Contacts of the strand formed by residues 78 - 87 (chain E) in PDB entry 1E81
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 GLY 78 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E SER* 4.7 3.5 + - - -
75E TYR 2.9 12.9 + - - -
76E GLY 2.9 3.7 + - - -
77E ASP* 1.3 78.4 - - - +
79E SER* 1.3 66.8 + - - +
80E SER* 3.7 4.5 + - - -
108E SER* 5.0 1.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E SER* 3.3 5.0 - - - -
75E TYR* 3.0 31.3 + - - -
77E ASP* 2.8 26.1 + - - -
78E GLY* 1.3 82.1 - - - +
80E SER* 1.3 60.3 + - - +
108E SER* 3.5 7.2 - - - -
110E SER* 2.9 30.8 + - - -
111E PHE* 3.2 24.5 - - - -
400E M91 4.1 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E TRP* 3.2 39.7 - - - -
71E TRP* 3.2 23.9 - - - -
72E SER* 4.5 0.3 + - - -
73E ILE* 3.0 49.0 + - - +
74E SER* 3.8 10.1 - - - -
75E TYR* 4.3 1.9 - - - -
78E GLY 4.4 3.5 + - - -
79E SER* 1.3 78.0 - - - +
81E SER* 1.3 63.4 + - - +
106E LYS 3.0 12.8 - - - -
107E VAL* 3.4 6.4 - - - -
108E SER* 2.6 54.0 + - - -
111E PHE* 3.6 4.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E TRP* 3.1 28.6 - - - -
72E SER* 3.9 13.5 - - - -
80E SER* 1.3 77.0 - - - +
82E GLY* 1.3 51.3 - - - +
104E ALA 3.4 1.0 - - - -
105E LYS* 2.5 30.1 + - - -
106E LYS* 2.7 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E THR* 3.5 9.8 - - - +
71E TRP* 3.1 33.4 + - - +
81E SER* 1.3 79.6 - - - +
83E ASP* 1.3 60.3 + - - -
103E SER 3.5 8.1 - - - -
105E LYS* 3.6 19.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E GLU* 2.3 43.9 - - - +
65E LEU* 4.3 10.5 - - + +
69E ALA 3.8 12.1 - - - +
70E THR* 4.6 2.7 - - + +
71E TRP* 3.0 18.4 + - - -
82E GLY* 1.3 72.1 - - - -
84E VAL* 1.3 66.8 + - - +
85E TYR* 3.8 6.9 - - - -
103E SER* 3.0 24.5 + - - +
105E LYS* 4.2 15.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E LEU* 3.9 4.7 - - - +
66E LEU* 2.9 41.8 + - + +
69E ALA* 3.8 34.2 + - + -
70E THR 4.2 1.6 - - - -
71E TRP* 3.9 11.2 - - + -
83E ASP* 1.3 84.1 - - - +
85E TYR* 1.3 80.3 + - - +
100E ALA* 4.3 13.2 - - + -
101E VAL 3.8 6.3 - - - +
102E GLU* 4.2 10.3 - - + -
131E VAL* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E GLU* 2.7 41.2 + - - -
56E TYR* 4.4 16.2 - + + +
58E PRO* 3.6 36.3 - - + +
63E ALA* 4.7 2.7 - - + -
64E LYS* 3.4 12.8 - - - +
65E LEU* 3.3 44.7 - - + +
66E LEU 4.3 0.4 - - - +
83E ASP* 3.8 4.5 - - - -
84E VAL* 1.3 79.2 - - - +
86E THR* 1.3 60.8 + - - +
87E ASP 4.1 0.2 - - - -
100E ALA* 3.5 3.6 - - - -
101E VAL* 2.6 45.5 + - + +
103E SER* 4.0 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E THR* 3.2 8.1 - - - +
64E LYS* 2.7 67.0 + - - +
66E LEU* 4.3 29.2 - - + -
85E TYR* 1.3 77.4 - - - +
87E ASP* 1.3 61.4 + - - +
98E GLY* 4.3 19.4 - - - +
99E GLN 3.2 9.4 - - - +
100E ALA* 4.8 5.2 - - - -
135E GLN* 5.3 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ILE* 4.4 2.5 - - + -
21E GLY* 3.2 13.4 - - - -
56E TYR* 2.6 29.7 + - - +
61E SER* 2.7 20.2 + - - -
63E THR* 2.4 44.6 + - - +
85E TYR 4.1 0.4 - - - -
86E THR* 1.3 73.3 - - - +
88E THR* 1.3 74.3 + - - +
89E VAL* 3.6 2.5 + - - -
96E VAL 3.8 0.2 - - - +
98E GLY 3.4 5.5 + - - +
99E GLN* 3.0 33.7 + - - +
101E VAL* 4.2 13.2 - - + +
----------------------------------------------------------
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