Contacts of the helix formed by residues 70 - 82 (chain A) in PDB entry 4ED5
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 70 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A THR* 3.7 5.7 - - - +
45A GLU* 4.7 1.3 + - + -
68A TYR* 3.5 10.8 - - - +
69A VAL* 1.3 96.6 - - + +
71A ALA* 1.3 62.2 + - - +
72A LYS* 3.8 7.3 + - - +
73A ASP* 3.2 34.3 + - - +
74A ALA* 3.3 15.4 + - - +
201A GOL 3.6 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLY* 3.6 27.1 - - - +
19A ARG 3.4 23.3 - - - +
20A THR* 3.7 2.3 - - - +
70A THR* 1.3 70.7 - - - +
72A LYS* 1.3 64.5 + - - +
74A ALA* 3.4 2.4 + - - +
75A GLU* 3.0 23.7 + - - +
95A TYR* 4.6 1.2 + - - -
201A GOL 2.8 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A THR* 3.4 7.2 + - - +
71A ALA* 1.3 77.0 - - - +
73A ASP* 1.3 60.1 + - - +
75A GLU* 3.4 12.7 + - - +
76A ARG* 2.9 29.6 + - - +
201A GOL 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 3.4 9.1 - - + +
44A GLY* 3.6 21.6 - - - -
45A GLU* 3.9 8.1 + - - +
68A TYR* 3.8 23.3 - - + -
69A VAL* 6.0 0.2 - - - +
70A THR* 3.2 27.8 + - - +
71A ALA 3.2 0.4 - - - -
72A LYS* 1.3 78.2 - - - +
74A ALA* 1.3 59.8 + - - +
76A ARG* 3.3 22.4 + - - -
77A ALA* 2.9 30.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
19A ARG 3.7 15.3 - - - +
20A THR* 3.6 29.2 - - - +
22A LEU* 3.7 6.1 - - + +
68A TYR* 3.6 14.2 - - + -
70A THR 3.3 5.2 + - - +
71A ALA 3.6 7.9 - - - +
73A ASP* 1.3 76.9 - - - +
75A GLU* 1.3 63.5 + - - +
77A ALA* 3.2 4.2 + - - +
78A ILE* 3.1 26.4 + - - +
95A TYR* 4.2 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA 3.0 15.8 + - - +
72A LYS* 3.7 12.2 - - - +
74A ALA* 1.3 77.2 - - - +
76A ARG* 1.3 61.4 + - - +
78A ILE* 3.3 7.7 + - - +
79A ASN* 3.2 34.3 + - - +
95A TYR* 3.4 19.2 + - - +
208A EDO 3.8 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A SER 5.0 2.0 + - - -
43A ILE* 2.5 49.1 + - + +
72A LYS 2.9 17.5 + - - +
73A ASP* 3.5 20.5 + - - +
75A GLU* 1.3 76.4 - - - +
77A ALA* 1.3 55.5 + - - +
79A ASN* 3.4 7.1 + - + +
80A THR* 2.8 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.7 7.2 - - + -
40A PHE* 4.4 5.6 - - + -
43A ILE* 3.7 16.3 - - + +
68A TYR* 3.4 35.4 - - + +
73A ASP 2.9 11.7 + - - +
74A ALA 3.2 9.1 + - - +
76A ARG* 1.3 72.9 - - - +
78A ILE* 1.3 62.6 + - - +
81A LEU* 2.8 35.3 + - + +
82A ASN 3.8 0.5 + - - -
93A VAL* 4.2 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.6 20.9 - - + -
74A ALA 3.1 10.5 + - - +
75A GLU* 3.5 5.6 - - - +
77A ALA* 1.3 75.7 - - - +
79A ASN* 1.3 66.2 + - - +
82A ASN* 3.0 32.3 + - + +
93A VAL* 3.7 19.1 - - + +
94A SER* 4.3 0.7 - - - -
95A TYR* 3.4 53.4 - - + +
206A M2M 3.6 26.0 - - - +
208A EDO 3.8 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLU* 3.2 29.5 + - - +
76A ARG* 3.9 8.1 - - + +
78A ILE* 1.3 81.0 - - - +
80A THR* 1.3 61.4 + - - +
82A ASN* 4.9 3.1 + - - +
208A EDO 4.2 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 3.8 24.9 - - + +
76A ARG* 2.8 33.4 + - - +
79A ASN* 1.3 79.9 - - - +
81A LEU* 1.3 69.8 + - + +
82A ASN 3.7 3.6 - - - +
84A LEU* 5.2 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 4.4 13.2 - - + +
40A PHE* 3.7 43.1 - - + -
42A SER* 5.1 3.4 - - - +
43A ILE* 3.9 21.5 - - + -
77A ALA* 2.8 18.8 + - + +
80A THR* 1.3 91.9 - - + +
82A ASN* 1.3 69.1 + - - +
83A GLY 3.2 0.2 + - - -
84A LEU* 2.9 43.3 + - + +
91A ILE* 3.4 13.2 - - + +
93A VAL* 3.8 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE* 3.0 23.1 + - + +
79A ASN 5.0 2.7 - - - +
80A THR 4.4 5.0 - - - +
81A LEU* 1.3 78.0 - - - +
83A GLY* 1.3 60.9 + - - +
84A LEU 3.5 0.3 + - - -
93A VAL* 3.0 37.8 + - - +
206A M2M 3.1 64.1 + - - +
----------------------------------------------------------
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