Contacts of the strand formed by residues 46 - 53 (chain A) in PDB entry 2J51
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 GLY 46 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASP* 3.6 4.7 - - - -
43A GLY* 2.7 40.2 + - - -
44A ALA 3.2 2.2 + - - -
45A PHE* 1.3 79.9 - - - +
47A LYS* 1.3 61.7 + - - -
48A VAL* 4.0 3.9 + - - +
64A VAL 4.7 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLU* 4.8 11.2 - - - +
41A GLY 3.6 12.8 - - - +
42A ASP* 4.0 12.0 + - + +
46A GLY* 1.3 75.1 - - - -
48A VAL* 1.3 61.9 + - - +
49A TYR* 4.1 33.0 - - + +
63A LYS* 4.6 0.2 - - - -
64A VAL 3.9 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLU* 3.7 4.2 - - - +
40A LEU* 2.9 30.0 + - + -
41A GLY* 3.1 24.2 + - - +
42A ASP* 5.0 1.6 - - - +
43A GLY 5.6 0.9 - - - +
46A GLY 4.7 5.6 - - - +
47A LYS* 1.3 76.8 - - - +
49A TYR* 1.3 67.5 + - - +
61A ALA* 4.1 13.0 - - + -
62A ALA 3.4 17.0 - - - +
63A LYS* 4.3 11.0 - - + +
1314A DKI 3.2 39.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ILE* 3.7 42.2 - - + -
38A GLY 3.3 16.2 - - - +
39A GLU* 3.9 26.8 + - + -
40A LEU* 3.8 5.5 - - - +
47A LYS* 4.1 24.4 - - + +
48A VAL* 1.3 74.3 - - - +
50A LYS* 1.3 60.7 + - - +
61A ALA* 3.4 5.2 - - - -
62A ALA* 2.8 40.6 + - + +
64A VAL* 3.7 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ILE* 3.5 3.8 - - - -
37A ILE* 2.7 67.1 + - + +
38A GLY* 2.9 17.2 + - - +
40A LEU* 3.7 27.9 - - + +
49A TYR* 1.3 71.7 - - - +
51A ALA* 1.3 57.2 + - - +
59A LEU* 4.5 12.2 - - + +
60A ALA 3.6 4.9 - - - +
110A PHE* 3.7 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TRP* 4.2 12.1 - - + -
35A GLU 3.3 10.3 - - - +
36A ILE* 4.7 4.9 - - + -
37A ILE* 4.4 2.5 - - - -
49A TYR 3.7 0.2 + - - -
50A LYS* 1.3 74.9 - - - +
52A GLN* 1.3 60.5 + - - +
53A ASN 4.4 0.2 - - - -
59A LEU* 3.4 9.0 - - - +
60A ALA 2.8 36.0 + - - +
62A ALA* 4.1 12.1 - - + -
105A TRP* 6.0 0.9 - - + -
107A LEU* 4.0 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TRP* 3.7 3.8 - - - -
35A GLU* 2.7 49.6 + - + +
37A ILE* 3.8 24.0 - - + +
51A ALA* 1.3 75.7 - - - +
53A ASN* 1.3 67.4 + - - +
54A LYS* 3.3 1.2 + - - -
57A SER* 3.4 41.3 + - - +
58A VAL 3.6 2.5 - - - -
59A LEU* 3.6 16.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.6 12.0 + - - +
34A TRP* 3.3 46.5 - - + +
52A GLN* 1.3 71.2 - - - +
54A LYS* 1.3 63.9 + - - +
55A GLU* 3.0 16.3 + - - +
56A THR* 2.9 47.1 + - - +
57A SER* 2.8 28.2 + - - -
58A VAL* 2.9 14.1 + - + +
96A ASP* 5.4 0.8 + - - -
----------------------------------------------------------
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