Contacts of the helix formed by residues 40 - 53 (chain A) in PDB entry 2BHT
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 VAL 40 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLU* 3.1 42.7 - - + +
35A ASN* 3.6 1.1 - - - +
39A SER* 1.3 69.9 - - - +
41A LYS* 1.3 90.2 + - + +
42A ASP 2.9 1.7 + - - -
43A ARG* 3.1 23.0 + - - +
44A ALA 4.3 0.5 + - - -
150A HIS* 3.9 25.1 + - + +
178A THR* 3.9 8.5 - - - +
278A ILE* 4.9 9.0 - - + -
280A CYS* 2.7 33.7 + - + +
320A PLP 4.9 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER* 2.9 11.8 + - - +
40A VAL* 1.3 88.1 - - + +
42A ASP* 1.3 62.7 + - - +
43A ARG 3.0 1.1 + - - -
44A ALA* 3.3 11.1 + - + +
45A ALA* 3.1 23.0 + - - +
69A SER* 5.0 2.0 + - - -
71A ASN* 3.3 24.3 - - + +
72A THR* 3.3 41.5 + - + +
75A ALA* 3.9 7.0 - - + -
140A GLN* 5.2 2.2 + - - -
146A ASN* 6.1 1.6 - - - +
175A THR* 6.3 0.7 - - - -
320A PLP 1.5 95.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.8 21.7 - - + +
35A ASN* 3.1 20.2 - - + +
36A PRO 3.6 1.0 - - - -
37A ALA* 2.7 51.7 + - - +
38A GLY 3.5 0.3 + - - -
39A SER* 3.1 11.4 + - - +
40A VAL 2.9 2.6 + - - -
41A LYS* 1.3 78.6 - - - +
43A ARG* 1.3 62.5 + - - +
45A ALA* 3.9 2.0 - - - +
46A LEU* 3.0 25.6 + - - +
75A ALA* 3.4 15.2 - - - +
78A MET* 3.2 12.8 - - + +
79A ILE* 4.1 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.0 15.7 - - + +
9A GLY* 3.6 14.3 - - - -
11A THR* 3.4 14.8 + - - +
32A GLU* 2.5 46.4 + - - +
35A ASN* 4.2 7.6 - - - +
40A VAL* 3.2 17.5 - - - +
41A LYS 3.0 0.4 - - - -
42A ASP* 1.3 78.7 - - - +
44A ALA* 1.3 60.6 + - - +
46A LEU* 3.8 2.9 - - - +
47A SER* 3.3 24.3 + - - -
149A ALA* 3.4 16.6 - - + +
150A HIS* 4.6 5.6 - - + -
153A THR* 3.4 11.3 + - - +
154A THR* 2.9 35.9 + - - +
157A GLU* 2.6 39.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL 4.3 0.2 + - - -
41A LYS* 3.3 14.4 + - + +
42A ASP 3.3 0.2 - - - -
43A ARG* 1.3 77.3 - - - +
45A ALA* 1.3 59.7 + - - +
47A SER* 3.4 2.2 - - - -
48A MET* 2.8 41.9 + - + +
72A THR* 5.4 6.1 - - + -
146A ASN* 3.6 39.9 - - + +
149A ALA* 4.1 8.9 - - - +
150A HIS* 4.6 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS 3.1 16.8 + - - +
42A ASP 3.9 0.2 - - - +
44A ALA* 1.3 77.5 - - - +
46A LEU* 1.3 60.9 + - - +
48A MET* 4.4 3.1 - - - +
49A ILE* 2.8 30.9 + - + +
72A THR* 5.8 2.2 - - + +
75A ALA* 3.7 13.5 - - + -
76A LEU* 3.6 29.4 - - + +
79A ILE* 3.3 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLU* 4.0 35.4 - - + +
8A ILE* 4.6 12.8 - - + -
42A ASP 3.0 17.8 + - - +
43A ARG* 3.8 4.7 - - - +
44A ALA 3.2 0.2 - - - -
45A ALA* 1.3 78.0 - - - +
47A SER* 1.3 56.0 + - - +
49A ILE* 3.0 1.7 + - - +
50A VAL* 2.8 51.3 + - + +
79A ILE* 3.7 14.8 - - + +
83A LYS* 3.9 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG 3.3 17.0 + - - -
44A ALA 3.4 3.4 - - - -
46A LEU* 1.3 76.1 - - - +
48A MET* 1.3 53.4 + - - +
50A VAL* 3.9 6.1 - - - -
51A GLU* 2.6 48.6 + - - +
145A ASP* 2.4 29.7 + - - -
148A LYS* 4.4 4.9 - - - +
149A ALA* 3.7 17.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA* 2.8 34.0 + - + +
45A ALA* 3.7 5.2 - - - +
47A SER* 1.3 73.6 - - - +
49A ILE* 1.3 64.2 + - + +
51A GLU* 4.1 1.2 - - - +
52A ALA* 3.3 21.3 + - - +
66A GLU* 4.1 10.5 - - - +
72A THR* 5.7 3.1 - - + -
76A LEU* 3.8 26.0 - - + -
138A LEU* 3.3 29.0 - - + +
140A GLN* 3.8 41.1 - - + -
143A ASN* 3.9 11.0 - - - -
145A ASP* 3.9 21.6 - - + +
146A ASN* 4.0 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA* 2.8 19.4 + - + +
46A LEU 3.8 3.8 - - - +
48A MET* 1.3 76.3 - - + +
50A VAL* 1.3 63.1 + - + +
52A ALA* 3.4 1.8 + - - -
53A GLU* 2.8 42.6 + - + +
58A ILE* 3.7 13.0 - - + +
64A LEU* 4.7 12.8 - - + -
76A LEU* 4.5 18.8 - - + +
79A ILE* 3.7 23.8 - - + -
80A ALA 6.0 0.4 - - - +
83A LYS* 3.3 29.6 - - + -
85A TYR* 3.3 28.3 - - + -
87A MET* 6.4 0.2 - - - -
138A LEU* 5.1 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 2.8 51.4 + - + +
47A SER* 3.7 6.7 - - - +
49A ILE* 1.3 72.4 - - - +
51A GLU* 1.3 69.6 + - + +
53A GLU* 2.8 25.5 + - - +
54A LYS* 3.3 19.8 + - - +
83A LYS* 3.0 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 2.6 38.1 + - - +
48A MET 4.1 0.2 - - - +
50A VAL* 1.3 77.2 - - + +
52A ALA* 1.3 57.5 + - - +
54A LYS* 2.7 59.1 + - - +
55A ARG* 2.9 19.7 + - - +
145A ASP* 3.3 29.4 - - - +
148A LYS* 2.5 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A MET 3.3 16.1 + - - +
49A ILE 3.7 0.2 - - - -
50A VAL 3.2 0.2 - - - -
51A GLU* 1.3 77.7 - - - +
53A GLU* 1.3 55.8 + - - +
54A LYS 3.0 4.7 - - - -
55A ARG* 4.0 8.5 - - + +
56A GLY 3.7 0.2 + - - -
57A ARG* 2.9 52.7 + - + +
58A ILE* 3.0 24.0 + - + -
138A LEU* 4.6 7.4 - - + -
145A ASP* 4.9 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 2.8 37.6 + - + +
50A VAL* 2.8 35.8 + - - +
51A GLU 3.5 0.2 - - - -
52A ALA* 1.3 76.1 - - - +
54A LYS* 1.3 59.6 + - - +
56A GLY* 3.9 9.1 + - - -
58A ILE* 3.8 13.4 - - + +
60A PRO* 4.2 9.4 - - + +
83A LYS* 3.8 8.4 + - - +
85A TYR* 2.6 34.1 + - - +
----------------------------------------------------------
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