Contacts of the helix formed by residues 68 - 77 (chain J) in PDB entry 2IVB
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 68 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J ASP 4.0 1.2 + - - -
67J LEU* 1.3 77.6 - - - +
69J GLU* 1.3 66.3 + - - +
70J ASP* 3.6 8.3 + - - +
71J SER* 2.6 36.5 + - - -
72J ILE* 3.1 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59J ARG* 5.9 2.1 - - - +
67J LEU 5.0 0.7 - - - +
68J ASP* 1.3 74.3 - - - +
70J ASP* 1.3 64.0 + - - +
72J ILE* 3.3 28.4 + - - +
73J LEU* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 70 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 3.9 25.4 - - + +
24D LYS* 3.3 32.1 + - - +
68J ASP* 3.4 8.9 - - - +
69J GLU* 1.3 78.8 - - - +
71J SER* 1.3 57.9 + - - +
73J LEU* 3.3 8.6 + - - +
74J LEU* 2.8 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 71 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J LEU* 3.5 29.9 - - - +
67J LEU* 4.0 18.2 - - - +
68J ASP* 2.6 30.6 + - - -
70J ASP* 1.3 77.8 - - - +
72J ILE* 1.3 62.1 + - - +
74J LEU* 3.3 9.5 + - - +
75J LEU* 3.2 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58J ALA* 3.7 21.2 - - + +
59J ARG* 4.0 21.5 - - + +
62J GLY* 3.9 28.9 - - - -
63J ALA* 5.0 0.4 - - - +
67J LEU* 3.5 24.9 - - + +
68J ASP 3.1 15.1 + - - +
69J GLU* 3.3 29.6 + - - +
71J SER* 1.3 77.4 - - - +
73J LEU* 1.3 61.1 + - - +
75J LEU* 3.5 15.7 + - - +
76J GLN* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 4.4 11.7 - - + -
23D ALA* 4.0 26.7 - - + +
24D LYS* 3.7 42.8 - - + +
3J GLN* 5.7 3.1 - - + -
69J GLU 2.9 13.9 + - - +
70J ASP* 3.4 10.8 - - - +
72J ILE* 1.3 76.9 - - - +
74J LEU* 1.3 62.5 + - - +
76J GLN* 3.0 37.3 + - + +
77J MET* 3.6 8.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 4.2 22.2 - - + -
5J GLN* 3.8 18.6 - - - +
10J ILE* 3.8 32.8 - - + +
11J ARG* 2.9 28.4 + - - -
14J LEU* 3.9 20.6 - - + -
70J ASP* 2.8 30.4 + - + +
71J SER* 3.7 10.5 - - - +
73J LEU* 1.3 72.6 - - - +
75J LEU* 1.3 59.7 + - - +
77J MET* 3.1 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J ARG* 3.9 13.7 + - - +
14J LEU* 4.0 14.4 - - + -
18J ILE* 4.2 7.6 - - + -
46J ALA* 3.7 25.6 - - + +
47J LEU* 4.1 14.6 - - + +
52J ALA* 3.6 6.2 - - - -
53J LEU* 2.9 32.7 + - + +
58J ALA* 4.3 10.5 - - + +
61J VAL* 4.0 22.9 - - + -
67J LEU* 3.8 28.9 - - + -
71J SER 3.2 15.3 + - - +
72J ILE* 3.7 13.5 - - - +
73J LEU 3.2 0.4 - - - -
74J LEU* 1.3 77.0 - - - +
76J GLN* 1.3 59.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 76 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J ILE* 6.0 0.9 - - - +
3J GLN* 4.3 4.1 + - - +
52J ALA* 3.6 10.3 - - - +
53J LEU 3.4 22.6 - - - +
55J ALA* 3.3 34.7 - - - +
58J ALA* 3.7 10.3 - - + +
59J ARG* 5.0 4.7 + - - +
72J ILE* 3.0 31.8 - - - +
73J LEU* 3.0 22.9 + - + +
75J LEU* 1.3 76.2 - - - +
77J MET* 1.3 62.0 + - + +
78J ILE* 3.6 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 77 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 4.6 11.0 - - + +
20D LEU* 5.4 1.3 - - - -
23D ALA* 4.1 19.5 - - + -
3J GLN* 3.3 21.5 - - + -
4J SER 3.4 34.5 - - - +
5J GLN* 3.2 37.2 - - + +
11J ARG* 2.9 21.4 + - - +
52J ALA* 3.2 12.2 - - - +
73J LEU* 3.6 13.0 - - + +
74J LEU* 3.1 30.4 + - - +
76J GLN* 1.3 78.3 - - - +
78J ILE* 1.3 60.5 + - - +
79J PRO* 3.3 0.5 - - - +
----------------------------------------------------------
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