Contacts of the helix formed by residues 69 - 74 (chain A) in PDB entry 1LK9
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 LEU 69 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLY 3.3 6.0 + - - +
67A LEU 3.0 1.4 - - - -
68A PHE* 1.4 114.2 - - + +
70A GLU* 1.3 67.1 + - - +
71A GLU 3.1 2.2 - - - -
72A TYR* 3.0 13.4 + - + +
73A TRP* 3.2 18.6 + - + +
232A HIS* 3.8 12.1 - - + +
251A LYS 4.7 1.6 - - - +
252A PHE 3.4 26.2 - - - +
253A THR* 3.5 27.6 - - - +
254A GLY* 3.8 4.5 - - - +
314A LEU* 3.7 21.1 - - + -
317A PHE* 3.9 19.1 - - + -
318A GLY* 4.3 0.2 - - - -
90B MET* 3.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 2.9 52.0 + - - +
27A PHE* 4.6 4.2 - - - -
67A LEU* 3.0 24.3 + - + +
69A LEU* 1.3 77.7 - - - +
71A GLU* 1.3 63.8 + - - +
73A TRP* 3.2 3.3 + - - +
74A LYS* 3.0 44.7 + - + +
407A THR* 5.6 1.4 - - - +
910A SO4 4.9 8.1 + - - +
87B TRP* 4.0 24.6 - - + +
90B MET* 3.6 21.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE 4.2 0.8 + - - -
69A LEU 3.1 0.2 - - - -
70A GLU* 1.3 81.5 - - - +
72A TYR* 1.4 62.0 + - - +
74A LYS* 3.5 13.7 + - - +
75A GLN* 3.2 36.7 + - - +
317A PHE* 3.5 17.9 - - + -
321A LYS* 2.8 38.6 + - - +
910A SO4 3.6 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.0 14.5 + - + +
71A GLU* 1.4 79.6 - - - +
73A TRP* 1.3 97.4 + + - +
75A GLN* 2.8 22.2 + - - +
76A HIS* 3.1 51.2 + + - -
299A GLU* 5.0 2.4 + - - +
300A VAL* 5.1 1.9 - - - -
303A MET* 3.8 8.3 - - - +
311A MET 3.8 8.5 - - - -
312A ARG 2.7 24.0 + - - -
314A LEU* 3.3 37.2 + - + +
317A PHE* 3.7 46.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.2 22.6 + - - +
70A GLU 3.2 6.6 + - - +
72A TYR* 1.3 105.1 - + - +
74A LYS* 1.3 59.5 + - - +
75A GLN 3.0 0.2 - - - -
76A HIS* 3.0 27.7 + - + -
77A LYS* 3.4 8.5 + - - -
80A SER* 3.5 22.7 - - - -
253A THR* 2.9 32.6 + - - +
255A HIS* 3.5 10.6 - + - -
296A VAL* 3.6 36.8 - - + -
299A GLU* 4.2 10.1 - - + -
300A VAL* 3.8 15.9 - - + -
314A LEU* 4.2 3.9 - - + +
86B PRO* 3.4 43.2 - - + +
87B TRP* 4.2 7.6 - - + -
90B MET* 3.7 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLY 4.5 6.3 + - - -
25A ARG* 4.3 14.8 - - - +
70A GLU* 3.0 41.8 + - + +
71A GLU* 3.8 9.4 - - - +
72A TYR 3.2 0.6 - - - -
73A TRP* 1.3 76.3 - - - +
75A GLN* 1.3 57.8 + - + +
76A HIS 3.4 0.2 - - - -
77A LYS* 3.1 35.8 + - + +
87B TRP* 3.7 47.3 - - + +
----------------------------------------------------------
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