Contacts of the strand formed by residues 77 - 82 (chain E) in PDB entry 3AB0
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 ILE 77 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E SER* 4.2 17.7 - - - +
22E CYS 3.2 4.9 - - - +
23E SER* 3.2 26.9 - - - +
29E PHE* 4.2 4.3 - - - -
70E SER 4.1 0.2 - - - +
71E ARG* 3.5 6.4 - - - +
72E ASP* 3.1 30.0 + - + +
75E ARG* 3.4 35.7 - - + +
76E ASN* 1.3 79.7 - - - +
78E LEU* 1.3 71.5 + - - +
79E THR* 4.0 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E SER* 3.3 5.2 - - - -
22E CYS* 2.7 46.5 + - + +
29E PHE* 4.4 10.7 - - + -
34E MET* 3.7 35.0 - - + +
35E SER 4.0 9.4 - - - +
36E TRP* 3.5 28.3 - - + +
51E ILE* 4.1 15.3 - - + -
69E THR* 4.0 11.9 - - - +
70E SER 3.7 13.9 - - - +
71E ARG* 4.5 4.3 - - + -
76E ASN 4.3 0.4 - - - -
77E ILE* 1.3 75.9 - - - +
79E THR* 1.3 60.5 + - - +
95E CYS* 3.8 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E LYS* 4.1 16.6 - - + -
20E LEU 3.3 12.5 + - - +
21E SER* 4.8 1.5 + - - +
36E TRP* 3.3 5.6 + - - -
68E THR 5.1 0.7 - - - +
69E THR* 2.9 29.2 + - - -
70E SER* 3.0 31.9 + - - +
71E ARG* 5.5 0.3 - - - -
77E ILE* 4.0 13.7 + - - +
78E LEU* 1.3 78.4 + - - +
80E LEU* 1.3 64.1 + - - +
81E GLN* 4.1 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU* 3.0 44.4 + - + +
36E TRP* 3.5 35.0 - - + +
48E VAL* 3.9 5.8 - - + -
49E ALA* 3.9 22.2 - - + -
67E PHE* 3.8 29.8 - - + -
68E THR 3.3 7.9 - - - +
69E THR* 4.0 8.5 - - - -
79E THR* 1.3 73.0 - - - +
81E GLN* 1.3 63.1 + - - +
82E MET* 3.2 18.0 + - + +
93E TYR* 3.9 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E SER* 5.3 3.3 - - - -
18E LEU* 3.2 18.8 + - - +
19E LYS* 3.4 31.5 - - - +
66E ARG 3.7 2.4 - - - +
67E PHE* 3.3 3.3 - - - -
68E THR* 2.7 50.3 + - - +
79E THR* 4.1 7.8 - - + +
80E LEU* 1.3 69.4 - - - +
82E MET* 1.3 64.6 + - - +
83E SER* 6.1 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E SER* 3.3 4.9 - - - -
18E LEU* 2.6 72.0 + - + +
20E LEU* 3.7 22.2 - - + -
67E PHE* 3.6 47.3 - - + -
80E LEU* 3.6 15.9 - - + +
81E GLN* 1.3 75.4 - - - +
83E SER* 1.3 62.4 + - - +
85E LEU* 3.9 12.6 - - + -
93E TYR* 3.9 20.9 - - - -
112E VAL* 3.8 16.6 - - + -
----------------------------------------------------------
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