Contacts of the helix formed by residues 79 - 93 (chain E) in PDB entry 5U0A
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 ASP 79 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E GLY 3.9 1.2 + - - -
78E TRP* 1.3 76.0 - - - +
80E ALA* 1.3 65.3 + - - +
81E ASP* 3.1 33.0 + - - +
82E LEU* 3.1 19.9 + - + +
83E ALA* 2.7 27.6 + - - +
135E ARG* 4.4 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E ARG* 3.8 35.5 + - - +
78E TRP 3.9 0.8 + - - -
79E ASP* 1.3 79.1 + - - +
81E ASP* 1.3 62.8 + - - +
83E ALA* 3.2 3.5 + - - +
84E ASP* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E ASP* 3.1 14.4 + - - +
80E ALA* 1.3 82.6 - - - +
82E LEU* 1.3 60.1 + - + +
84E ASP* 3.4 6.2 + - - +
85E ALA* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E TRP* 3.2 23.8 - - + -
79E ASP* 3.1 22.0 + - + +
81E ASP* 1.3 77.8 - - + +
83E ALA* 1.3 61.4 + - - +
85E ALA* 3.8 2.3 - - - +
86E GLY 2.9 23.2 + - - -
135E ARG* 4.4 27.4 - - + +
138E VAL* 4.4 4.4 - - + +
139E ALA* 4.1 35.7 - - + +
142E ALA* 4.3 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E ALA* 3.8 27.9 - - - +
73E LEU* 3.9 17.9 - - + +
74E ARG* 4.0 10.8 - - - +
78E TRP* 3.9 10.2 - - + -
79E ASP 2.7 21.6 + - - +
80E ALA* 3.2 8.9 + - - +
82E LEU* 1.3 73.6 - - - +
84E ASP* 1.3 57.0 + - - +
86E GLY* 3.4 0.7 + - - -
87E ALA* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 84 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E ILE* 4.4 2.3 - - - +
70E ALA* 4.7 7.8 - - + +
74E ARG* 5.7 2.0 - - - +
80E ALA 3.0 15.0 + - - +
81E ASP* 3.8 7.0 - - - +
82E LEU 3.3 0.2 - - - -
83E ALA* 1.3 78.2 - - - +
85E ALA* 1.3 57.6 + - - +
87E ALA* 3.4 4.6 + - - +
88E ARG* 3.0 52.0 + - - +
105E GLU* 5.8 0.3 - - - +
110E ALA* 4.3 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E ASP 3.0 17.2 + - - +
82E LEU* 4.1 4.3 - - - +
84E ASP* 1.3 77.8 - - - +
86E GLY* 1.3 58.2 + - - +
88E ARG* 3.3 11.3 + - - +
89E GLN* 2.9 36.4 + - + +
138E VAL* 4.2 4.3 - - + +
142E ALA* 3.9 30.1 - - + -
147E PRO* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E LEU* 4.3 11.9 - - - -
78E TRP* 4.4 2.5 - - - -
82E LEU 2.9 17.6 + - - -
83E ALA 3.8 0.9 - - - -
85E ALA* 1.3 76.3 - - - +
87E ALA* 1.3 58.7 + - - +
89E GLN* 3.1 7.2 + - - +
90E VAL* 3.0 30.5 + - - +
131E ALA* 4.1 3.8 - - - +
138E VAL* 3.7 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E ILE* 3.4 39.8 - - + +
69E ILE* 3.9 18.3 - - + +
70E ALA* 4.2 3.6 - - + +
73E LEU* 4.2 1.2 - - - +
83E ALA 2.9 17.8 + - - +
84E ASP 4.0 1.3 - - - +
86E GLY* 1.3 72.8 - - - +
88E ARG* 1.3 65.6 + - - +
90E VAL* 3.0 21.9 + - - +
91E VAL* 3.3 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E ILE* 4.6 11.2 - - + -
84E ASP* 3.0 43.6 + - - +
85E ALA* 3.6 10.1 - - - +
86E GLY 3.2 0.2 - - - -
87E ALA* 1.3 76.6 - - - +
89E GLN* 1.3 60.7 + - + +
91E VAL* 3.4 10.8 - - + +
92E LEU* 2.9 36.4 + - + +
102E LEU* 4.1 12.9 - - + +
105E GLU* 3.3 19.6 + - - -
111E PRO* 3.2 37.3 - - - +
147E PRO* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E ALA* 2.9 25.2 + - + +
86E GLY* 3.1 10.9 + - - +
88E ARG* 1.3 78.1 - - - +
90E VAL* 1.3 63.6 + - - +
92E LEU* 3.9 7.3 - - - +
93E SER* 2.9 28.6 + - - -
138E VAL* 4.3 17.5 - - + -
141E GLU* 4.3 10.2 + - + +
142E ALA* 5.4 0.6 - - - +
147E PRO* 3.2 38.8 - - - +
148E LYS 2.7 26.7 + - - +
149E GLY* 3.9 1.4 - - - -
150E ILE* 3.8 9.0 + - + +
151E LEU* 3.3 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E ILE* 3.9 27.6 - - + -
86E GLY 3.0 15.6 + - - +
87E ALA* 3.0 13.0 + - - +
89E GLN* 1.3 77.7 - - - +
91E VAL* 1.3 60.5 + - + +
93E SER* 3.1 7.7 + - - -
94E VAL* 3.1 25.6 - - - +
127E LEU* 4.4 25.1 - - + +
131E ALA* 3.5 25.1 - - + +
151E LEU* 4.4 4.9 - - + -
156E ILE* 3.9 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E ILE* 4.0 18.2 - - + -
66E ILE* 3.7 39.9 - - + -
69E ILE* 5.7 1.3 - - + -
87E ALA 3.3 4.4 + - - +
88E ARG* 3.4 12.1 - - - +
90E VAL* 1.3 83.9 - - + +
92E LEU* 1.3 65.9 + - + +
93E SER 3.4 0.2 - - - -
94E VAL* 3.9 6.2 + - - +
99E GLY* 3.9 0.2 - - - -
100E ILE* 3.1 43.6 + - + +
102E LEU* 4.3 15.3 - - + -
113E THR* 4.5 5.6 - - + -
117E PHE* 5.2 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E ARG* 2.9 22.7 + - + +
89E GLN* 3.9 17.7 - - - +
90E VAL 3.3 0.4 - - - -
91E VAL* 1.3 80.7 - - + +
93E SER* 1.3 59.3 + - - +
94E VAL 3.3 2.1 + - - -
98E SER* 2.8 34.9 - - - +
99E GLY* 4.0 16.6 - - - +
100E ILE 5.3 2.7 - - - +
102E LEU* 6.1 4.5 - - + -
147E PRO* 3.1 35.0 - - + +
148E LYS* 4.5 2.2 - - - -
149E GLY* 3.9 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E GLN 2.9 17.7 + - - -
90E VAL 3.1 10.6 + - - -
91E VAL 3.4 0.2 - - - -
92E LEU* 1.3 77.0 - - - +
94E VAL* 1.3 56.6 + - - +
98E SER 5.3 0.2 - - - -
149E GLY* 3.5 22.0 - - - +
151E LEU* 3.6 25.8 - - - +
153E ALA* 3.7 20.4 - - - +
156E ILE* 3.1 19.3 - - - +
----------------------------------------------------------
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