Contacts of the strand formed by residues 81 - 91 (chain E) in PDB entry 1ACB
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 GLN 81 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E VAL 3.3 3.6 - - - +
67E VAL* 3.4 2.4 - - - -
68E ALA* 2.9 41.3 + - + +
79E LYS 4.8 5.9 + - - +
80E ILE* 1.3 76.1 - - - +
82E LYS* 1.3 64.0 + - - +
83E LEU* 3.7 16.1 + - + +
111E ALA 4.9 0.2 - - - +
112E ALA* 3.7 8.1 - - - +
113E SER* 2.8 56.0 + - - +
115E SER* 4.4 4.2 + - - -
118E VAL* 3.4 28.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E GLN* 4.3 13.0 - - - +
38E GLY* 6.4 0.2 - - - -
65E VAL* 4.3 19.3 - - + -
66E VAL 3.5 4.9 - - - -
67E VAL* 4.1 26.5 - - + -
80E ILE* 4.3 22.9 + - + +
81E GLN* 1.3 74.9 - - - +
83E LEU* 1.3 61.9 + - - +
84E LYS* 4.3 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E LEU* 5.3 2.5 - - + -
65E VAL* 3.6 7.7 - - - +
66E VAL* 2.8 58.0 + - + +
68E ALA* 4.4 14.1 - - + -
81E GLN* 4.3 18.4 - - + +
82E LYS* 1.3 75.4 - - - +
84E LYS* 1.3 62.7 + - - +
108E LEU* 3.8 32.1 - - + -
110E THR* 3.6 25.4 - - + +
111E ALA 3.9 13.5 - - - +
112E ALA* 3.9 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E LYS* 5.7 5.1 - - - +
62E THR 3.9 19.3 + - - +
63E SER* 4.2 9.1 + - - +
64E ASP 4.0 12.7 + - - -
65E VAL* 4.6 13.8 - - + +
82E LYS 5.6 1.3 - - - +
83E LEU* 1.3 75.1 - - - +
85E ILE* 1.3 60.3 - - - +
108E LEU* 3.3 10.2 - - - +
109E SER* 2.7 41.9 + - - +
110E THR* 4.1 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E LEU* 5.9 0.9 - - + -
60E VAL* 3.9 25.6 - - + -
61E THR 4.0 2.0 - - - +
62E THR* 3.7 29.2 + - + +
64E ASP* 3.5 25.1 + - + +
65E VAL 4.6 1.1 - - - +
66E VAL* 3.8 28.3 - - + -
83E LEU 4.4 0.4 - - - +
84E LYS* 1.3 79.5 - - - +
86E ALA* 1.3 62.4 + - - +
87E LYS 3.8 15.0 - - - +
88E VAL* 4.2 13.5 - - + -
106E LEU* 4.0 16.6 - - + -
107E LYS 3.4 14.1 - - - +
108E LEU* 4.3 1.1 - - + +
109E SER* 4.0 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E THR* 3.7 9.7 - - - +
85E ILE* 1.3 75.4 - - - +
87E LYS* 1.3 64.9 + - + +
107E LYS* 2.4 30.3 + - + +
108E LEU 3.8 3.8 - - - +
109E SER* 3.5 29.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E THR* 4.3 4.9 - - - -
85E ILE* 3.6 2.3 - - - +
86E ALA* 1.3 82.9 - - + +
88E VAL* 1.3 65.9 + - - +
89E PHE* 3.9 33.1 - - + -
106E LEU* 3.6 1.9 - - - -
107E LYS* 2.8 36.6 + - + +
245E ASN* 5.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E VAL* 3.9 30.1 - - + +
61E THR* 4.1 20.4 - - - -
62E THR* 4.2 7.0 - - + +
85E ILE* 4.2 12.1 - - + -
87E LYS* 1.3 80.1 - - - +
89E PHE* 1.3 70.2 + - - +
90E LYS* 3.9 6.1 + - + +
104E THR* 3.5 25.4 - - + -
105E LEU 3.6 2.2 - - - -
106E LEU* 3.9 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E TRP* 3.3 36.3 - + - -
87E LYS* 3.9 40.6 - - + -
88E VAL* 1.3 78.0 - - - +
90E LYS* 1.3 59.8 + - - +
104E THR* 4.0 1.6 - - - -
105E LEU* 2.6 42.4 + - + +
107E LYS* 4.1 8.1 - - + -
237E TRP* 3.3 13.6 - - + -
241E THR* 3.8 21.1 - - + -
245E ASN* 3.2 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E ALA* 4.0 16.2 - - + +
88E VAL* 3.9 7.5 + - + +
89E PHE* 1.3 74.1 - - - +
91E ASN* 1.3 73.6 + - - +
92E SER* 3.1 5.5 + - - -
94E TYR* 3.3 35.4 - - + -
104E THR* 3.4 22.0 - - + +
237E TRP* 4.0 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E LYS* 1.3 76.4 - - - +
92E SER* 1.3 58.7 + - - +
93E LYS* 2.9 21.7 + - - +
94E TYR* 2.7 33.7 + - + +
101E ASN* 4.0 14.0 - - - +
103E ILE* 3.2 40.1 + - + +
234E LEU* 4.3 12.1 - - - +
237E TRP* 3.3 46.9 + - + +
----------------------------------------------------------
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