Contacts of the helix formed by residues 78 - 92 (chain E) in PDB entry 3LUE
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 ASN 78 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E ARG* 4.4 15.8 - - - +
69E TYR* 2.7 43.7 + - - +
70E PRO* 3.6 14.3 + - + +
76E VAL* 3.5 10.4 - - - +
77E THR* 1.3 85.1 + - - +
79E TRP* 1.3 60.0 + - - +
80E ASP* 3.9 3.4 + - - +
81E ASP* 3.0 8.4 + - - +
82E MET* 3.1 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E VAL* 3.7 43.7 + - + -
77E THR 4.1 5.3 + - - -
78E ASN* 1.3 74.6 - - - +
80E ASP* 1.3 65.2 + - - +
82E MET* 3.6 5.6 + - + +
83E GLU* 3.0 29.6 + - - +
86E TRP* 4.1 20.9 - + - -
115E ASN* 4.1 34.5 - - + +
118E LYS* 3.4 48.5 - - + +
119E MET* 4.2 13.2 - - + -
122E ILE* 3.5 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E LEU 4.4 11.4 - - - +
68E LYS* 5.2 1.1 - - - -
69E TYR* 1.3 67.0 - - + +
78E ASN* 3.6 4.2 + - - -
79E TRP* 1.3 79.2 + - - +
81E ASP 1.3 47.2 - - - +
83E GLU* 4.0 12.6 - - + +
118E LYS* 5.7 0.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
34E ILE* 1.7 50.9 - - + +
62E ARG* 4.8 0.4 + - - -
67E LEU* 3.2 31.0 - - - +
69E TYR* 0.4 442.2 + - + +
70E PRO* 4.2 0.2 - - - -
78E ASN* 2.9 9.7 + - - +
80E ASP* 1.3 65.9 - - - +
82E MET* 1.3 51.4 + - - +
84E LYS* 3.4 0.2 - - - +
85E ILE* 3.1 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ASN* 3.2 27.6 - - - +
17E CYS* 4.7 0.4 - - - -
69E TYR* 2.3 2.0 - - - -
70E PRO* 3.8 7.9 - - + +
71E ILE* 3.4 38.1 - - + -
76E VAL* 3.5 24.0 - - + -
78E ASN 3.1 19.5 + - - +
79E TRP* 3.9 7.9 - - + +
81E ASP* 1.3 73.9 - - - +
83E GLU* 1.3 63.4 + - - +
85E ILE* 2.8 43.4 + - + +
86E TRP* 3.1 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E TYR* 2.8 21.3 - - + +
79E TRP* 3.0 21.7 + - - +
80E ASP* 3.3 10.7 - - - +
82E MET* 1.3 74.6 - - - +
84E LYS* 1.3 64.1 + - - +
86E TRP* 3.3 10.0 + - - +
87E HIS* 3.1 21.1 + - - +
118E LYS* 4.5 6.2 + - - -
122E ILE* 3.9 37.0 - - + +
126E THR* 3.9 23.0 + - - +
127E PHE* 4.0 6.0 - - + -
120N LYS* 5.4 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E ILE* 2.7 25.7 - - + +
35E VAL* 2.6 20.6 + - - +
67E LEU 2.9 5.2 - - - -
68E LYS* 0.4 253.1 + - + +
69E TYR* 0.8 211.2 - - + +
83E GLU* 1.3 64.4 - - - +
85E ILE* 1.3 62.7 + - - +
86E TRP 3.2 0.3 + - - -
87E HIS 3.3 0.5 + - - -
88E HIS* 3.0 20.4 + - - +
122N VAL* 3.4 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E CYS* 3.9 16.4 - - - -
31E PHE* 4.0 12.8 - - + -
32E PRO 5.1 1.3 - - - +
33E SER* 4.2 31.4 - - - +
34E ILE* 5.1 11.7 - - + +
69E TYR* 4.8 0.7 - - + -
70E PRO* 3.6 26.0 - - + -
71E ILE* 5.0 0.2 - - + -
81E ASP 3.1 9.6 + - - +
82E MET* 2.8 35.0 + - + +
84E LYS* 1.3 75.6 - - - +
86E TRP* 1.3 61.1 + - + +
88E HIS* 3.2 9.5 + - - +
89E THR* 2.8 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E VAL* 3.7 20.7 - - + +
12E ASN* 2.9 38.1 + - - -
76E VAL* 5.6 1.6 - - + -
79E TRP* 4.1 17.3 - + - -
82E MET* 3.1 47.2 + - + +
83E GLU* 3.8 5.8 - - - +
85E ILE* 1.3 77.1 - - + +
87E HIS* 1.3 63.7 + - - +
89E THR* 2.8 28.8 + - - -
90E PHE* 3.1 15.9 + + + -
105E LEU* 4.4 10.8 - - + -
119E MET* 4.2 27.6 - - + -
122E ILE* 4.1 22.2 - - + -
123E MET* 3.5 28.5 - - + -
127E PHE* 3.9 12.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E TYR 4.6 2.4 + - - -
83E GLU 3.1 13.4 + - - +
84E LYS* 3.4 9.4 - - - +
86E TRP* 1.3 72.0 - - - +
88E HIS* 1.3 58.0 + - - +
90E PHE* 3.5 0.8 + - - -
91E TYR* 2.9 76.7 + + + +
92E ASN* 5.4 2.5 - - - -
127E PHE* 3.7 17.7 - - + -
118N GLY 5.6 0.9 - - - -
119N VAL* 4.4 8.5 - - + -
120N LYS* 4.0 44.9 + - + +
122N VAL* 4.2 7.9 - - + -
143N THR* 4.1 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E PHE* 4.2 21.6 - + - +
84E LYS 3.0 11.9 + - - +
85E ILE* 3.3 9.6 - - - +
87E HIS* 1.3 72.3 - - - +
89E THR* 1.3 58.7 + - - +
92E ASN* 3.0 46.8 + - + +
93E GLU* 2.7 65.3 + - - +
122N VAL* 4.3 18.8 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
10E VAL* 3.9 22.3 - - + +
19E ALA* 3.7 30.7 - - + -
31E PHE* 3.5 17.0 - - + -
85E ILE* 2.8 17.7 + - - +
86E TRP* 2.8 27.3 + - - -
88E HIS* 1.3 72.9 - - - +
90E PHE* 1.3 57.9 + - + +
93E GLU* 3.3 8.4 + - - +
94E LEU* 2.7 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E LEU* 3.3 34.3 - - + -
10E VAL* 4.5 17.5 - - + -
86E TRP* 3.1 30.0 + + + -
87E HIS* 4.1 2.2 - - - +
89E THR* 1.3 79.5 - - + +
91E TYR* 1.3 61.5 + + + +
94E LEU* 4.8 0.7 - - + -
95E ARG 2.8 30.7 + - - -
96E VAL* 2.8 24.1 + - + +
98E PRO* 3.6 32.3 - - + -
103E VAL* 4.0 17.5 - - + -
105E LEU* 5.6 0.4 - - + -
123E MET* 4.0 29.6 - - + -
127E PHE* 4.2 19.3 - + + -
142N TRP* 3.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E HIS* 2.9 69.9 + + + +
90E PHE* 1.3 65.3 - - + +
92E ASN* 1.3 65.0 + - - +
95E ARG* 4.6 0.2 - - - -
96E VAL 4.0 0.4 - - - -
98E PRO* 3.7 25.5 - - + +
99E GLU* 4.8 3.8 + - - -
127E PHE* 4.1 20.1 + + - -
142N TRP* 1.2 57.7 - - + +
143N THR* 4.6 6.3 - - + +
146N LEU* 1.0 129.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E HIS* 5.4 3.1 - - - -
88E HIS* 3.0 43.1 + - + +
91E TYR* 1.3 94.7 + - - +
93E GLU* 1.3 72.4 + - - +
95E ARG* 3.5 18.2 - - - +
43N TRP* 4.6 4.9 - - - -
47N GLN* 4.3 4.5 + - - +
122N VAL* 5.0 5.9 - - - +
124N ILE* 4.2 14.0 - - - +
139N GLY* 2.7 45.4 + - - -
142N TRP* 3.7 0.7 - - - -
143N THR* 3.3 9.8 + - - -
----------------------------------------------------------
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