Contacts of the helix formed by residues 57 - 69 (chain A) in PDB entry 2L8K
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 ASP 57 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 5.2 1.9 - - - +
55A ASP* 3.7 13.6 + - - +
56A ARG* 1.3 83.8 - - - +
58A ALA* 1.3 62.7 + - - +
59A ALA* 3.2 2.9 - - + +
60A ARG* 3.8 41.8 + - + +
61A SER* 2.9 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLN 6.1 0.9 - - - -
55A ASP 5.1 2.0 + - - -
56A ARG 3.4 6.5 + - - +
57A ASP* 1.3 69.3 - - - +
59A ALA* 1.3 59.7 + - - +
61A SER* 2.5 24.2 + - - -
62A ARG* 3.4 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASP* 3.2 2.8 - - + +
58A ALA* 1.3 76.7 - - - +
60A ARG* 1.3 65.2 + - - +
62A ARG* 3.3 21.8 + - - +
63A ARG* 3.7 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 2.8 40.5 + - - -
14A PHE* 6.4 2.5 - - + -
55A ASP* 4.9 3.6 - - - +
57A ASP* 3.4 34.4 + - + +
59A ALA* 1.3 75.7 - - - +
61A SER* 1.3 62.0 + - - +
63A ARG* 2.9 20.4 + - + +
64A LEU* 2.7 35.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.4 34.4 + - - -
53A GLN* 4.7 2.0 + - - -
55A ASP* 4.8 2.4 + - - -
57A ASP 2.9 15.0 + - - -
58A ALA* 2.5 31.4 + - - -
60A ARG* 1.3 73.3 - - - +
62A ARG* 1.3 48.4 + - - +
64A LEU* 3.5 12.6 - - - +
65A MET* 2.6 47.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ALA 3.6 13.2 - - - +
59A ALA* 3.3 13.6 + - - +
60A ARG 3.1 0.6 - - - -
61A SER* 1.3 79.7 + - - +
63A ARG* 1.3 62.7 + - + +
65A MET* 3.5 11.0 - - + +
66A ALA* 3.2 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ALA 3.7 6.7 + - - +
60A ARG* 2.9 17.3 + - + +
62A ARG* 1.3 82.5 - - + +
64A LEU* 1.3 64.8 + - + +
66A ALA* 3.4 5.3 + - - +
67A LYS* 3.3 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 3.5 33.7 - - + +
17A LEU* 5.5 3.1 - - + -
18A SER* 5.5 9.2 - - - +
21A LEU* 3.5 17.3 - - + +
52A LEU* 3.4 32.8 - - + -
55A ASP* 5.3 0.4 - - - +
60A ARG* 2.7 41.3 - - + +
61A SER* 3.5 14.1 - - - +
63A ARG* 1.3 74.4 - - + +
65A MET* 1.3 58.7 - - - +
66A ALA 3.1 2.7 - - - -
67A LYS* 2.9 15.9 + - - +
68A LEU* 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASN* 3.3 27.8 - - - +
52A LEU* 3.5 24.2 - - + -
53A GLN* 3.2 41.7 - - + +
61A SER* 2.6 34.9 + - - +
62A ARG* 3.5 15.3 - - + +
64A LEU* 1.3 74.2 - - - +
66A ALA* 1.3 59.3 + - - +
68A LEU* 3.7 3.5 + - - +
69A ALA* 3.4 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 3.2 16.3 + - - +
63A ARG* 3.8 8.5 - - - +
64A LEU 3.1 0.8 - - - -
65A MET* 1.3 76.7 - - - +
67A LYS* 1.3 65.3 + - - +
68A LEU 3.2 0.4 - - - -
69A ALA* 3.2 21.3 + - - +
70A ASP* 3.8 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER* 3.7 18.0 + - - +
21A LEU* 3.6 39.6 - - + +
22A ASP* 3.7 29.7 + - - +
63A ARG* 3.3 23.3 + - - +
64A LEU* 2.9 17.2 + - - +
66A ALA* 1.3 78.6 - - - +
68A LEU* 1.3 61.7 + - - +
70A ASP* 3.5 14.6 + - - +
71A PHE* 4.0 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.8 1.1 - - + -
21A LEU* 3.4 23.1 - - + +
45A ARG* 3.4 32.5 - - + +
48A LEU* 3.7 16.4 - - + -
49A ASN* 3.2 59.9 - - + +
52A LEU* 4.4 6.7 - - + -
64A LEU 2.8 14.9 + - - +
65A MET 3.9 4.3 - - - +
67A LYS* 1.3 75.6 - - - +
69A ALA* 1.3 57.2 + - - +
70A ASP 2.9 5.6 - - - -
71A PHE* 2.7 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ARG* 5.0 7.3 + - - +
65A MET 3.4 11.7 + - - +
66A ALA* 3.2 18.1 + - - +
68A LEU* 1.3 82.3 - - - +
70A ASP* 1.3 61.9 + - - +
71A PHE 3.3 1.3 + - - +
----------------------------------------------------------
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