Contacts of the helix formed by residues 65 - 72 (chain A) in PDB entry 5J6Y
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 65 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLY* 1.3 75.2 - - - -
66A HIS* 1.3 67.7 + - - +
67A LEU 3.3 2.9 - - - -
68A GLN* 3.3 25.2 + - + +
69A GLU* 2.9 43.8 + - - +
81A ASP* 5.1 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A SER 3.5 11.7 + - - -
59A SER* 3.0 27.5 + - - -
60A ASP 2.7 25.9 + - - +
61A VAL* 3.6 4.7 - - - +
63A LYS* 3.0 22.2 + - + +
64A GLY* 5.5 1.3 - - - -
65A THR* 1.3 83.4 + - - +
67A LEU* 1.3 57.4 + - - +
69A GLU* 3.2 25.6 + - - +
70A PHE* 2.9 30.5 + - - +
160A TYR* 3.2 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 3.6 53.8 - - + -
61A VAL* 3.3 20.3 + - + +
62A ALA* 5.8 0.2 - - - -
63A LYS 4.5 0.6 + - - -
64A GLY 4.9 1.3 + - - +
65A THR 3.3 0.6 - - - -
66A HIS* 1.3 77.9 - - - +
68A GLN* 1.3 63.4 + - - +
70A PHE* 3.2 16.1 + - + +
71A LEU* 2.9 52.3 + - + +
78A LEU* 4.3 15.9 - - + -
82A PRO* 3.9 21.1 - - + -
90A ILE* 4.8 5.4 - - + -
153A TRP* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLY 4.0 3.5 - - - +
65A THR* 3.3 35.2 - - + +
67A LEU* 1.3 84.6 + - - +
69A GLU* 1.3 64.1 + - + +
72A GLY* 3.0 20.1 + - - -
75A ALA* 3.4 21.8 - - + +
78A LEU* 3.9 23.6 - - + +
81A ASP* 3.0 42.3 + - - +
82A PRO* 4.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY* 5.0 1.8 + - - -
65A THR* 2.9 34.9 + - - +
66A HIS* 3.3 27.4 - - - +
67A LEU 3.2 0.2 - - - -
68A GLN* 1.3 76.3 - - + +
70A PHE* 1.3 64.8 + - - +
72A GLY* 3.3 12.5 + - - -
160A TYR* 4.5 5.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A SER 4.5 0.5 - - - +
54A TYR* 3.2 48.6 - + + -
55A GLY* 3.0 35.2 + - - +
61A VAL* 4.0 15.5 - - + -
66A HIS 2.9 16.5 + - - +
67A LEU* 3.5 7.2 - - + +
69A GLU* 1.3 78.4 - - - +
71A LEU* 1.3 75.5 + - + +
72A GLY* 3.4 0.7 + - - -
90A ILE* 4.5 6.3 - - + -
153A TRP* 3.4 51.8 - + - -
160A TYR* 3.6 23.0 - + + -
161A VAL* 4.0 4.5 - - - -
162A PHE* 3.9 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 3.8 34.1 - - + -
51A ASN 5.2 0.2 - - - +
53A SER 5.7 0.2 - - - -
54A TYR* 3.6 40.5 - - + -
67A LEU* 2.9 41.4 + - + +
70A PHE* 1.3 88.7 - - + +
72A GLY* 1.3 65.5 + - - +
73A SER* 3.1 2.4 + - - -
74A ASP* 3.0 19.2 + - + +
75A ALA* 3.9 15.9 - - + +
78A LEU* 4.0 27.6 - - + -
90A ILE* 4.9 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLN 3.0 13.4 + - - +
69A GLU* 3.3 8.7 + - - -
70A PHE 3.3 3.2 - - - -
71A LEU* 1.3 73.6 - - - +
73A SER* 1.3 57.2 + - - -
75A ALA* 2.9 26.2 + - - +
76A SER 4.4 1.2 + - - -
307A CA 4.4 11.9 - - - -
----------------------------------------------------------
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