Contacts of the helix formed by residues 66 - 79 (chain A) in PDB entry 3ASZ
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 66 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A MET* 5.7 0.2 - - - -
42A TYR* 2.8 24.9 + - + +
44A LYS* 3.8 19.0 - - + +
45A ASP 5.1 0.7 + - - -
65A PHE* 1.3 68.9 - - - +
67A LEU* 1.3 64.9 + - - +
68A ALA* 3.9 8.8 + - - +
69A LEU* 3.3 29.1 + - + +
70A TYR* 3.1 20.7 + - - +
95A ARG* 3.1 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A MET* 4.1 13.2 - - + -
62A PRO 5.9 1.1 - - - +
65A PHE* 3.0 10.9 + - + +
66A ASP* 1.3 74.4 - - - +
68A ALA* 1.3 55.0 + - - +
70A TYR* 4.3 5.4 - - + -
71A LEU* 2.7 42.7 + - + +
118A PRO* 3.9 19.7 - - + -
120A GLU* 3.6 24.7 - - + +
121A LEU* 3.8 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASP* 3.2 8.2 - - - +
67A LEU* 1.3 78.2 - - - +
69A LEU* 1.3 57.6 + - - +
71A LEU* 3.8 6.7 - - - +
72A GLU* 3.0 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR* 4.0 18.8 - - + -
66A ASP* 3.3 22.1 + - + +
67A LEU 3.3 0.4 - - - -
68A ALA* 1.3 76.6 - - - +
70A TYR* 1.3 60.8 + - - +
72A GLU* 3.4 18.3 + - - +
73A HIS* 2.9 52.6 + - + +
86A PRO* 4.1 10.1 - - + -
95A ARG* 3.8 35.9 - - - +
99A ARG* 4.2 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 2.7 44.8 + - + +
39A MET* 3.7 34.8 + - + -
42A TYR* 3.5 36.9 - + + -
66A ASP 3.1 13.1 + - - +
67A LEU* 3.6 10.8 - - - +
69A LEU* 1.3 77.7 - - - +
71A LEU* 1.3 56.6 + - - +
73A HIS* 3.3 3.6 + - - +
74A ALA* 2.9 28.2 + - + +
110A LEU* 3.3 31.5 - - + +
111A GLU 3.5 4.2 + - - -
115A VAL* 3.8 6.0 - - + +
121A LEU* 3.8 37.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
67A LEU* 2.7 29.5 + - + +
68A ALA* 3.8 7.2 - - - +
70A TYR* 1.3 74.4 - - - +
72A GLU* 1.3 63.1 + - - +
74A ALA* 3.1 5.6 + - - +
75A GLN* 2.9 50.3 + - - +
120A GLU* 4.0 34.3 - - + +
121A LEU* 4.3 10.3 - - + -
124A LEU* 3.9 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ALA 3.0 19.7 + - - +
69A LEU* 3.5 19.6 - - - +
70A TYR 3.3 0.2 - - - -
71A LEU* 1.3 75.7 - - - +
73A HIS* 1.3 72.3 + - + +
75A GLN* 3.4 15.2 + - - +
76A ALA* 3.0 28.4 + - + +
79A ARG* 5.3 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 3.9 9.4 - - + -
42A TYR* 2.8 29.0 + - + +
69A LEU* 2.9 39.7 + - + +
70A TYR 3.7 3.4 - - - +
72A GLU* 1.3 91.9 + - + +
74A ALA* 1.3 65.0 + - - +
76A ALA* 3.2 2.8 + - + +
77A LEU* 3.0 26.9 + - - +
83A VAL* 3.6 27.3 - - + +
84A GLU* 3.2 33.5 + - - +
86A PRO* 4.0 8.5 - - + -
99A ARG* 4.1 3.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 4.0 8.4 - - - +
70A TYR* 2.9 14.0 + - + +
71A LEU* 3.1 9.6 + - - +
73A HIS* 1.3 74.3 - - - +
75A GLN* 1.3 58.5 + - - +
77A LEU* 3.2 8.1 + - - +
78A LEU* 2.9 34.2 + - + +
108A VAL* 5.5 2.0 - - + +
110A LEU* 4.2 25.8 - - + -
121A LEU* 5.0 2.9 - - + -
124A LEU* 4.0 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 2.9 47.6 + - + +
72A GLU* 3.6 15.9 + - - +
74A ALA* 1.3 74.5 - - - +
76A ALA* 1.3 63.8 + - - +
78A LEU* 3.1 10.4 + - + +
79A ARG* 3.0 49.0 + - + +
124A LEU* 4.7 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLU* 3.0 15.0 + - + +
73A HIS* 3.2 9.8 + - + +
75A GLN* 1.3 75.1 - - - +
77A LEU* 1.3 61.2 + - - +
79A ARG* 3.0 23.4 + - - +
81A LEU* 2.8 43.1 + - + +
82A PRO 4.7 1.6 - - - +
83A VAL* 3.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PRO* 4.1 7.8 - - - +
35A ALA* 4.2 17.3 - - + +
37A LEU* 3.6 39.7 - - + -
73A HIS 3.0 12.5 + - - +
74A ALA* 3.5 7.2 - - - +
76A ALA* 1.3 76.8 - - - +
78A LEU* 1.3 63.6 + - - +
80A GLY* 3.2 12.5 + - - -
81A LEU 3.6 17.0 - - - +
83A VAL* 4.1 8.3 - - + -
102A VAL* 3.9 24.9 - - + +
103A ARG 4.1 13.9 - - - +
104A PRO* 4.1 12.6 - - + +
105A ALA 4.9 2.1 - - - +
108A VAL* 4.2 23.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
5A LYS* 5.0 1.6 - - - -
6A PRO* 3.6 35.1 - - + +
8A VAL* 3.3 31.4 - - + -
74A ALA* 2.9 23.1 + - + +
75A GLN* 3.1 12.5 + - + +
77A LEU* 1.3 76.7 - - - +
79A ARG* 1.3 60.2 + - + +
80A GLY 3.3 1.4 + - - -
108A VAL* 4.3 11.0 - - + -
124A LEU* 3.8 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLU* 5.3 3.0 + - - +
75A GLN* 3.0 42.1 + - + +
76A ALA* 3.0 19.3 + - - +
78A LEU* 1.3 77.8 - - + +
80A GLY* 1.3 62.9 + - - +
81A LEU* 3.4 29.0 + - + +
----------------------------------------------------------
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