Contacts of the helix formed by residues 117 - 132 (chain E) in PDB entry 5BXD
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 LEU 117 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E TYR* 3.8 26.5 - - + -
54E SER* 3.7 23.6 - - - +
56E ILE* 4.1 5.6 - - + -
87E ILE* 3.7 33.4 - - + +
90E PHE* 4.2 14.6 - - + -
91E LEU* 3.9 20.6 - - + -
112E ALA* 3.1 9.8 + - + +
115E PHE* 4.1 9.2 - - + +
116E GLN* 1.3 72.9 - - - +
118E GLN* 1.3 64.2 + - - +
119E PRO* 3.4 3.8 - - - -
120E MET* 3.1 22.6 + - + +
121E LEU* 3.1 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E GLU 5.4 4.5 + - - +
113E LYS 5.1 1.0 + - - -
116E GLN* 3.3 40.6 + - - +
117E LEU* 1.3 71.8 - - - +
119E PRO* 1.3 72.4 - - + +
121E LEU* 3.2 25.2 + - - +
122E LEU* 3.0 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 119 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E TYR* 4.0 27.6 - - + +
53E GLU 6.1 1.1 - - - +
90E PHE* 3.8 15.7 - - + -
117E LEU* 3.6 5.2 - - + -
118E GLN* 1.3 93.6 - - + +
120E MET* 1.3 60.3 + - - +
122E LEU* 3.4 10.1 + - + +
123E GLU* 3.3 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 120 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E TYR 3.6 26.5 - - - +
87E ILE* 3.9 19.5 - - + -
90E PHE* 3.4 48.4 - - + -
96E LEU* 4.0 24.5 - - + -
108E LEU* 4.0 23.6 - - + -
112E ALA* 4.0 10.5 - - + -
117E LEU* 3.1 19.3 + - + +
119E PRO* 1.3 76.7 - - - +
121E LEU* 1.3 61.0 + - - +
123E GLU* 3.2 4.6 + - - +
124E MET* 2.9 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E TYR* 3.6 48.0 - - + +
112E ALA* 3.6 26.7 - - + +
113E LYS* 3.8 23.1 - - + +
117E LEU 3.1 14.0 + - - +
118E GLN* 3.2 37.9 + - - +
120E MET* 1.3 76.8 - - - +
122E LEU* 1.3 56.0 + - - +
124E MET* 3.3 4.9 + - - +
125E GLU* 2.9 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E GLN 3.0 12.7 + - - +
119E PRO* 3.6 12.1 - - + +
120E MET 3.2 0.2 - - - -
121E LEU* 1.3 77.0 - - - +
123E GLU* 1.3 65.3 + - - +
125E GLU* 3.4 12.5 + - + +
126E ARG* 3.2 61.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E PHE* 4.6 11.2 - - + -
94E SER 5.2 4.7 - - - +
95E LYS* 5.8 0.2 - - - -
96E LEU* 3.8 27.1 + - + +
119E PRO 3.3 14.2 + - - +
120E MET* 3.2 9.5 + - - +
122E LEU* 1.3 80.7 - - - +
124E MET* 1.3 56.8 + - - +
126E ARG* 3.3 35.1 + - - +
127E TRP* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 124 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E LEU* 3.8 24.7 - - + -
98E ILE* 5.4 2.7 - - + -
105E TYR* 3.2 46.8 + - + +
108E LEU* 3.6 29.8 - - + -
109E TYR* 3.6 40.8 - - + +
112E ALA* 4.3 14.6 - - - -
120E MET* 2.9 23.4 + - + +
121E LEU* 3.7 5.6 - - - +
122E LEU 3.3 0.2 - - - -
123E GLU* 1.3 77.0 - - - +
125E GLU* 1.3 56.8 + - - +
127E TRP* 3.2 1.5 + - - +
128E LYS 2.9 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E TYR* 3.9 6.8 + - - -
109E TYR* 2.9 33.5 + - + +
121E LEU* 2.9 21.7 + - + +
122E LEU* 3.6 14.1 - - + +
123E GLU 3.3 0.2 - - - -
124E MET* 1.3 74.9 - - - +
126E ARG* 1.3 58.9 + - + +
128E LYS* 3.4 17.6 + - - +
129E GLN* 2.9 50.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 126 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E LEU* 3.2 46.4 + - + +
123E GLU* 3.6 31.1 + - - +
125E GLU* 1.3 74.3 - - + +
127E TRP* 1.3 65.6 + - - +
129E GLN* 3.3 17.3 + - - +
130E ASP* 3.3 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 127 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E LEU* 3.8 17.5 - - + -
98E ILE* 3.4 23.9 + - + +
99E PRO 3.6 9.5 + - - -
100E ASP* 3.9 3.3 - - - +
101E ASP 4.9 0.7 - - - -
102E PHE* 3.6 44.6 - + + -
105E TYR* 3.5 37.7 - + + -
123E GLU 2.9 13.2 + - - +
124E MET 3.4 7.2 - - - +
126E ARG* 1.3 78.4 - - - +
128E LYS* 1.3 65.6 + - - +
130E ASP* 3.4 7.2 + - - -
131E ARG* 3.0 79.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E TYR* 3.5 37.8 + - + +
124E MET 2.9 16.4 + - - +
125E GLU* 3.7 17.8 + - - +
127E TRP* 1.3 84.7 - - + +
129E GLN* 1.3 60.4 + - + +
131E ARG* 2.9 4.7 + - - +
132E GLU* 2.8 56.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 129 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E GLU* 2.9 38.6 + - - +
126E ARG* 3.3 17.3 + - - +
128E LYS* 1.3 76.1 - - + +
130E ASP* 1.3 64.4 + - - +
131E ARG 3.5 0.3 + - - -
132E GLU* 3.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 130 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E ARG* 3.3 15.1 + - - +
127E TRP* 3.7 9.0 - - - +
128E LYS 3.1 1.0 - - - -
129E GLN* 1.3 79.6 - - - +
131E ARG* 1.3 72.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E ASP* 2.8 47.5 + - - +
101E ASP* 5.7 0.4 - - - +
127E TRP* 3.0 82.9 + - + +
128E LYS* 2.9 5.6 + - - +
130E ASP* 1.3 93.5 + - + +
132E GLU* 1.3 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E LYS* 2.8 46.2 + - + +
129E GLN* 3.9 28.8 + - - +
130E ASP 3.8 0.4 - - - -
131E ARG* 1.3 82.0 - - - +
----------------------------------------------------------
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