Contacts of the helix formed by residues 84 - 94 (chain A) in PDB entry 5ABT
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 84 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ARG* 1.3 90.4 - - + +
85A GLU* 1.3 64.1 + - - +
86A GLU* 3.3 21.6 + - - +
87A ASP* 3.0 42.0 + - - +
88A VAL* 3.2 15.6 + - - +
111A VAL* 6.1 0.4 - - - -
115A TRP* 3.4 8.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 1.3 73.7 - - - +
86A GLU* 1.3 70.8 + - - +
88A VAL* 3.4 1.6 + - - -
89A ALA* 3.0 23.6 + - - +
114A GLY 5.8 2.2 - - - -
115A TRP* 3.4 30.7 + - + +
118A ARG* 2.7 44.2 + - + +
119A PHE* 3.3 22.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 3.1 22.6 - - - +
85A GLU* 1.3 93.4 + - + +
87A ASP* 1.3 66.3 + - - +
89A ALA* 3.4 7.8 + - - +
90A ALA* 3.0 25.5 + - - +
118A ARG* 5.3 3.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 3.2 30.3 + - - +
81A GLY 4.2 1.4 - - - +
82A VAL* 3.9 13.2 - - + -
83A ARG* 2.9 27.4 + - - +
84A THR* 3.0 30.7 + - - +
86A GLU* 1.3 77.8 - - - +
88A VAL* 1.3 62.5 + - - +
90A ALA* 3.4 5.1 + - - +
91A LEU* 3.2 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 3.7 18.6 - - + -
84A THR 3.2 13.8 + - - +
85A GLU 3.6 6.5 - - - +
86A GLU 3.3 0.2 - - - -
87A ASP* 1.3 76.3 - - - +
89A ALA* 1.3 62.7 + - - +
91A LEU* 3.2 4.5 + - - +
92A LEU* 3.1 33.3 + - + +
99A VAL* 4.0 16.2 - - + -
101A ILE* 4.2 5.8 - - + -
115A TRP* 3.9 24.2 - - + -
119A PHE* 3.6 25.8 - - + -
124A LEU* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLU 3.0 15.8 + - - +
86A GLU* 3.7 8.3 - - - +
87A ASP 3.3 0.2 - - - -
88A VAL* 1.3 77.1 - - - +
90A ALA* 1.3 58.2 + - - +
92A LEU* 3.4 4.4 + - - +
93A LYS* 2.9 29.7 + - - +
118A ARG* 3.5 28.7 - - - +
119A PHE* 3.8 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 6.5 0.4 - - + -
66A LYS* 5.4 5.9 - - - -
86A GLU 3.0 18.2 + - - +
87A ASP* 3.7 6.5 - - - +
88A VAL 3.2 0.4 - - - -
89A ALA* 1.3 73.2 - - - +
91A LEU* 1.3 65.8 + - + +
93A LYS* 3.4 10.0 + - - +
94A ALA* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 3.7 20.4 - - - +
62A ILE* 6.2 5.2 - - + -
65A ILE* 4.2 20.6 - - + -
66A LYS* 6.4 1.6 - - + -
78A VAL* 4.4 16.4 - - + +
82A VAL* 3.7 30.3 - - + -
87A ASP 3.2 13.3 + - - +
88A VAL 3.7 5.8 - - - +
90A ALA* 1.3 78.3 - - + +
92A LEU* 1.3 62.0 + - - +
94A ALA* 3.0 14.7 + - + -
95A GLY 3.4 0.2 + - - -
96A VAL* 3.1 39.6 + - + +
99A VAL* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 3.1 20.7 + - + +
89A ALA 3.7 5.6 - - - +
91A LEU* 1.3 76.1 - - - +
93A LYS* 1.3 64.3 + - - +
95A GLY* 3.1 14.6 + - - -
96A VAL 3.4 22.8 + - - +
97A ALA 4.1 13.7 - - - +
99A VAL* 4.0 16.8 - - + -
119A PHE* 3.5 35.0 - - + -
123A ALA* 4.2 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ALA 2.9 18.3 + - - +
90A ALA* 3.6 9.6 - - - +
91A LEU 3.2 0.2 - - - -
92A LEU* 1.3 76.8 - - - +
94A ALA* 1.3 57.9 + - - +
95A GLY* 3.1 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LYS* 4.0 39.1 - - + +
69A VAL* 3.6 16.8 - - + +
70A ALA* 5.2 4.0 + - - +
90A ALA 3.1 14.7 + - - +
91A LEU* 3.0 11.3 + - + +
93A LYS* 1.3 76.0 - - - +
95A GLY* 1.3 56.6 + - - +
96A VAL* 3.5 4.0 - - + -
----------------------------------------------------------
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