Contacts of the helix formed by residues 21 - 32 (chain C) in PDB entry 5LPN
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 GLY 21 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C VAL* 1.3 80.5 - - - +
22C LYS* 1.3 55.4 + - - +
24C CYS* 2.8 5.5 + - - +
25C VAL* 2.6 38.6 + - - +
88C VAL* 4.2 1.1 - - - -
122C ASN* 3.6 13.1 + - - -
202C GNP 2.9 30.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU* 4.1 14.0 - - + +
15C ILE 3.9 3.6 - - - -
16C GLY* 2.7 58.7 + - - +
17C ASP 2.7 19.0 + - - +
20C VAL* 3.3 2.6 - - - +
21C GLY* 1.3 73.9 - - - +
23C THR* 1.3 65.8 + - - +
25C VAL* 2.9 27.8 - - - +
26C LEU* 3.0 11.3 + - - +
64C ASP* 3.6 12.8 - - - +
65C THR* 3.6 25.1 - - + +
88C VAL* 3.6 17.5 - - + +
202C GNP 3.0 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LYS* 1.3 75.1 - - - +
24C CYS* 1.3 57.1 + - - +
26C LEU* 3.9 2.8 - - + +
27C PHE* 2.9 34.0 + - + +
39C ILE 5.4 4.7 - - - +
41C THR* 2.7 9.6 + - - +
64C ASP* 2.9 23.8 + - - +
201C MG 2.0 32.3 - - - -
202C GNP 2.9 13.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLY 2.8 7.9 + - - +
23C THR* 1.3 77.9 - - - +
25C VAL* 1.3 59.6 + - - +
27C PHE* 3.9 5.5 - - - +
28C ARG* 2.9 22.9 + - - +
33C ALA 4.6 1.0 - - - +
34C PHE* 4.1 14.6 - - + -
35C ASN 4.6 7.0 - - - -
37C THR 5.3 3.1 - - - -
153C ALA* 3.2 11.5 - - - +
202C GNP 3.4 66.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU* 4.6 10.5 - - + -
21C GLY 2.6 20.3 + - - +
22C LYS* 2.9 31.4 - - - +
24C CYS* 1.3 72.8 - - - +
26C LEU* 1.3 66.0 + - - +
28C ARG* 3.2 2.6 + - - +
29C PHE* 3.1 21.3 + - - +
88C VAL* 5.2 2.0 - - + -
120C LEU* 4.2 28.7 - - + -
122C ASN* 4.5 11.6 - - + +
151C THR* 4.9 2.7 - - - +
153C ALA* 4.2 8.7 - - - +
159C ILE* 3.4 27.6 - - + +
162C ALA* 6.5 0.2 - - + -
163C PHE* 4.4 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU* 3.8 24.0 - - + -
22C LYS 3.0 16.1 + - - +
23C THR* 4.0 5.4 - - + +
25C VAL* 1.3 78.7 - - - +
27C PHE* 1.3 57.0 + - - +
29C PHE* 3.2 2.6 + - + -
30C SER* 2.7 42.3 + - - +
46C PHE* 5.3 0.2 - - - -
47C LYS* 4.5 20.0 - - + +
62C ILE* 3.9 48.5 - - + +
64C ASP* 3.9 21.8 - - + +
163C PHE* 4.4 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C THR* 2.9 26.9 + - + +
24C CYS* 3.9 7.2 - - - +
25C VAL 3.2 0.2 - - - -
26C LEU* 1.3 77.6 - - - +
28C ARG* 1.3 59.1 + - - +
30C SER* 3.1 8.2 + - - -
31C ASP* 2.9 46.2 + - + -
32C ASP 3.6 2.8 + - - -
33C ALA* 3.8 32.9 - - + +
34C PHE* 4.8 2.5 - - - -
35C ASN* 3.8 17.5 - - + -
47C LYS* 6.2 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C CYS 2.9 18.2 + - - +
25C VAL 3.7 3.6 - - - +
27C PHE* 1.3 76.2 - - - +
29C PHE* 1.3 57.7 + - - +
32C ASP* 2.8 26.5 + - - +
33C ALA 3.1 22.1 + - - +
153C ALA* 3.5 27.1 - - + +
156C ASN* 3.6 12.3 - - - +
159C ILE* 4.3 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C VAL 3.1 8.4 + - - +
26C LEU* 3.8 3.4 - - + +
28C ARG* 1.3 78.2 - - - +
30C SER* 1.3 70.3 + - - +
31C ASP 3.4 0.5 + - - -
32C ASP* 4.1 2.4 + - - +
49C LYS* 3.7 53.5 + - + -
51C VAL* 4.4 11.4 - - + -
60C LEU* 5.2 4.9 - - + -
62C ILE* 4.3 15.0 - - + -
159C ILE* 3.5 8.5 - - + +
160C GLU* 3.8 37.2 - - + -
163C PHE* 3.1 62.8 - + + -
164C LEU* 4.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 2.7 39.9 + - - +
27C PHE* 3.1 12.5 + - - -
29C PHE* 1.3 81.3 - - - +
31C ASP* 1.3 82.9 + - - +
47C LYS* 4.6 17.3 - - - +
48C ILE 5.9 1.8 - - - -
49C LYS* 4.5 20.8 - - - +
62C ILE* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PHE* 2.9 35.7 + - + +
30C SER* 1.3 114.1 + - - +
32C ASP* 1.3 74.7 + - - +
33C ALA* 3.4 6.7 + - + +
47C LYS* 5.8 0.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
27C PHE 3.6 0.2 + - - -
28C ARG 2.8 23.7 + - - +
29C PHE 4.1 2.1 + - - +
30C SER 3.9 0.8 - - - -
31C ASP* 1.3 76.4 - - - +
33C ALA* 1.3 57.7 + - - +
156C ASN* 2.7 33.1 + - - +
----------------------------------------------------------
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