Contacts of the helix formed by residues 74 - 89 (chain E) in PDB entry 1JT6
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 74 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E LYS* 1.3 91.8 - - + +
75E ASN* 1.3 59.9 + - - +
76E ARG* 3.6 6.4 + - - +
77E GLU* 2.8 46.4 + - - +
78E LYS* 2.9 28.6 + - - +
139E GLU* 3.2 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E LYS 5.5 0.6 + - - -
74E THR* 1.3 69.4 - - - +
76E ARG* 1.3 64.9 + - - +
77E GLU 2.9 2.0 - - - -
78E LYS* 4.0 19.4 - - - +
79E PHE* 3.0 24.3 + - - +
129E VAL* 5.8 0.5 - - - +
130E ILE* 3.4 33.3 - - + +
133E GLU* 3.4 30.1 + - - +
134E GLY 3.7 12.2 - - - +
137E ASN* 4.1 6.5 - - - +
139E GLU* 2.6 31.0 + - - +
140E TRP* 3.8 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E THR* 3.2 6.3 - - - +
75E ASN* 1.3 76.8 - - - +
77E GLU* 1.3 63.5 + - - +
79E PHE* 3.7 4.4 - - - +
80E TYR* 3.1 69.2 + - - -
139E GLU* 2.9 19.2 + - + +
140E TRP* 3.7 17.4 - - + -
180E GLN* 5.1 7.1 - - - +
183E LEU* 4.0 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E ALA* 3.5 14.7 - - + +
73E LYS* 2.9 21.4 + - - +
74E THR* 2.8 50.5 + - - +
75E ASN 2.9 0.2 - - - -
76E ARG* 1.3 81.7 - - - +
78E LYS* 1.3 62.2 + - - +
79E PHE 3.1 1.8 - - - -
80E TYR* 3.1 9.4 + - + +
81E LEU* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E TRP* 3.1 12.0 - - + -
69E GLN* 3.4 50.8 + - + +
70E ILE* 5.3 3.0 - - - +
72E ALA* 2.8 34.2 + - + +
73E LYS 3.5 13.7 + - - -
74E THR 2.9 15.4 + - - +
75E ASN* 3.7 23.5 + - - +
77E GLU* 1.3 75.3 - - - +
79E PHE* 1.3 56.3 + - - +
81E LEU* 4.4 0.9 - - - -
82E TYR* 2.8 33.4 + - - +
130E ILE* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E ASN 3.0 15.5 + - - +
76E ARG* 3.7 6.3 - - - +
78E LYS* 1.3 74.7 - - - +
80E TYR* 1.3 64.1 + - - +
82E TYR* 4.0 0.8 - - - +
83E ASN* 3.2 48.6 + - - -
127E TYR* 3.4 37.0 - + - -
130E ILE* 4.1 16.1 - - + +
131E PHE* 3.8 19.7 - + - -
140E TRP* 5.1 0.7 - - + -
152E ALA* 4.1 6.7 - - + -
156E VAL* 5.3 0.2 - - + -
178E PHE* 4.7 5.2 - + - -
179E SER* 4.1 17.9 - - - -
182E PHE* 3.7 28.0 - + + -
183E LEU* 3.5 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E ARG* 3.1 59.3 + - - -
77E GLU* 3.1 10.4 + - + +
79E PHE* 1.3 76.0 - - - +
81E LEU* 1.3 67.8 + - - +
83E ASN* 3.3 4.9 + - - +
84E GLU* 3.1 23.3 + - - +
175E MET* 5.5 0.7 - - - +
176E ASN* 3.4 45.1 - - + +
179E SER* 3.5 18.5 + - - -
180E GLN* 3.0 37.0 + - - +
183E LEU* 3.7 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E TRP* 4.2 9.2 - - + -
68E GLU* 3.5 35.7 - - + +
69E GLN* 4.6 0.7 - - - -
71E LYS* 4.2 13.5 - - + -
72E ALA* 4.3 13.5 - - + -
77E GLU 3.0 16.4 + - - +
78E LYS* 3.8 5.2 - - - +
80E TYR* 1.3 78.1 - - - +
82E TYR* 1.3 58.6 + - - +
84E GLU* 3.0 20.0 + - - +
85E LEU* 2.8 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E TRP* 3.2 40.4 + + - -
65E TRP* 3.4 43.2 - + + -
78E LYS 2.8 20.2 + - - +
79E PHE* 4.0 4.0 - - - +
80E TYR 3.3 0.2 - - - -
81E LEU* 1.3 77.8 - - - +
83E ASN* 1.3 64.4 + - - +
85E LEU* 3.3 5.0 + - - +
86E SER* 3.1 32.5 + - - -
93E TYR* 3.4 10.2 + - - -
123E TYR* 4.3 8.0 + - - +
126E ALA* 3.8 26.1 - - + +
127E TYR* 3.2 46.5 - + - -
130E ILE* 4.5 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E PHE* 3.2 33.7 + - - +
80E TYR 3.9 1.8 - - - +
82E TYR* 1.3 78.0 - - - +
84E GLU* 1.3 61.8 + - - +
86E SER* 3.6 12.4 - - - -
87E LEU* 3.9 2.4 + - - +
127E TYR* 2.7 44.1 + - - -
156E VAL* 3.5 15.3 - - + +
175E MET* 3.3 42.3 - - + +
178E PHE* 4.1 1.4 - - - -
179E SER* 3.1 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E TYR 3.1 12.6 + - - +
81E LEU* 3.0 24.8 + - - +
83E ASN* 1.3 74.4 - - - +
85E LEU* 1.3 70.7 + - - +
86E SER 3.1 0.9 - - - -
87E LEU* 2.9 23.3 + - + +
88E THR* 3.6 7.7 + - - +
172E ILE* 3.7 39.6 - - + +
175E MET* 4.3 5.8 - - + +
176E ASN* 3.8 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E TRP* 4.1 20.2 - - + -
64E GLN* 5.3 7.6 - - + +
65E TRP* 3.6 29.6 - - + -
68E GLU* 3.3 40.2 - - + +
81E LEU* 2.8 29.5 + - + +
82E TYR 3.5 8.1 - - - +
84E GLU* 1.3 79.9 - - + +
86E SER* 1.3 53.7 + - - +
88E THR* 2.7 33.4 + - - +
89E THR* 2.8 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E TRP* 4.0 2.8 - - - -
82E TYR* 3.1 23.4 + - - -
83E ASN* 3.6 13.0 - - - -
84E GLU 3.1 0.2 - - - -
85E LEU* 1.3 77.3 - - - +
87E LEU* 1.3 59.0 + - - +
88E THR 3.3 0.4 + - - -
89E THR* 3.9 8.3 - - - +
93E TYR* 3.0 51.7 + - - +
156E VAL* 4.3 5.2 - - - +
160E VAL* 3.6 26.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E ASN 3.9 9.2 - - - +
84E GLU* 2.9 12.3 + - - +
86E SER* 1.3 77.7 - - - +
88E THR* 1.3 61.6 + - + +
89E THR 5.0 1.5 - - - +
159E ILE* 4.7 2.5 - - + +
160E VAL* 3.7 26.5 - - + +
163E THR* 4.5 2.2 - - - +
164E HIS* 5.4 1.0 + - - -
168E ILE* 4.2 10.0 - - + +
171E ARG* 2.9 83.9 + - + +
172E ILE* 3.8 13.5 - - + +
175E MET* 3.6 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 5.1 8.6 - - - +
84E GLU 4.3 6.7 - - - +
85E LEU* 2.7 28.1 + - - +
87E LEU* 1.3 78.8 - - + +
89E THR* 1.3 68.3 + - - +
90E GLU* 3.6 1.4 + - - +
168E ILE* 3.8 26.0 - - + -
172E ILE* 4.7 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E TRP* 3.5 19.0 - - + -
64E GLN* 2.4 38.1 + - - +
85E LEU* 2.8 13.9 + - - +
86E SER* 3.9 5.5 - - - +
87E LEU 5.0 1.2 - - - +
88E THR* 1.3 82.5 + - - +
90E GLU* 1.3 61.7 + - - +
91E TYR* 3.2 27.6 + - - +
93E TYR* 3.8 16.2 - - + +
94E PRO* 4.2 10.4 - - - +
----------------------------------------------------------
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