Contacts of the helix formed by residues 64 - 79 (chain B) in PDB entry 4BZ5
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 SER 64 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B HIS* 1.3 75.8 - - - +
65B THR* 1.3 64.2 + - - +
66B GLU* 3.2 17.7 - - - +
67B TYR* 3.1 20.1 + - - +
68B VAL* 3.1 22.3 + - - +
145B ARG* 3.0 39.0 + - - +
146B SER* 2.6 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TYR* 3.1 34.1 + - + +
60B THR* 4.0 16.8 - - + +
63B HIS 3.7 0.8 + - - -
64B SER* 1.3 73.5 - - - +
66B GLU* 1.3 67.9 + - - +
68B VAL 3.4 0.7 + - - -
69B ASP* 2.9 37.4 + - - -
145B ARG* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER* 3.2 27.5 + - - +
65B THR* 1.3 89.7 + - - +
67B TYR* 1.3 60.3 + - - +
69B ASP* 3.5 10.2 + - - +
70B ALA* 3.1 23.4 + - - +
95B PHE* 3.8 24.2 - - + -
145B ARG* 4.6 5.4 + - - -
146B SER* 4.4 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B HIS* 3.9 20.0 - + + -
64B SER* 3.1 21.7 + - - +
66B GLU* 1.3 75.9 - - - +
68B VAL* 1.3 68.6 + - + +
70B ALA* 3.1 3.2 + - - +
71B LEU* 2.9 26.5 + - + +
95B PHE* 3.7 38.4 - + + -
97B LEU* 4.0 15.8 - - + +
144B LYS 4.5 2.0 - - - -
145B ARG 3.8 13.2 - - - +
146B SER* 3.7 17.7 - - - -
147B GLU 4.0 1.3 - - - -
148B ALA* 3.3 39.5 + - - +
153B TYR* 2.6 32.5 + - - +
154B LEU* 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B MET* 5.7 0.7 - - - -
56B TYR* 3.7 28.0 - - + -
59B VAL* 3.8 22.9 - - + -
60B THR* 3.9 9.9 - - + -
63B HIS* 3.7 23.1 - - + -
64B SER 3.1 17.3 + - - +
65B THR 3.9 2.9 - - - +
67B TYR* 1.3 75.7 - - + +
69B ASP* 1.3 64.1 + - - +
71B LEU* 3.2 8.4 + - - +
72B LYS* 3.0 33.0 + - - +
108B PHE* 4.1 15.2 - - + -
154B LEU* 4.7 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TYR* 2.7 31.4 + - - -
65B THR* 2.9 25.8 + - - +
66B GLU* 3.6 9.2 - - - +
68B VAL* 1.3 76.6 - - - +
70B ALA* 1.3 56.3 + - - +
72B LYS* 3.4 12.4 + - - +
73B LYS* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLU 3.1 11.1 + - - +
67B TYR 3.1 8.3 + - - +
69B ASP* 1.3 74.6 - - - +
71B LEU* 1.3 62.2 + - - +
73B LYS* 3.2 5.9 + - - -
74B LEU* 2.8 29.3 + - - +
91B LEU* 4.8 10.3 - - + -
92B MET* 3.5 11.7 - - - +
95B PHE* 3.5 33.9 - - + -
97B LEU* 4.1 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 2.9 17.7 + - + +
68B VAL* 3.7 8.3 - - - +
70B ALA* 1.3 73.6 - - - +
72B LYS* 1.3 64.4 + - - +
74B LEU* 3.3 7.0 + - + +
75B GLN* 3.2 16.5 + - - +
97B LEU* 3.6 32.7 - - + +
107B VAL* 4.2 13.3 - - + +
108B PHE* 3.7 30.9 - - + +
111B SER* 4.3 4.5 - - - -
153B TYR* 3.8 28.0 - - + +
154B LEU* 3.7 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PRO* 5.5 3.8 + - - +
55B MET* 4.0 14.6 - - - +
56B TYR* 3.2 36.3 - - - +
68B VAL* 3.0 19.4 + - - +
69B ASP* 3.5 14.3 + - - +
71B LEU* 1.3 77.9 - - - +
73B LYS* 1.3 61.8 + - - +
75B GLN* 3.3 5.9 + - - +
76B MET* 3.1 20.9 + - - +
108B PHE* 3.8 42.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ASP 3.0 14.7 + - - +
70B ALA* 3.2 9.4 + - - +
72B LYS* 1.3 74.0 - - - +
74B LEU* 1.3 61.3 + - - +
76B MET* 3.2 15.3 + - + +
77B LEU* 2.8 46.5 + - + +
88B ASP* 3.0 32.0 + - - +
91B LEU* 4.4 19.0 - - + +
92B MET* 3.8 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ALA 2.8 13.3 + - - +
71B LEU* 3.5 11.2 - - + +
72B LYS 3.2 0.4 - - - -
73B LYS* 1.3 76.6 - - - +
75B GLN* 1.3 62.4 + - - +
77B LEU* 3.4 4.3 + - + +
78B HIS* 3.1 55.4 + - + +
84B LEU* 5.4 2.2 - - + -
92B MET* 3.6 30.5 - - + +
97B LEU* 3.8 39.0 - - + +
102B PRO 4.4 3.6 - - - +
103B GLY* 3.6 26.9 - - - +
107B VAL* 4.0 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU 3.2 3.6 + - - -
72B LYS 3.5 8.5 - - - +
73B LYS 3.2 0.2 - - - -
74B LEU* 1.3 78.9 - - - +
76B MET* 1.3 63.2 + - - +
78B HIS* 3.1 3.3 + - - +
79B CYS* 3.1 28.2 + - - -
104B PHE 4.3 3.4 - - - -
105B PRO 3.2 21.0 - - - +
106B SER* 3.2 9.5 - - - -
107B VAL* 3.7 17.1 - - + +
108B PHE* 2.8 36.4 + - + +
109B ASP* 3.0 36.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LYS 3.1 13.5 + - - +
73B LYS* 3.2 16.6 + - - +
75B GLN* 1.3 76.6 - - - +
77B LEU* 1.3 67.0 + - + +
79B CYS* 3.2 15.7 + - - +
80B GLU* 3.4 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LYS* 2.8 35.6 + - + +
74B LEU* 3.7 6.7 - - + +
76B MET* 1.3 76.8 - - + +
78B HIS* 1.3 62.5 + - + +
79B CYS 3.2 0.2 - - - -
80B GLU* 3.3 36.0 + - - +
82B LYS* 4.6 7.6 - - - +
84B LEU* 3.6 44.7 - - + +
88B ASP* 3.8 25.8 - - - +
92B MET* 3.6 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 3.1 45.5 + - + +
75B GLN 3.1 2.9 + - - +
77B LEU* 1.3 80.8 - - + +
79B CYS* 1.3 57.9 + - - +
80B GLU 3.4 5.6 - - - +
84B LEU* 4.8 12.9 - - + +
103B GLY* 3.4 36.4 + - - -
104B PHE* 3.7 25.7 + - - +
105B PRO* 3.8 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLN* 3.1 19.0 + - - +
76B MET* 3.2 9.4 + - - +
77B LEU 3.2 0.6 - - - -
78B HIS* 1.3 77.7 - - - +
80B GLU* 1.3 60.2 + - - +
105B PRO* 3.1 39.5 - - - -
----------------------------------------------------------
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