Contacts of the helix formed by residues 91 - 104 (chain E) in PDB entry 3ECS
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 LYS 91 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E LEU* 3.6 28.0 - - + -
35E LYS 5.4 1.1 - - - -
37E ASP 3.6 15.5 + - - -
40E GLU* 4.3 9.9 - - - +
46E ARG* 3.3 34.4 - - - +
88E LYS* 4.5 16.0 - - - +
89E CYS* 2.6 12.2 + - - +
90E LYS* 1.3 78.4 - - - +
92E ILE* 1.3 56.5 + - - +
93E MSE 2.8 10.9 + - - +
94E ILE* 3.3 37.2 + - + +
95E GLU* 4.1 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E LEU 5.1 0.4 - - - +
89E CYS* 3.5 11.4 + - - +
90E LYS* 3.5 42.8 - - + +
91E LYS* 1.3 77.8 - - - +
93E MSE 1.3 63.7 + - - +
94E ILE 3.2 0.2 - - - -
95E GLU* 3.0 54.2 - - - +
96E ARG* 2.9 37.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E LEU* 4.1 20.1 - - + +
43E GLN* 5.6 4.9 - - - +
46E ARG* 4.6 27.8 - - + -
47E ALA* 6.0 4.9 - - + +
50E THR* 6.4 2.5 - - + -
73E LEU* 5.5 1.8 - - + +
76E ILE* 3.2 56.5 - - + +
77E SER* 5.3 1.8 - - - +
78E LEU 6.0 0.2 - - - +
90E LYS* 3.1 35.4 - - + +
91E LYS* 4.3 4.5 - - - -
92E ILE* 1.3 80.5 - - - +
94E ILE* 1.3 52.9 + - - +
96E ARG* 3.0 12.0 + - - +
97E GLY* 2.7 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E LEU* 3.9 8.9 - - + +
34E LEU* 3.3 24.0 - - + -
35E LYS* 3.5 61.2 - - + +
91E LYS* 3.3 31.8 + - + +
92E ILE 3.2 0.4 - - - -
93E MSE 1.3 77.6 - - - +
95E GLU* 1.3 57.1 + - - +
97E GLY* 3.4 1.2 + - - -
98E GLU* 3.1 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 95 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E LYS 4.1 1.2 + - - +
92E ILE* 3.0 50.9 + - + +
94E ILE* 1.3 77.2 - - - +
96E ARG* 1.3 78.8 + - - +
98E GLU* 3.6 11.7 + - - +
99E LEU* 3.2 20.6 + - - +
102E ARG* 4.7 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 96 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E PHE* 3.3 27.4 - - + +
76E ILE* 4.1 19.5 - - + -
78E LEU 4.4 13.3 + - - +
90E LYS* 5.3 0.4 - - - +
92E ILE* 2.9 66.7 + - - +
93E MSE 3.2 11.4 - - - +
95E GLU* 1.3 89.0 + - - +
97E GLY* 1.3 59.7 + - - +
99E LEU* 2.9 15.4 + - - +
100E PHE 2.8 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 97 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E LEU* 4.3 8.5 - - - +
72E PHE* 3.4 31.9 - - - -
76E ILE* 3.7 3.5 - - - +
93E MSE 2.7 18.9 + - - -
94E ILE 3.8 2.7 - - - -
95E GLU 3.3 0.2 - - - -
96E ARG* 1.3 74.4 - - - +
98E GLU* 1.3 55.4 + - - +
100E PHE* 3.3 3.7 + - - +
101E LEU* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E LEU* 3.7 9.7 - - + +
35E LYS* 2.8 39.9 + - - -
94E ILE* 3.1 24.5 + - - +
95E GLU* 4.0 10.3 - - - +
96E ARG 3.2 0.4 - - - -
97E GLY* 1.3 74.5 - - - +
99E LEU* 1.3 59.7 + - - +
101E LEU* 3.8 9.9 - - + +
102E ARG* 2.9 46.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E PHE* 3.9 20.6 - - + -
95E GLU 3.2 13.4 + - - +
96E ARG* 2.9 17.6 + - - +
98E GLU* 1.3 77.4 - - - +
100E PHE* 1.3 52.6 + - - +
102E ARG* 3.3 26.0 + - + +
103E ARG* 2.8 57.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 100 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E ILE* 3.7 26.9 - - + -
68E GLY 4.4 2.5 - - - -
71E LEU* 3.9 29.6 - - + -
72E PHE* 3.7 35.0 - + + -
75E PHE* 3.4 44.2 - + + -
96E ARG 2.8 8.6 + - - +
97E GLY* 3.6 6.5 - - - +
99E LEU* 1.3 77.8 - - - +
101E LEU* 1.3 55.3 + - - +
103E ARG* 3.5 6.1 + - + +
104E ILE* 3.1 50.8 + - + +
233E PHE* 5.0 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E VAL* 4.2 23.8 - - + +
27E ILE* 3.2 32.8 - - + -
28E ARG* 3.4 45.1 - - + +
31E LEU* 5.5 11.0 - - + -
97E GLY 2.9 16.4 + - - +
98E GLU* 3.9 11.7 - - + +
99E LEU 3.3 0.2 - - - -
100E PHE* 1.3 76.7 - - - +
102E ARG* 1.3 63.4 + - - +
104E ILE* 3.8 7.1 - - + +
105E SER* 3.5 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E GLU 4.7 2.8 + - - -
98E GLU* 2.9 32.5 + - - +
99E LEU* 3.6 39.2 - - + +
101E LEU* 1.3 78.7 - - - +
103E ARG* 1.3 63.5 + - + +
105E SER* 3.1 21.1 + - - -
106E LEU* 3.5 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E PHE* 5.1 8.6 - - - -
99E LEU* 2.8 41.7 + - + +
100E PHE* 3.7 9.6 - - + +
102E ARG* 1.3 81.1 - - + +
104E ILE* 1.3 61.7 + - + +
105E SER 3.4 0.7 + - - -
106E LEU* 3.7 17.7 + - - +
107E SER* 4.3 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E VAL* 3.4 43.7 - - + -
27E ILE* 5.3 2.0 - - + -
100E PHE* 3.1 49.8 + - + +
101E LEU* 3.8 15.7 - - + +
103E ARG* 1.3 74.2 - - + +
105E SER* 1.3 64.5 + - - +
106E LEU 3.1 7.7 + - - -
107E SER* 3.3 23.8 + - - +
108E ARG 5.2 0.2 + - - -
232E SER* 5.8 3.6 - - - +
233E PHE* 4.2 24.8 - - + +
----------------------------------------------------------
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