Contacts of the helix formed by residues 20 - 37 (chain P) 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 P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K ALA 3.3 15.7 - - - +
38K PRO* 3.5 25.6 - - + -
16P PHE* 3.3 29.4 - - + +
17P ASP* 3.1 5.6 - - - +
19P GLY* 1.3 81.1 - - - +
21P ASP* 1.3 62.8 + - - +
22P ASN 3.1 3.4 - - - +
23P LEU* 3.1 28.0 + - + +
57P TYR* 3.2 39.4 - - + -
5V TRP* 3.6 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 21 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P ASP* 2.5 23.0 + - - +
18P THR* 3.8 10.9 + - - +
19P GLY 3.7 1.4 - - - -
20P VAL* 1.3 74.1 - - - +
22P ASN* 1.3 69.7 + - - +
24P GLN* 3.9 11.3 + - - +
25P THR* 4.0 10.9 + - - -
57P TYR* 5.0 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 22 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20P VAL* 3.1 1.2 - - - +
21P ASP* 1.3 86.1 - - - +
23P LEU* 1.3 66.2 + - - +
24P GLN 3.2 0.7 - - - -
25P THR* 3.0 10.6 + - - -
26P GLN* 2.8 33.9 + - + +
3V THR 5.5 1.0 + - - -
4V PRO* 5.3 2.4 - - - +
5V TRP* 3.8 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K PRO* 5.8 1.6 - - + -
20P VAL* 3.1 29.2 + - + +
22P ASN* 1.3 78.3 - - - +
24P GLN* 1.3 64.3 + - - +
26P GLN* 3.2 4.3 + - - +
27P VAL* 3.0 21.7 + - - +
50P LYS* 3.5 30.3 - - + +
53P GLU* 3.7 32.1 - - + +
54P TYR* 4.4 5.8 - - + -
57P TYR* 3.8 24.7 - - + +
5V TRP* 3.7 36.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 24 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J ALA* 5.4 4.8 - - - +
20P VAL 3.7 2.0 + - - -
21P ASP* 4.2 7.8 - - - +
22P ASN 3.2 0.4 - - - -
23P LEU* 1.3 78.9 - - - +
25P THR* 1.3 56.8 + - - +
27P VAL* 3.3 8.0 - - - +
28P THR* 2.7 44.7 + - - +
54P TYR* 4.0 17.2 + - + +
57P TYR* 2.8 32.8 + - + +
58P ARG* 3.6 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 25 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21P ASP 4.0 8.5 + - - -
22P ASN* 3.0 14.9 + - - -
24P GLN* 1.3 80.0 - - - +
26P GLN* 1.3 59.3 + - + +
28P THR* 3.4 5.0 + - - -
29P GLU* 3.0 51.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 26 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22P ASN* 2.8 24.4 + - + +
23P LEU* 3.6 4.4 - - - +
25P THR* 1.3 80.2 - - + +
27P VAL* 1.3 57.7 + - - +
29P GLU* 3.4 8.5 + - - +
30P ALA* 2.9 28.2 + - - +
50P LYS* 2.9 39.9 + - + +
4V PRO* 4.4 8.7 - - - +
5V TRP* 3.0 58.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23P LEU 3.0 16.3 + - - +
24P GLN 3.3 11.2 - - - +
26P GLN* 1.3 73.7 - - - +
28P THR* 1.3 67.8 + - - +
30P ALA* 3.7 4.9 - - - -
31P LEU* 3.0 22.0 + - - +
47P TYR* 3.4 30.3 - - + +
50P LYS* 3.8 13.7 - - + +
51P LEU* 3.7 35.7 - - + +
54P TYR* 3.8 28.3 - - + -
68U PHE* 6.1 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 28 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P GLN* 2.7 33.1 + - - +
25P THR* 3.7 6.7 - - - -
27P VAL* 1.3 79.0 - - - +
29P GLU* 1.3 61.4 + - + +
31P LEU* 3.2 11.7 + - + +
32P ASP* 2.9 40.6 + - - +
54P TYR* 5.8 0.5 - - - -
68U PHE* 6.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P THR* 3.0 40.4 + - + +
26P GLN* 3.8 7.3 - - - +
28P THR* 1.3 74.7 - - + +
30P ALA* 1.3 61.1 + - - +
32P ASP* 3.3 13.8 + - - +
33P LYS* 3.0 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P GLN 2.9 18.8 + - - +
27P VAL* 3.7 8.1 - - - +
29P GLU* 1.3 77.2 - - - +
31P LEU* 1.3 57.0 + - - +
33P LYS* 4.0 7.5 - - - +
34P LEU* 2.9 30.7 + - - +
43P LEU* 4.8 6.6 - - + +
46P ALA* 4.8 5.6 - - + -
47P TYR* 3.8 32.0 - - + +
50P LYS* 4.9 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27P VAL 3.0 15.1 + - - +
28P THR* 3.2 13.2 + - + +
30P ALA* 1.3 74.1 - - - +
32P ASP* 1.3 62.7 + - - +
34P LEU* 4.3 5.8 - - + -
35P ALA* 2.8 35.0 + - + +
47P TYR* 3.6 30.7 - - + +
12U VAL* 5.1 7.4 - - + +
15U LYS* 5.0 22.7 - - + -
16U PHE* 5.3 12.6 - - + +
64U THR* 4.4 14.4 - - + +
68U PHE* 3.8 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 32 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P THR* 2.9 31.0 + - - +
29P GLU* 3.3 17.4 + - - +
31P LEU* 1.3 81.2 - - - +
33P LYS* 1.3 62.7 + - + +
35P ALA* 3.5 15.4 - - - +
36P ALA* 3.7 6.6 + - - +
15U LYS* 5.3 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29P GLU* 3.0 31.5 + - - +
30P ALA* 4.0 3.4 - - - +
32P ASP* 1.3 76.2 - - + +
34P LEU* 1.3 66.2 + - - +
36P ALA* 2.9 19.2 + - - +
37P LYS 3.2 8.1 + - - -
43P LEU* 3.5 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P ALA 2.9 19.1 + - - +
31P LEU* 3.2 7.6 + - + +
33P LYS* 1.3 75.5 - - - +
35P ALA* 1.3 59.7 + - - +
37P LYS 3.0 14.0 - - - +
38P PRO* 2.8 54.7 - - + +
43P LEU* 3.5 29.8 - - + +
44P LEU* 3.6 25.6 - - + +
47P TYR* 3.3 39.0 - - + -
16U PHE* 5.4 6.5 - - + -
60U ALA* 6.2 2.2 - - + -
64U THR* 5.4 4.7 - - + -
79a PHE* 5.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31P LEU* 2.8 19.4 + - + +
32P ASP* 3.5 10.3 - - - +
33P LYS 3.1 0.2 - - - -
34P LEU* 1.3 76.5 - - - +
36P ALA* 1.3 60.1 + - - +
38P PRO* 3.6 1.0 - - - +
15U LYS 3.4 26.0 - - - +
16U PHE* 3.6 26.4 - - + +
19U GLY* 3.2 22.8 - - - +
20U VAL* 3.3 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32P ASP 3.7 4.4 + - - +
33P LYS* 2.9 14.3 + - - +
35P ALA* 1.3 80.9 - - - +
37P LYS* 1.3 68.8 + - + +
38P PRO* 3.6 0.4 - - - -
19U GLY* 3.5 14.2 - - - +
5a TRP* 2.7 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P LYS 3.2 2.6 + - - -
34P LEU* 3.0 12.0 + - - +
36P ALA* 1.3 89.9 - - + +
38P PRO* 1.3 66.9 - - - +
39P SER 3.0 3.5 + - - +
40P ASP* 3.1 26.0 + - + +
43P LEU* 3.7 12.7 - - + +
6a SER 3.5 22.7 - - - +
7a GLY* 4.2 1.8 - - - -
8a TYR* 4.0 26.2 - - + +
11a ASP* 2.8 22.3 + - - +
----------------------------------------------------------
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