Contacts of the helix formed by residues 58 - 71 (chain A) in PDB entry 3BQY
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 ALA 58 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A MSE 4.7 3.4 - - - -
53A TYR* 4.5 6.1 - - - -
56A PHE* 3.1 8.8 + - - +
57A ALA* 1.3 78.5 - - + +
59A LYS* 1.3 65.1 + - - +
60A GLN* 3.2 13.5 - - + +
61A ASP* 3.0 30.2 + - - +
62A LEU 3.4 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 5.2 6.8 + - + +
34A ASP 5.9 0.8 + - - -
36A LEU* 3.4 31.3 + - + +
37A THR* 4.4 14.0 - - - +
38A MSE 4.1 33.3 - - + +
53A TYR* 4.9 1.4 - - - -
58A ALA* 1.3 73.0 - - - +
60A GLN* 1.3 57.4 + - - +
62A LEU* 3.1 11.0 + - + +
63A LEU* 2.9 47.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ALA* 3.2 9.4 - - + +
59A LYS* 1.3 78.0 - - - +
61A ASP* 1.3 69.5 + - - +
63A LEU* 3.7 13.3 - - + +
64A THR* 2.9 34.4 + - - +
115A HIS* 3.6 51.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 3.9 14.7 - - + -
57A ALA* 3.6 14.8 - - - +
58A ALA* 3.0 35.8 + - - +
60A GLN* 1.3 85.4 + - - +
62A LEU* 1.3 65.2 + - - +
64A THR* 3.4 7.6 + - - +
65A ALA* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A THR* 4.3 7.6 - - + -
21A VAL* 4.4 6.5 - - + -
24A ALA* 4.1 22.4 - - + -
36A LEU* 4.9 8.5 - - + -
37A THR 6.0 0.7 - - - +
38A MSE 4.0 15.0 - - - -
41A LEU* 3.4 26.0 - - + -
56A PHE* 3.6 43.7 - - + -
58A ALA 3.4 3.2 + - - +
59A LYS* 3.1 17.4 + - + +
61A ASP* 1.3 78.9 - - - +
63A LEU* 1.3 57.5 + - + +
65A ALA* 3.1 4.3 + - - +
66A MSE 2.9 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.8 31.9 - - + -
36A LEU* 4.2 6.7 - - + -
59A LYS* 2.9 43.4 + - + +
60A GLN* 3.7 13.7 - - + +
62A LEU* 1.3 72.0 - - + +
64A THR* 1.3 55.8 + - - +
66A MSE 3.2 22.3 + - - +
67A ALA* 2.9 30.9 + - - +
110A VAL* 3.6 23.5 - - + +
113A GLY 6.0 2.5 - - - +
114A THR* 5.5 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLN* 2.9 24.3 + - - +
61A ASP* 3.7 8.3 - - - +
62A LEU 3.2 0.2 - - - -
63A LEU* 1.3 75.1 - - - +
65A ALA* 1.3 58.0 + - - +
67A ALA* 3.3 3.8 + - - +
68A GLU* 3.0 30.1 + - + +
114A THR* 3.4 19.6 + - - +
115A HIS* 3.0 26.9 + - - +
116A ALA* 3.6 31.0 - - + +
118A GLY 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 3.9 15.3 - - + +
56A PHE* 3.9 19.5 - - + -
61A ASP 3.0 13.8 + - - +
62A LEU 3.5 7.4 - - - +
64A THR* 1.3 74.5 - - - +
66A MSE 1.3 59.1 + - - +
68A GLU* 3.4 7.3 + - - +
69A HIS* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 4.0 22.0 - - + +
24A ALA* 3.8 22.2 - - + +
25A LEU* 3.9 17.2 - - + +
28A LEU* 3.7 30.5 - - + -
36A LEU* 3.7 20.0 - - + -
62A LEU* 2.9 39.0 + - + +
63A LEU* 3.4 25.8 - - + +
65A ALA* 1.3 72.6 - - - +
67A ALA* 1.3 59.1 + - - +
69A HIS* 3.2 3.6 + - - +
70A MSE 2.9 35.8 + - + +
110A VAL* 4.2 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU 2.9 16.6 + - - +
64A THR 3.3 4.9 + - - +
66A MSE 1.3 75.3 - - - +
68A GLU* 1.3 62.7 + - - +
70A MSE 3.3 20.3 + - - +
71A VAL* 3.4 18.7 + - - +
110A VAL* 4.0 10.9 - - + +
111A PHE* 4.0 33.1 - - + -
114A THR* 4.1 14.1 - - + +
121A THR* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A THR* 3.0 19.1 + - + +
65A ALA* 3.8 7.0 - - - +
66A MSE 3.3 0.2 - - - -
67A ALA* 1.3 78.8 - - - +
69A HIS* 1.3 61.2 + - - +
71A VAL* 3.4 11.5 + - - +
118A GLY* 3.3 30.5 + - - +
119A PRO* 3.1 13.2 - - + +
120A ASN* 2.6 70.4 + - - +
121A THR* 3.5 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 4.1 16.2 - - + -
22A GLN* 4.0 20.2 - - - -
25A LEU* 3.4 20.3 - - + +
65A ALA 3.0 17.4 + - - +
66A MSE 3.6 4.5 - - - +
68A GLU* 1.3 76.3 - - - +
70A MSE 1.3 65.6 + - - +
72A ASP* 3.1 26.9 + - + +
104A HIS* 5.7 1.5 - + - -
120A ASN* 4.5 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.5 26.7 - - + -
28A LEU* 3.7 22.0 - - + -
66A MSE 2.9 20.8 + - + +
67A ALA* 3.3 14.1 + - - +
69A HIS* 1.3 75.5 - - - +
71A VAL* 1.3 63.6 + - + +
72A ASP* 3.4 3.3 + - - +
100A ALA* 3.3 23.4 - - - +
101A LEU* 4.5 9.6 - - + -
104A HIS* 3.6 36.5 + - + +
107A GLY* 3.8 25.6 - - - +
110A VAL* 3.8 24.2 - - + -
111A PHE* 5.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ALA 3.4 15.5 - - - +
68A GLU 3.4 9.2 - - - +
69A HIS 3.1 0.4 - - - -
70A MSE 1.3 78.2 - - - +
72A ASP* 1.3 66.2 + - - +
73A GLY 3.2 1.0 + - - -
74A VAL* 3.0 31.0 + - + +
75A ALA 4.7 0.2 + - - -
97A LEU* 3.9 21.3 - - + -
100A ALA* 4.5 1.6 - - + -
101A LEU* 4.4 9.0 - - + -
111A PHE* 3.8 23.8 - - + -
120A ASN* 3.8 18.9 - - + +
121A THR* 3.7 26.2 - - - +
124A PHE* 6.1 2.0 - - + -
----------------------------------------------------------
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