Contacts of the helix formed by residues 63 - 78 (chain C) in PDB entry 4DHX
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 THR 63 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C HIS 3.6 9.8 + - - +
62C VAL* 1.3 85.1 - - - +
64C VAL* 1.3 53.2 + - - +
65C ASP* 3.7 6.2 + - - +
66C ASP* 3.0 28.7 + - + +
67C LEU* 2.7 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1225A PHE* 4.3 14.8 - - + -
1228A ALA* 4.8 13.9 - - + -
1229A LYS* 3.3 32.5 - - - +
1232A LEU* 5.3 13.0 - - + -
63C THR* 1.3 70.4 - - - +
65C ASP* 1.3 60.3 + - - +
67C LEU* 3.0 9.9 + - + +
68C VAL* 2.7 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1225A PHE* 5.3 6.4 - - - -
63C THR* 3.4 6.0 + - - +
64C VAL* 1.3 82.4 - - - +
66C ASP* 1.3 61.4 + - - +
68C VAL* 3.5 8.8 + - - +
69C ALA* 3.2 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C LYS* 4.7 9.9 - - - -
61C HIS 5.4 1.6 - - - +
62C VAL* 4.8 9.2 - - - +
63C THR* 3.0 31.9 + - + +
65C ASP* 1.3 75.2 - - - +
67C LEU* 1.3 61.3 + - - +
69C ALA* 3.2 16.0 + - - +
70C GLU* 2.6 36.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1228A ALA* 4.2 24.7 - - + -
1232A LEU* 4.5 23.1 - - + -
50C CYS* 4.6 13.5 - - + +
53C VAL* 3.1 39.0 - - + -
54C ILE* 4.8 11.9 - - + -
62C VAL* 4.9 13.0 - - + -
63C THR 2.7 17.8 + - - +
64C VAL* 3.0 15.2 + - + +
66C ASP* 1.3 74.0 - - - +
68C VAL* 1.3 63.2 + - - +
69C ALA 3.1 0.5 + - - -
70C GLU* 3.2 5.9 + - - +
71C ILE* 3.0 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1224A ILE* 4.9 11.4 - - + +
1225A PHE* 4.5 19.3 - - + -
1228A ALA* 5.4 3.6 - - + -
64C VAL* 2.7 34.5 + - + +
65C ASP* 3.8 8.7 - - - +
67C LEU* 1.3 72.0 - - + +
69C ALA* 1.3 60.2 + - - +
71C ILE* 3.1 10.5 - - + -
72C THR* 2.9 49.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ASP 3.2 12.5 + - - +
66C ASP* 3.2 15.7 + - - +
67C LEU 3.1 0.4 - - - -
68C VAL* 1.3 79.3 - - - +
70C GLU* 1.3 65.7 + - - +
72C THR* 3.6 2.8 + - - -
73C PRO* 3.3 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C HIS* 3.5 16.4 - - + -
53C VAL* 4.3 24.1 - - + +
57C LYS* 4.2 18.3 + - - -
62C VAL* 5.8 0.2 - - - +
66C ASP* 2.6 41.3 - - - +
67C LEU* 3.2 7.1 + - - +
69C ALA* 1.3 83.3 - - - +
71C ILE* 1.3 61.3 + - - +
73C PRO* 3.9 8.6 - - - +
74C LYS* 4.8 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1224A ILE* 3.8 28.3 - - + +
1227A THR* 5.1 0.2 - - + -
1228A ALA* 5.1 3.4 - - + -
46C LEU* 3.4 31.2 - - + -
49C HIS* 4.0 13.7 - - - +
50C CYS* 3.2 33.9 - - - -
53C VAL* 6.1 1.1 - - + -
67C LEU* 3.0 24.8 + - + +
68C VAL* 3.1 18.6 - - + +
70C GLU* 1.3 79.3 - - - +
72C THR* 1.3 69.7 + - - +
73C PRO* 3.3 1.1 - - - -
74C LYS* 3.0 7.6 + - - +
75C GLY 2.9 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1221A VAL* 6.1 3.8 - - + -
1224A ILE* 3.9 32.3 - - + +
68C VAL* 2.9 40.6 + - + +
69C ALA* 3.6 4.0 + - - -
71C ILE* 1.3 80.0 - - - +
73C PRO* 1.3 73.6 - - - +
75C GLY* 3.1 0.7 + - - -
76C ARG* 2.9 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ALA 3.3 16.6 - - - +
70C GLU* 3.9 7.6 - - - +
71C ILE 3.4 3.6 - - - -
72C THR* 1.3 100.0 - - - +
74C LYS* 1.3 60.7 + - - +
76C ARG* 3.5 7.3 + - + +
77C ALA* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C GLN* 4.8 5.1 + - - +
46C LEU* 5.0 1.6 - - + -
49C HIS* 3.8 49.7 - - + +
70C GLU 4.8 0.8 + - - +
71C ILE 3.0 8.8 + - - +
73C PRO* 1.3 80.9 - - - +
75C GLY* 1.3 58.0 + - - +
77C ALA* 3.0 10.4 + - + +
78C LEU* 2.9 65.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1220A LEU* 4.3 2.7 - - - -
1224A ILE* 4.3 6.5 - - - -
42C TRP* 2.8 39.5 + - - -
46C LEU* 3.9 18.1 - - - +
71C ILE 2.9 14.0 + - - -
72C THR 3.1 3.5 + - - -
74C LYS* 1.3 77.8 - - - +
76C ARG* 1.3 61.5 + - - +
78C LEU* 3.5 2.2 + - - -
79C VAL* 3.5 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1217A ASP* 3.5 34.6 + - - +
1220A LEU* 3.8 22.9 - - + +
1221A VAL* 3.3 27.3 - - - +
1224A ILE* 5.0 4.0 - - + -
72C THR* 2.9 30.5 + - - +
73C PRO* 3.9 6.1 - - + +
75C GLY* 1.3 76.5 - - - +
77C ALA* 1.3 60.4 + - - +
79C VAL* 3.6 17.0 + - - +
84C LYS* 4.6 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C PRO 3.2 16.0 + - - +
74C LYS* 3.0 12.9 + - + +
76C ARG* 1.3 75.1 - - - +
78C LEU* 1.3 65.5 + - + +
79C VAL 3.2 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C CYS* 5.1 1.2 - - - -
42C TRP* 3.2 30.3 - - + +
45C GLN* 3.4 47.6 - - + +
46C LEU* 3.9 25.1 - - + +
74C LYS* 2.9 49.7 + - + +
76C ARG 3.3 0.6 - - - -
77C ALA* 1.3 77.4 - - + +
79C VAL* 1.3 61.6 + - - +
80C PRO* 3.1 10.7 - - - +
----------------------------------------------------------
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