Contacts of the helix formed by residues 10 - 21 (chain A) in PDB entry 1BL0
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 10 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASP* 1.4 76.3 - - - +
11A ILE* 1.3 56.7 + - - +
14A HIS* 2.8 46.0 + - + +
51A GLU* 3.2 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASP 2.8 11.2 + - - +
10A ALA* 1.3 82.2 - - - +
12A THR* 1.3 71.2 + - + +
14A HIS* 4.0 4.6 - - - +
15A SER* 3.6 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASP* 2.6 30.6 + - - +
11A ILE* 1.3 83.5 - - + +
13A ILE* 1.3 64.7 + - - +
14A HIS 3.2 1.1 - - - -
15A SER* 3.0 8.5 + - - -
16A ILE* 3.0 22.7 + - - +
39A TYR* 4.4 19.5 - - - +
44A LEU* 5.9 1.9 - - - +
47A MET* 3.2 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASP 2.5 15.9 + - - +
10A ALA 4.4 0.4 - - - +
12A THR* 1.3 76.0 - - - +
14A HIS* 1.4 64.1 + - - +
15A SER 3.0 1.7 + - - -
16A ILE* 3.2 15.5 - - + +
17A LEU* 3.1 25.4 + - + +
44A LEU* 3.8 17.7 - - + -
47A MET* 3.6 26.2 - - + -
48A PHE* 3.5 39.7 - - + +
51A GLU* 3.5 36.8 - - + -
52A THR* 4.0 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA* 2.8 33.5 + - + +
11A ILE* 4.0 6.5 - - - +
12A THR 3.2 0.2 - - - -
13A ILE* 1.4 81.0 - - + +
15A SER* 1.3 56.9 + - - +
17A LEU* 3.7 22.0 - - + +
18A ASP* 2.8 19.1 - - - +
51A GLU* 4.4 17.5 - - - -
52A THR* 5.9 2.9 - - + -
124A LEU* 5.7 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.6 12.0 + - - -
12A THR* 3.0 12.1 + - - -
13A ILE 3.0 1.2 - - - -
14A HIS* 1.3 77.3 - - - +
16A ILE* 1.3 57.9 + - - +
17A LEU 3.0 1.3 - - - -
18A ASP* 2.6 32.4 + - - +
19A TRP* 3.1 9.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR* 3.0 12.4 + - - +
13A ILE* 3.2 20.2 - - + +
15A SER* 1.3 75.2 + - - +
17A LEU* 1.3 60.8 + - - +
19A TRP* 3.3 21.5 + - + +
20A ILE* 2.9 37.6 + - + +
34A SER* 4.3 16.8 - - - +
37A SER* 3.8 35.2 - - - +
44A LEU* 4.5 18.2 - - + -
48A PHE* 3.9 27.6 - - + -
56A LEU* 5.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 3.1 34.5 + - + +
14A HIS* 3.7 23.1 - - + +
15A SER 2.9 0.4 + - - -
16A ILE* 1.3 81.7 - - + +
18A ASP* 1.4 63.7 + - - +
20A ILE* 2.9 15.8 + - + +
21A GLU* 3.0 18.4 + - - +
48A PHE* 3.2 35.7 - - + -
52A THR* 4.4 8.7 - - + -
59A TYR* 4.0 19.5 - - + +
123A PRO 4.4 11.7 - - - +
124A LEU* 4.4 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A HIS 2.8 27.2 - - - +
15A SER* 2.6 15.8 + - - +
17A LEU* 1.4 68.6 - - - +
19A TRP* 1.3 67.0 + - - +
21A GLU* 3.2 5.8 + - - +
22A ASP* 2.8 36.1 + - - +
124A LEU* 6.0 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER* 3.1 8.9 + - - +
16A ILE* 3.6 28.7 - - + +
18A ASP* 1.3 80.6 - - - +
20A ILE* 1.3 71.3 + - + +
22A ASP* 3.4 7.7 + - + -
23A ASN* 2.8 56.2 + - - +
27A PRO* 5.9 1.1 - - + -
29A SER* 4.0 18.4 - - - -
33A VAL* 3.7 30.1 - - + -
34A SER* 4.0 22.0 - - - -
36A ARG* 4.1 24.9 - - - +
37A SER* 4.6 12.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 2.9 27.9 + - + +
17A LEU* 2.9 12.1 + - - +
19A TRP* 1.3 89.1 - - + +
21A GLU* 1.3 60.2 + - - +
22A ASP 3.0 1.1 - - - -
23A ASN* 2.7 23.5 + - - -
24A LEU* 3.0 35.8 + - + +
29A SER* 4.9 6.7 - - - +
34A SER* 4.6 9.2 - - - +
48A PHE* 4.5 3.1 - - + -
56A LEU* 3.9 28.0 - - + -
59A TYR* 4.5 17.0 - - + -
60A ILE* 4.2 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 3.0 19.7 + - - +
18A ASP* 4.0 5.4 - - - +
20A ILE* 1.3 72.6 - - - +
22A ASP* 1.3 58.4 + - - +
23A ASN 2.9 12.7 + - - -
24A LEU* 3.7 19.0 - - + +
25A GLU* 5.3 4.0 + - - +
59A TYR* 3.0 20.4 + - - -
63A ARG* 2.3 51.9 + - - +
67A GLU* 6.4 0.2 - - - -
123A PRO* 3.0 28.2 - - + +
----------------------------------------------------------
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