Contacts of the helix formed by residues 14 - 25 (chain A) in PDB entry 1BTB
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 SER 14 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER* 3.2 9.3 + - - -
13A ILE* 1.3 85.1 - - - +
15A ASP* 1.3 57.1 + - - +
17A HIS* 3.1 3.6 + - - +
18A GLN* 2.8 32.4 + - - +
32A GLU* 3.6 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 3.9 6.4 - - - +
10A ILE* 3.2 16.9 + - + +
11A ARG* 3.2 43.6 + - - +
12A SER* 2.7 20.6 + - - +
14A SER* 1.3 80.0 - - - +
16A LEU* 1.3 61.8 + - - +
18A GLN* 2.9 23.6 + - - +
19A THR* 3.0 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.3 36.8 - - + -
10A ILE* 3.0 23.0 - - + +
12A SER 3.0 2.9 + - - +
13A ILE* 2.6 27.4 + - + +
15A ASP* 1.3 71.8 - - - +
17A HIS* 1.3 62.9 + - + +
18A GLN 3.1 0.3 + - - -
19A THR* 3.4 1.3 + - + -
20A LEU* 3.0 34.7 + - + +
53A TRP* 3.5 16.4 - - + -
59A SER* 4.2 5.2 - - - +
66A GLY 3.5 10.5 - - - +
67A ALA* 3.3 37.0 - - + +
70A VAL* 3.9 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 3.0 38.4 + - + +
14A SER 3.7 4.9 - - - +
16A LEU* 1.3 74.8 - - - +
18A GLN* 1.3 56.4 + - - +
20A LEU* 4.2 3.3 - - - +
21A LYS* 2.9 17.0 + - - +
30A TYR* 2.9 48.3 + - + -
32A GLU* 2.6 61.2 + - + +
33A ASN* 4.4 7.3 - - - -
34A LEU* 5.1 1.8 - - + -
70A VAL* 3.1 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A SER* 2.8 16.3 + - - +
15A ASP* 2.9 22.1 + - - +
17A HIS* 1.3 75.9 - - - +
19A THR* 1.3 67.6 + - - +
21A LYS* 3.2 11.1 + - + +
22A LYS* 3.0 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL 3.6 11.0 + - - +
5A ILE* 4.0 18.6 - - + -
6A ASN* 4.8 9.3 + - - +
9A GLN* 5.8 3.3 - - - +
10A ILE* 4.8 6.3 - - + -
15A ASP* 3.0 12.7 + - - -
16A LEU 4.1 4.7 - - - +
18A GLN* 1.3 80.4 + - - +
20A LEU* 1.3 68.6 + - + +
22A LYS* 3.2 8.8 + - - +
23A GLU* 2.9 47.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.2 26.0 - - + -
16A LEU* 3.0 25.1 + - + +
17A HIS* 3.9 7.2 - - - +
19A THR* 1.3 73.6 - - - +
21A LYS* 1.3 69.2 + - - +
23A GLU* 2.6 41.4 + - - +
24A LEU* 2.7 28.3 + - + -
30A TYR* 4.4 9.4 - - - +
37A LEU* 4.5 0.9 - - + -
51A LEU* 4.0 3.4 - - + -
70A VAL* 2.9 42.0 - - + -
74A PHE* 3.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A HIS 2.9 18.2 + - - +
18A GLN* 3.4 11.7 - - + +
20A LEU* 1.3 78.5 - - - +
22A LYS* 1.3 67.1 + - + +
24A LEU* 3.9 0.4 - - - +
25A ALA* 2.5 35.9 + - - +
26A LEU* 2.9 47.6 + - + +
27A PRO 3.3 18.0 + - - -
28A GLU* 4.6 11.5 - - - +
30A TYR* 3.5 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 3.0 32.9 + - - +
19A THR* 3.3 12.8 - - - +
20A LEU 2.7 4.2 + - - -
21A LYS* 1.3 87.6 - - + +
23A GLU* 1.3 68.3 + - + +
25A ALA* 2.9 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LYS* 4.9 14.1 - - - +
2A LYS 4.6 7.3 - - - +
3A ALA* 3.1 31.6 - - + +
4A VAL* 2.4 44.7 + - + +
5A ILE 3.6 0.8 + - - -
19A THR* 2.9 22.4 + - + +
20A LEU* 2.6 36.0 + - - +
22A LYS* 1.3 79.1 - - + +
24A LEU* 1.3 62.0 + - + +
25A ALA* 2.8 6.6 + - - +
49A LEU* 5.9 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA* 5.5 0.9 - - + -
20A LEU* 2.7 53.3 + - + +
21A LYS 3.9 0.9 - - - +
23A GLU* 1.3 74.2 - - + +
25A ALA* 1.3 70.7 + - - +
26A LEU* 3.3 19.6 + - + +
37A LEU* 4.2 9.0 - - + -
41A LEU* 3.0 37.0 - - + -
44A TRP* 4.0 10.7 + - - -
45A VAL* 3.2 31.2 - - + +
49A LEU* 4.1 5.4 - - + -
74A PHE* 3.5 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 2.5 21.1 + - - +
22A LYS* 3.3 9.9 - - - +
23A GLU 2.8 5.9 + - - +
24A LEU* 1.3 79.7 - - - +
26A LEU* 1.3 65.8 + - - +
44A TRP* 3.2 13.9 + - - -
----------------------------------------------------------
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