Contacts of the helix formed by residues 67 - 81 (chain A) in PDB entry 3VOD
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 67 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LYS* 5.4 1.1 - - - +
66A VAL* 1.3 75.4 - - - +
68A LEU* 1.3 63.7 + - - +
69A GLY* 3.2 17.6 + - - -
70A ALA* 3.3 21.2 + - + +
71A LEU* 2.9 28.5 + - - +
67B ASP* 5.7 0.8 - - + +
70B ALA* 4.2 27.3 + - + +
73B ARG* 4.6 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO* 4.2 22.7 - - + +
58A VAL* 4.5 11.2 - - + +
61A LYS* 4.0 38.9 - - + +
66A VAL 3.6 3.8 + - - -
67A ASP* 1.3 76.5 + - - +
69A GLY* 1.3 54.4 + - - +
71A LEU* 3.8 8.2 - - + +
72A THR* 2.7 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 3.2 13.5 + - - -
68A LEU* 1.3 79.3 - - - +
70A ALA* 1.3 61.3 + - - +
72A THR* 3.4 4.8 + - - -
73A ARG* 3.2 37.1 + - - +
73B ARG* 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A VAL* 5.8 2.7 - - + -
67A ASP* 3.3 25.3 + - + +
69A GLY* 1.3 75.0 - - - +
71A LEU* 1.3 56.8 + - - +
73A ARG* 3.6 12.4 + - - +
74A MET* 2.9 34.6 + - + +
67B ASP* 4.1 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 4.1 21.5 - - + -
57A PRO* 3.6 12.6 - - + +
60A LEU* 3.9 27.1 - - + -
61A LYS* 3.6 37.9 - - + +
64A LEU* 4.2 5.4 - - + -
66A VAL* 4.0 10.0 - - + +
67A ASP 2.9 18.1 + - - +
68A LEU* 3.8 8.5 - - + +
69A GLY 3.2 0.2 - - - -
70A ALA* 1.3 75.0 - - - +
72A THR* 1.3 56.9 + - - +
74A MET* 3.5 9.4 - - + -
75A LEU* 2.6 54.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO* 5.6 3.3 - - - +
68A LEU* 2.7 36.2 + - - +
69A GLY* 3.9 5.1 - - - -
71A LEU* 1.3 75.8 - - - +
73A ARG* 1.3 57.4 + - - +
75A LEU* 3.5 11.3 + - + +
76A ASP* 3.0 32.4 + - - +
86A ARG* 4.0 17.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLY* 3.2 25.9 + - - +
70A ALA* 3.7 8.6 - - - +
72A THR* 1.3 75.5 - - - +
74A MET* 1.3 58.7 + - - +
76A ASP* 3.1 10.1 + - - +
77A ARG* 2.9 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ALA* 3.7 38.1 - - + +
42A GLN* 3.8 19.3 - - + -
45A VAL* 3.5 25.4 - - + -
64A LEU* 5.4 0.4 - - + -
66A VAL* 5.2 13.2 - - + -
70A ALA* 2.9 20.1 + - + +
71A LEU* 3.6 19.1 - - + +
73A ARG* 1.3 75.2 - - - +
75A LEU* 1.3 61.0 + - - +
77A ARG* 3.4 14.5 + - - +
78A LEU* 3.2 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 4.4 8.3 - - + -
49A ILE* 4.2 21.8 - - + -
57A PRO* 4.2 28.9 - - + -
60A LEU* 4.3 7.6 - - + -
71A LEU* 2.6 45.6 + - + +
72A THR* 3.7 9.9 - - - +
74A MET* 1.3 73.0 - - - +
76A ASP* 1.3 57.3 + - - +
78A LEU* 3.4 5.3 + - + +
79A VAL* 3.0 35.4 + - + +
84A VAL* 4.4 8.0 - - + +
86A ARG* 3.9 15.3 - - - +
98A VAL* 4.1 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A THR* 3.0 19.9 + - - +
73A ARG* 3.1 12.7 + - - +
75A LEU* 1.3 75.2 - - - +
77A ARG* 1.3 64.0 + - + +
79A VAL* 3.4 9.1 + - - +
80A SER* 3.1 22.0 + - - -
86A ARG* 3.4 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 4.7 19.5 - - - +
73A ARG* 2.9 28.8 + - - +
74A MET* 3.6 17.2 - - - +
75A LEU 3.3 0.2 - - - -
76A ASP* 1.3 76.2 - - + +
78A LEU* 1.3 60.3 + - + +
80A SER* 3.4 9.8 + - - -
81A LYS* 3.2 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 3.9 32.1 - - + +
45A VAL* 3.6 34.8 - - + -
46A LEU* 3.9 15.7 - - + -
74A MET* 3.2 25.4 + - + +
75A LEU* 3.4 6.3 + - + +
76A ASP 3.3 0.2 - - - -
77A ARG* 1.3 74.6 - - + +
79A VAL* 1.3 62.1 + - - +
81A LYS* 3.6 5.4 + - + +
82A GLY 3.3 2.9 + - - -
83A TRP* 3.1 54.7 + - + -
84A VAL* 3.4 20.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.0 24.1 + - + +
76A ASP* 3.6 10.5 - - - +
77A ARG 3.3 0.2 - - - -
78A LEU* 1.3 74.6 - - - +
80A SER* 1.3 64.2 + - - +
82A GLY* 3.0 14.7 + - - -
84A VAL* 3.4 33.2 - - + +
85A GLU* 5.0 1.3 - - - -
86A ARG* 4.5 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASP 3.1 13.9 + - - -
77A ARG* 3.4 13.2 - - - -
79A VAL* 1.3 77.4 - - - +
81A LYS* 1.3 64.3 + - - +
82A GLY* 3.2 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP* 4.0 15.0 + - - -
42A GLN* 4.2 17.0 + - - +
77A ARG* 3.2 19.8 + - - +
78A LEU* 3.8 6.7 - - + +
79A VAL 3.3 0.2 - - - -
80A SER* 1.3 77.2 - - - +
82A GLY* 1.3 61.9 + - - +
83A TRP* 3.6 58.5 + - + -
----------------------------------------------------------
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