Contacts of the strand formed by residues 59 - 66 (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 LEU 59 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 3.7 23.8 - - + -
50A LYS* 4.5 11.0 - - + +
51A ALA 3.4 7.2 - - - +
52A GLN* 3.6 28.7 - - + +
57A SER 4.2 3.6 - - - +
58A VAL* 1.3 79.0 - - - +
60A ALA* 1.3 62.7 + - - +
95A LEU* 3.6 10.4 - - - +
109A GLU* 5.3 0.2 - - - +
110A PHE* 3.4 52.8 + - + +
112A ALA* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TRP* 3.7 22.7 - - + -
50A LYS* 3.6 4.3 - - - +
51A ALA* 2.8 33.6 + - + +
59A LEU* 1.3 76.8 - - - +
61A ALA* 1.3 59.7 + - - +
95A LEU* 3.7 8.7 - - + -
107A LEU* 3.9 21.3 - - + -
108A ILE 3.3 12.6 - - - +
110A PHE* 3.8 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 3.7 15.3 - - + -
48A VAL* 4.1 7.4 - - + -
49A TYR 3.4 5.2 - - - -
60A ALA* 1.3 73.4 - - - +
62A ALA* 1.3 59.5 + - - +
63A LYS* 3.9 0.7 - - + -
106A ILE 3.4 2.3 - - - +
107A LEU* 3.4 4.0 - - - -
108A ILE* 2.9 35.3 + - + +
110A PHE* 4.2 3.0 - - - +
1314A DKI 3.5 47.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ILE* 5.7 0.2 - - + -
48A VAL* 3.4 5.5 - - - +
49A TYR* 2.8 51.0 + - + +
51A ALA* 4.1 10.5 - - + -
61A ALA* 1.3 71.2 - - - +
63A LYS* 1.3 62.9 + - - +
64A VAL* 3.7 1.9 + - + -
105A TRP* 4.4 20.0 - - + -
106A ILE 3.5 4.7 - - - -
107A LEU* 4.0 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 5.2 9.5 - - - +
47A LYS 4.6 4.3 - - - -
48A VAL* 4.3 6.8 - - + +
61A ALA 3.9 1.1 - - - +
62A ALA* 1.3 73.0 - - - +
64A VAL* 1.3 59.5 + - - +
65A ILE* 4.1 17.7 - - + +
79A GLU* 3.6 24.7 + - - +
104A LEU 3.5 0.8 - - - +
105A TRP* 3.2 7.1 - - - +
106A ILE* 2.9 52.7 + - + +
108A ILE* 3.5 30.1 - - + -
173A ASP* 4.9 5.9 + - - +
175A GLY* 6.2 0.2 - - - -
1314A DKI 3.8 38.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE 3.5 11.5 - - - +
46A GLY* 4.7 2.9 - - - -
47A LYS 3.9 12.1 + - - +
49A TYR* 3.7 34.1 - - + -
62A ALA 3.7 3.3 + - - +
63A LYS* 1.3 77.2 - - - +
65A ILE* 1.3 62.1 + - - +
66A ASP 3.9 1.7 + - - -
103A ASN* 3.8 21.5 - - + +
104A LEU 3.5 2.0 - - - -
105A TRP* 3.8 50.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 3.9 28.7 - - + +
63A LYS* 4.5 16.8 - - + +
64A VAL* 1.3 80.0 - - - +
66A ASP* 1.3 69.9 + - - +
67A THR* 3.2 2.0 + - + +
76A TYR* 3.7 54.7 - - + +
79A GLU* 5.5 0.7 - - - +
103A ASN* 3.2 6.0 - - - -
104A LEU* 2.9 47.3 + - + +
106A ILE* 4.2 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE 4.6 3.2 + - - -
64A VAL 3.9 3.0 + - - -
65A ILE* 1.3 77.6 - - - +
67A THR* 1.3 73.1 + - - +
68A LYS* 4.1 3.9 + - - +
72A GLU* 4.0 5.9 - - - +
76A TYR* 4.7 1.9 + - - -
102A ASN* 3.8 7.8 - - - +
103A ASN* 3.3 16.5 + - - +
----------------------------------------------------------
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