Contacts of the helix formed by residues 56 - 70 (chain F) in PDB entry 4LQL
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 56 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F PRO* 4.8 11.0 - - + -
55F THR* 1.3 92.9 + - + +
57F ALA* 1.3 60.1 + - - +
58F ASP* 3.1 8.5 - - - +
59F SER* 2.3 48.9 + - - -
60F ILE* 3.2 12.6 + - - +
88F ASN* 4.4 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F THR* 1.3 72.2 - - - +
58F ASP* 1.3 53.2 + - - +
59F SER 3.3 0.2 - - - -
60F ILE 4.3 0.7 - - - -
61F THR* 2.7 30.7 + - - -
87F LYS 4.9 2.2 - - - +
88F ASN* 3.3 48.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 58 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A HIS* 4.3 21.2 + - - -
177A LYS* 5.4 6.8 + - - -
56F THR* 3.1 6.7 - - - +
57F ALA* 1.3 78.1 - - - +
59F SER* 1.3 60.2 + - - +
61F THR* 4.0 10.4 - - - +
62F LYS* 3.6 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F VAL 5.6 0.9 - - - -
54F ALA* 3.4 19.9 - - - +
55F THR 3.7 0.6 + - - -
56F THR* 2.3 50.1 + - - -
58F ASP* 1.3 78.9 - - - +
60F ILE* 1.3 67.8 + - - +
61F THR 3.0 1.3 - - - -
62F LYS* 3.4 2.9 + - - +
63F PHE* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 60 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F VAL* 5.0 4.3 - - + -
54F ALA* 3.7 22.4 - - + +
55F THR 5.4 1.3 - - - -
56F THR 3.2 17.7 + - - +
59F SER* 1.3 74.5 - - - +
61F THR* 1.3 65.8 + - - +
63F PHE* 3.7 6.1 - - + +
64F MET* 3.3 25.7 + - + +
88F ASN* 3.1 32.1 - - + +
89F TRP* 3.4 70.2 - - + +
92F GLY* 4.1 6.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A HIS* 6.1 4.0 - - + -
57F ALA 2.7 24.7 + - - -
58F ASP* 4.0 14.4 - - - +
60F ILE* 1.3 82.3 - - - +
62F LYS* 1.3 54.0 + - + +
64F MET* 3.2 3.1 + - - +
65F LYS* 2.7 42.4 + - + +
88F ASN 5.0 1.1 + - - -
91F ARG* 4.2 21.6 - - + +
92F GLY* 4.3 10.7 + - - +
95F LEU* 5.2 8.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ASP* 6.0 2.0 - - - +
58F ASP 3.6 13.5 + - - +
59F SER* 3.4 5.2 + - - +
61F THR* 1.3 76.3 - - + +
63F PHE* 1.3 55.9 + - - +
65F LYS* 3.5 11.1 - - + +
66F GLU* 2.5 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 63 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F TRP* 4.3 17.3 - + + -
12F VAL* 3.9 27.6 - - + -
51F LYS* 6.2 3.8 - - + -
52F LEU* 5.5 6.7 - - + +
59F SER 3.2 17.7 + - - +
60F ILE* 3.7 9.9 - - + +
62F LYS* 1.3 70.2 - - - +
64F MET* 1.3 58.6 + - + +
66F GLU* 2.6 27.5 + - - +
67F ALA* 2.6 19.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 64 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F ILE* 3.3 17.0 + - + +
61F THR 3.2 8.4 + - - +
63F PHE* 1.3 83.4 - - + +
65F LYS* 1.3 56.9 + - - +
67F ALA* 3.4 13.1 + - - +
68F ASN* 2.5 31.6 + - - -
76F VAL* 6.1 2.0 - - + -
89F TRP* 6.4 1.3 - - + -
92F GLY* 3.7 33.9 - - - +
93F THR 4.3 0.9 - - - +
95F LEU* 5.1 2.5 - - + -
96F LEU* 4.0 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASN 4.3 19.0 - - - +
69A TYR* 4.3 13.9 - - + +
71A ASP* 4.7 14.6 - - - +
61F THR* 2.7 27.9 + - + +
62F LYS* 3.5 16.4 - - + +
64F MET* 1.3 74.0 - - - +
66F GLU* 1.3 65.2 + - - +
67F ALA 3.4 0.2 + - - -
68F ASN* 3.5 20.8 - - - +
69F TYR* 3.8 4.2 + - - +
95F LEU* 5.0 11.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 4.1 28.2 - - + +
10F TRP* 4.2 16.8 - - + -
62F LYS 2.5 24.5 + - - +
63F PHE* 2.6 10.6 + - - +
65F LYS* 1.3 69.1 - - - +
67F ALA* 1.3 66.7 + - - +
69F TYR* 3.8 2.6 + - - +
70F ASN* 3.3 18.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F TRP* 3.7 22.7 - - + -
63F PHE* 2.6 14.6 + - + +
64F MET* 3.5 13.0 - - - +
65F LYS 3.3 0.2 - - - -
66F GLU* 1.3 68.4 - - - +
68F ASN* 1.3 69.8 + - - +
70F ASN* 2.7 26.5 + - - +
73F VAL* 3.8 16.4 - - + -
76F VAL* 4.8 15.7 - - + -
96F LEU* 5.5 4.0 - - + -
98F LYS* 4.0 6.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 68 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LYS* 4.6 10.5 - - + +
68A ASN* 6.3 3.8 - - + -
64F MET 2.5 27.9 + - - -
65F LYS* 3.5 12.6 - - - +
67F ALA* 1.3 76.3 - - - +
69F TYR* 1.3 63.3 + - - +
71F ASP* 4.0 7.6 + - - +
95F LEU* 3.5 18.6 + - - +
96F LEU* 4.7 1.5 - - - +
97F GLN* 3.1 42.4 + - + +
98F LYS* 3.6 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 69 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LYS* 3.9 17.0 - - + +
66A GLU* 3.3 46.7 - - + +
69A TYR* 3.6 51.6 - + + -
65F LYS 3.8 3.1 + - - +
66F GLU 4.4 0.7 - - - +
67F ALA 3.0 2.0 + - - -
68F ASN* 1.3 73.8 - - - +
70F ASN* 1.3 59.1 + - + +
71F ASP* 2.5 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 70 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F TRP* 4.1 22.0 - - + -
66F GLU* 3.3 13.4 + - + +
67F ALA 2.7 17.0 + - - +
69F TYR* 1.3 73.8 - - - +
71F ASP* 1.3 51.2 + - - +
72F ASP* 2.8 26.6 + - - -
73F VAL* 2.9 29.6 + - + +
98F LYS* 4.1 0.2 + - - -
----------------------------------------------------------
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