Contacts of the helix formed by residues 51 - 63 (chain A) in PDB entry 3BQT
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 CYS 51 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 3.4 9.0 - - - -
49A SER 3.8 5.8 - - - +
50A VAL* 1.3 84.3 - - - +
52A MSE 1.3 78.5 + - - +
53A SER 3.0 1.3 - - - -
54A GLU* 2.8 23.3 + - - +
55A LEU 3.2 7.6 + - - -
82A HIS* 4.1 18.2 - - + -
49B SER* 4.8 6.1 - - - -
50B VAL 4.7 0.2 - - - -
51B CYS* 2.1 58.1 - - + -
52B MSE 5.0 0.4 - - - +
53B SER 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A CYS* 1.3 76.9 - - - +
53A SER* 1.3 62.0 + - - +
55A LEU* 3.1 12.2 + - - +
56A TYR* 3.0 72.0 + - + +
78A LEU 4.1 2.9 - - - +
79A LYS* 3.3 37.0 - - + -
82A HIS* 3.1 53.3 - - + +
49B SER* 5.6 5.6 - - - +
51B CYS* 3.8 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A CYS 2.9 0.8 + - - -
52A MSE 1.3 78.8 - - - +
54A GLU* 1.3 79.8 + - - +
56A TYR* 3.3 7.6 + - - +
57A ALA* 2.9 28.5 + - - +
67A TRP* 5.1 9.4 + - - +
51B CYS* 3.2 13.8 - - - +
53B SER* 4.1 5.1 - - - -
54B GLU* 3.2 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.4 26.6 - - + +
40A PHE* 4.5 2.5 - - + -
43A ILE* 6.1 1.1 - - + -
49A SER 4.7 0.7 - - - +
50A VAL* 3.5 26.2 - - + -
51A CYS* 2.8 34.5 + - - +
53A SER* 1.3 89.8 - - - +
55A LEU* 1.3 55.5 + - - +
57A ALA* 3.4 8.2 - - + +
58A LEU* 2.8 36.8 + - + +
53B SER* 2.6 31.0 + - - -
67B TRP* 5.5 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER* 4.1 11.4 - - - +
37A LYS* 4.6 4.5 - - - +
40A PHE* 3.7 33.3 - - + -
51A CYS 3.2 4.0 + - - -
52A MSE 3.1 15.8 + - - +
54A GLU* 1.3 76.3 - - - +
56A TYR* 1.3 63.5 + - + +
58A LEU* 3.1 5.9 + - - +
59A GLU* 3.1 19.8 + - - +
78A LEU* 3.6 51.1 - - + +
81A PHE* 3.8 19.1 - - + -
82A HIS* 3.6 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A MSE 3.0 48.5 + - + +
53A SER* 3.6 7.9 - - - +
55A LEU* 1.3 76.7 - - + +
57A ALA* 1.3 56.8 + - - +
59A GLU* 3.3 4.2 + - - +
60A GLY* 2.7 34.0 + - - -
67A TRP* 3.3 59.8 - + + +
70A LEU* 4.1 5.9 - - + +
75A LYS* 3.1 36.5 + - + +
78A LEU* 3.7 38.6 - - + -
79A LYS* 4.0 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN* 3.5 32.8 - - + +
12A ILE* 5.2 0.3 + - - +
16A LEU* 4.0 20.9 - - + -
53A SER 2.9 18.6 + - - +
54A GLU* 3.4 11.2 - - + +
56A TYR* 1.3 77.1 - - - +
58A LEU* 1.3 63.7 + - - +
60A GLY 3.2 0.7 + - - -
61A ALA* 3.1 21.0 + - - +
67A TRP* 4.4 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 5.9 1.1 - - + -
16A LEU* 4.3 18.4 - - + -
20A LEU* 3.7 34.3 - - + -
31A LEU* 4.2 15.7 - - + +
36A SER* 3.5 19.7 - - - +
39A ALA* 3.7 26.5 - - + -
40A PHE* 3.8 20.0 - - + +
43A ILE* 5.0 2.9 - - + -
54A GLU* 2.8 22.9 + - + +
55A LEU* 3.1 2.9 + - - +
57A ALA* 1.3 78.1 - - - +
59A GLU* 1.3 59.8 + - - +
60A GLY 3.1 0.2 - - - -
61A ALA* 3.3 8.6 + - + +
62A VAL* 3.2 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLY* 5.9 0.2 - - - -
36A SER* 3.1 27.3 + - - +
37A LYS* 5.8 1.0 - - - +
55A LEU 3.1 13.1 + - - +
56A TYR 3.6 0.7 - - - +
58A LEU* 1.3 73.5 - - - +
60A GLY* 1.3 65.1 + - - +
62A VAL* 3.8 16.9 - - - +
63A GLN* 3.2 50.1 + - - +
70A LEU* 3.8 17.0 - - + +
74A LYS* 3.6 33.9 + - - +
78A LEU* 4.1 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN* 3.4 7.2 - - - -
56A TYR 2.7 17.2 + - - -
57A ALA 3.6 0.2 - - - -
58A LEU 3.1 0.2 - - - -
59A GLU* 1.3 80.0 - - - +
61A ALA* 1.3 50.9 + - - +
63A GLN* 2.5 30.8 - - - +
65A ILE* 3.1 31.6 + - - +
67A TRP* 4.5 3.1 - - - -
70A LEU* 4.1 10.1 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
9A LEU* 3.7 40.0 - - + +
10A PRO* 3.6 26.9 - - - +
11A ASN* 3.8 1.4 + - - -
12A ILE* 5.1 5.6 - - + -
31A LEU* 4.6 7.0 - - + -
32A LYS* 4.5 4.3 - - - -
57A ALA 3.1 9.8 + - - +
58A LEU* 3.5 13.9 - - + +
60A GLY* 1.3 71.7 - - - +
62A VAL* 1.3 55.4 + - - +
63A GLN 2.7 16.7 - - - +
64A GLY* 4.5 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 6.1 0.2 - - + -
31A LEU* 3.7 36.6 - - + +
32A LYS* 4.2 36.3 + - + +
35A GLY* 4.5 5.4 - - - -
36A SER 4.5 8.1 - - - +
58A LEU 3.2 15.0 + - - +
59A GLU* 4.1 20.4 - - - +
60A GLY 3.2 0.8 - - - -
61A ALA* 1.3 73.6 - - - +
63A GLN* 1.3 64.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU* 3.2 35.6 + - - +
60A GLY 2.5 18.4 + - - +
61A ALA 2.7 8.7 - - - +
62A VAL* 1.3 81.7 - - + +
64A GLY* 1.3 57.0 + - - +
65A ILE* 3.8 24.2 - - + +
70A LEU* 3.4 18.6 - - + +
71A ASP* 4.9 5.1 + - - +
74A LYS* 4.4 12.5 - - - +
----------------------------------------------------------
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