Contacts of the helix formed by residues 43 - 52 (chain B) in PDB entry 4BL8
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 LYS 43 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ASN* 5.2 4.2 + - - -
41B PRO 3.7 0.6 + - - -
42B ASP* 1.3 78.2 - - + +
44B LEU* 1.3 64.1 + - - +
45B GLU* 3.1 18.2 - - - +
46B GLU* 3.1 22.6 + - + +
47B LYS* 3.0 26.1 + - + +
386B PRO* 3.3 28.3 - - + +
387B ASP* 3.1 30.3 + - - +
389B PRO* 4.4 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TRP* 4.0 11.0 - - + -
12B ILE* 3.4 17.3 - - - +
13B ASN* 3.3 44.7 + - + +
41B PRO* 3.6 28.0 + - + +
42B ASP 3.1 4.3 + - - -
43B LYS* 1.3 77.9 - - - +
45B GLU* 1.3 70.9 + - - +
47B LYS* 4.2 7.2 - - - -
48B PHE* 3.0 24.6 + - - +
61B ILE* 3.8 31.0 - - + -
62B PHE 3.9 9.2 - - - +
63B TRP* 4.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ASN* 4.9 0.3 - - - +
43B LYS* 3.7 17.2 - - - +
44B LEU* 1.3 84.4 + - - +
46B GLU* 1.3 78.4 + - + +
49B PRO* 3.5 11.0 - - - +
63B TRP* 3.2 49.2 - - + -
67B ARG* 3.8 35.3 + - - +
71B TYR* 2.8 31.3 + - - +
342B TYR* 4.7 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LYS* 3.1 22.4 + - + +
45B GLU* 1.3 95.8 - - + +
47B LYS* 1.3 60.9 + - - +
48B PHE 3.3 0.7 - - - -
49B PRO* 3.2 13.7 - - - +
50B GLN* 2.5 31.5 - - - +
67B ARG* 4.8 2.7 - - - +
342B TYR* 2.7 35.3 + - - +
382B ARG* 3.5 24.1 - - + +
386B PRO* 3.4 28.6 - - + +
389B PRO* 5.6 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TRP* 4.0 18.4 - - + -
41B PRO* 4.5 13.7 - - + +
42B ASP* 3.3 34.9 + - - +
43B LYS* 3.0 15.1 + - - +
44B LEU* 3.3 1.5 + - - +
46B GLU* 1.3 76.9 - - - +
48B PHE* 1.3 66.1 + - - +
50B GLN* 2.9 22.5 + - + +
51B VAL* 3.1 26.1 + - + +
386B PRO* 4.7 17.9 - - + -
387B ASP* 5.5 8.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TRP* 3.9 7.6 - - + -
44B LEU 3.0 11.4 + - - +
47B LYS* 1.3 75.6 - - - +
49B PRO* 1.3 72.3 - - + +
50B GLN 3.0 0.7 + - - -
51B VAL* 3.1 3.0 + - - +
52B ALA* 2.9 37.3 + - + +
58B PRO* 4.0 24.2 - - + -
61B ILE* 3.3 50.9 - - + -
71B TYR* 4.3 14.6 - + - +
76B LEU* 3.8 42.2 - - + -
77B LEU* 4.3 10.3 - - + -
268B ASN* 4.0 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLU 3.5 15.0 - - - +
46B GLU* 3.2 17.9 - - - +
48B PHE* 1.3 97.7 - - + +
50B GLN* 1.3 58.4 + - + +
52B ALA* 4.3 4.4 + - + +
67B ARG* 6.0 1.3 - - - +
71B TYR* 4.0 11.9 - - + -
76B LEU* 3.7 30.3 - - + +
383B ARG* 4.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU* 2.5 39.3 - - - +
47B LYS* 2.9 19.3 + - - +
48B PHE 3.0 0.6 + - - -
49B PRO* 1.3 82.2 - - + +
51B VAL* 1.3 66.2 + - + +
52B ALA 3.6 0.4 + - - -
54B THR* 4.7 8.1 - - - +
382B ARG 4.1 2.1 - - - +
383B ARG* 2.6 72.9 + - + +
386B PRO* 3.6 27.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TRP* 3.7 25.8 - - + -
47B LYS* 3.2 20.6 - - + +
48B PHE* 3.1 3.1 + - - +
50B GLN* 1.3 87.8 - - + +
52B ALA* 1.3 63.6 + - - +
53B ALA 3.3 2.5 - - - -
54B THR* 3.0 26.9 + - + +
56B ASP* 4.6 7.4 - - + +
57B GLY* 3.2 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PHE* 2.9 26.4 + - + +
49B PRO* 4.4 3.1 + - + +
50B GLN 3.6 2.2 - - - -
51B VAL* 1.3 79.6 - - - +
53B ALA* 1.3 59.2 + - + +
55B GLY* 4.1 4.9 + - - -
57B GLY* 4.5 2.9 + - - -
76B LEU* 3.6 37.0 - - + -
268B ASN* 3.1 31.4 + - - +
270B ALA* 3.7 9.2 - - - +
----------------------------------------------------------
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