Contacts of the helix formed by residues 25 - 37 (chain C) in PDB entry 3LDZ
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 ASP 25 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ALA* 5.6 3.1 - - - +
21C ASN* 5.9 4.6 - - - +
23C ALA 3.6 5.8 + - - +
24C GLU* 1.4 66.8 - - - +
26C TRP* 1.3 61.5 + - - +
27C GLY* 3.2 14.7 + - - -
28C LEU* 3.2 32.3 + - + +
29C ILE* 3.2 26.2 + - - +
8F LEU* 3.7 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLU* 3.3 57.8 + - + +
25C ASP* 1.3 69.1 + - - +
27C GLY* 1.3 58.9 + - - +
29C ILE* 3.7 39.5 - - + +
30C LEU* 3.0 36.6 + - + +
67C THR* 4.7 14.4 - - - -
71C ALA* 4.4 4.9 - - + -
8F LEU* 5.3 2.0 - - - +
44F ILE* 4.1 20.4 - - + -
46F ALA* 6.0 0.4 - - - -
47F GLY* 3.7 37.0 - - - -
68F HIS* 3.8 44.2 + + + -
70F VAL* 3.7 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ASP* 3.2 9.1 + - - -
26C TRP* 1.3 78.7 - - - +
28C LEU* 1.3 55.0 + - - +
30C LEU* 3.7 1.9 + - - +
31C ASP* 3.0 37.9 + - - +
8F LEU* 5.6 3.0 - - - +
42F ARG* 4.7 0.3 + - - -
70F VAL* 3.7 25.1 - - - +
72F ARG* 5.7 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ASP* 4.0 30.3 - - + +
15C LYS* 3.7 22.4 - - + +
16C ALA* 3.6 37.5 - - + +
25C ASP* 3.2 33.4 + - + +
27C GLY* 1.3 74.4 - - - +
29C ILE* 1.4 64.1 + - - +
31C ASP* 3.2 13.6 + - + +
32C ILE* 3.0 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ALA* 4.7 14.8 - - + +
24C GLU* 5.0 7.0 - - + -
25C ASP 3.2 16.9 + - - +
26C TRP* 3.4 40.8 + - + +
28C LEU* 1.4 74.4 - - - +
30C LEU* 1.4 59.3 + - + +
32C ILE* 3.1 7.6 + - - +
33C CYS* 3.0 29.2 + - - -
64C GLN 5.7 0.9 - - - +
67C THR* 4.3 16.6 - - - +
68C LEU* 3.9 28.9 - - + -
71C ALA* 3.4 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TRP* 3.0 21.0 + - + +
27C GLY 4.1 1.8 - - - +
29C ILE* 1.4 80.2 - - + +
31C ASP* 1.3 57.6 + - - +
33C CYS* 3.5 6.7 + - + +
34C ASP* 3.0 35.3 + - - +
75C ASN* 4.0 23.3 - - - +
42F ARG* 3.9 44.6 - - + +
44F ILE* 3.5 37.0 - - + -
47F GLY 5.1 1.1 - - - +
49F GLN* 4.3 15.9 - - + +
70F VAL* 4.0 10.8 - - + -
----------------------------------------------------------
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 GLY 3.0 27.5 + - - +
28C LEU* 3.5 17.9 - - + +
29C ILE 3.2 0.2 - - - -
30C LEU* 1.3 74.7 - - - +
32C ILE* 1.4 59.8 + - + +
34C ASP* 3.6 7.8 + - - +
35C LYS* 3.1 28.2 + - - +
42F ARG* 3.5 7.4 + - - -
72F ARG* 3.2 43.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C PHE* 4.0 8.1 - - + -
12C ASP* 3.6 45.8 - - + +
13C VAL* 4.1 3.1 - - + +
16C ALA* 3.7 17.5 - - + -
28C LEU* 3.0 21.1 + - + +
29C ILE 3.1 6.3 + - - +
31C ASP* 1.4 74.6 - - - +
33C CYS* 1.4 63.0 + - - +
35C LYS* 3.2 10.0 + - + +
36C VAL* 3.1 22.5 + - - +
46C CYS* 3.6 28.5 - - - -
68C LEU* 3.9 29.8 - - + -
72C CYS* 4.5 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ILE* 3.0 26.5 + - - -
30C LEU* 3.7 11.0 - - + +
31C ASP 3.4 0.2 - - - -
32C ILE* 1.4 75.8 - - - +
34C ASP* 1.3 62.4 + - - +
36C VAL* 3.4 16.6 + - - +
37C GLY* 3.6 4.2 + - - -
68C LEU* 5.3 0.2 - - - -
71C ALA 3.8 29.2 - - - -
72C CYS* 4.2 9.2 - - - -
75C ASN* 4.0 20.4 - - + +
76C CYS* 3.6 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 3.0 21.8 + - - +
31C ASP* 3.8 8.8 - - - +
33C CYS* 1.3 78.3 - - - +
35C LYS* 1.4 62.4 + - - +
37C GLY* 3.3 12.4 + - - -
38C GLN* 3.6 20.4 + - - +
42F ARG* 2.7 34.2 + - - -
49F GLN* 4.8 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C PRO* 2.8 40.2 + - - +
9C PHE* 3.7 29.8 - - + +
12C ASP* 3.5 20.2 + - - +
31C ASP 3.1 18.2 + - - +
32C ILE* 3.2 8.5 + - - +
34C ASP* 1.4 74.5 - - - +
36C VAL* 1.3 65.0 + - - +
38C GLN* 3.2 24.5 + - + +
39C SER* 4.1 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C PHE* 3.9 8.3 - - + -
32C ILE 3.1 15.7 + - - +
33C CYS 3.4 9.0 - - - +
35C LYS* 1.3 77.1 - - - +
37C GLY* 1.3 59.0 + - - +
38C GLN 3.0 5.9 + - - -
39C SER 3.2 20.1 + - - +
42C GLY* 3.7 5.4 - - - +
43C PRO* 3.6 34.4 - - + +
46C CYS* 3.8 34.5 - - + -
72C CYS* 4.7 2.5 - - - -
76C CYS* 4.0 28.3 - - + -
79C ILE* 4.6 2.9 - - + -
80C PHE* 4.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C CYS 3.6 4.3 + - - -
34C ASP* 3.3 9.0 + - - -
36C VAL* 1.3 78.5 - - - +
38C GLN* 1.3 68.3 + - - +
39C SER 3.5 1.9 + - - -
79C ILE* 5.0 11.7 - - - -
----------------------------------------------------------
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