALA* 1.3 90.3 - - + +
38C PRO* 1.3 66.9 - - - +
39C SER 3.0 3.7 + - - +
40C ASP* 3.1 26.2 + - + +
43C LEU* 3.7 14.5 - - + +
6N SER 3.5 23.6 - - - +
7N GLY* 4.8 1.6 - - - -
8N TYR* 4.0 26.4 - - + +
11N ASP* 2.8 22.1 + - - +
----------------------------------------------------------
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