Contacts of the helix formed by residues 42 - 50 (chain B) in PDB entry 3EBL
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 GLU 42 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE 3.9 14.8 - - - +
34B LEU* 2.9 36.8 + - + +
36B ARG* 2.7 41.4 + - + +
41B PHE* 1.3 72.9 - - - +
43B ARG* 1.3 57.9 + - - +
44B ASP 3.4 2.9 - - - -
45B LEU* 3.5 19.4 + - + +
46B GLY* 2.9 25.6 + - - -
36C ARG* 5.3 0.7 - - - -
42C GLU* 5.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 2.7 41.9 + - - +
42B GLU* 1.3 67.9 - - - +
44B ASP* 1.3 68.7 + - - +
46B GLY* 3.2 1.1 + - - -
47B GLU* 2.9 46.4 + - + +
125B VAL* 2.8 25.0 + - - +
126B HIS* 4.8 1.0 - - - +
156B ARG* 3.4 41.1 + - - +
157B ALA 2.8 29.1 + - - -
159B GLU* 3.1 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.7 22.8 - - + +
42B GLU 3.4 0.4 - - - -
43B ARG* 1.3 85.4 - - - +
45B LEU* 1.3 58.0 + - - +
47B GLU* 3.5 7.0 + - - +
48B TYR* 3.0 27.4 + - - +
37C ALA* 6.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 5.8 2.2 - - - +
33B ILE* 4.3 17.0 - - + -
34B LEU* 3.8 17.0 - - + -
42B GLU* 3.5 26.9 + - + +
43B ARG 3.3 0.2 - - - -
44B ASP* 1.3 77.2 - - - +
46B GLY* 1.3 58.8 + - - +
48B TYR* 3.1 15.7 + - + +
49B LEU* 2.9 58.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 3.8 25.0 - - - +
41B PHE* 4.7 6.7 - - - -
42B GLU 2.9 15.4 + - - -
43B ARG* 3.6 4.3 - - - -
45B LEU* 1.3 77.2 - - - +
47B GLU* 1.3 60.1 + - - +
49B LEU* 3.2 2.9 + - - +
50B ASP* 3.0 26.7 + - - +
52B ARG* 5.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 5.4 1.4 - - - +
43B ARG* 2.9 36.4 + - + +
44B ASP* 3.7 8.1 - - - +
46B GLY* 1.3 74.2 - - - +
48B TYR* 1.3 63.0 + - - +
50B ASP* 3.6 12.0 + - - +
52B ARG* 2.8 48.1 + - - +
156B ARG* 2.6 34.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 3.4 37.1 - - + +
60A LEU* 3.7 27.1 - - + -
132A THR* 3.7 24.7 + - + +
135A ASP* 2.7 30.8 + - - +
136A SER* 3.1 33.1 + - - -
139A ARG* 3.8 15.7 - - - -
44B ASP 3.0 18.2 + - - +
45B LEU* 3.1 14.6 + - + +
47B GLU* 1.3 78.8 - - - +
49B LEU* 1.3 76.8 + - + +
50B ASP 3.7 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 2.9 32.1 + - - +
132A THR* 4.4 2.2 - - + -
603A NO3 4.0 23.6 - - - +
604A NO3 3.9 17.7 - - - +
30B SER* 5.3 6.3 - - - +
33B ILE* 6.0 4.5 - - + -
34B LEU* 4.6 12.1 - - + -
45B LEU* 2.9 45.4 + - + +
46B GLY* 4.1 3.8 - - - +
48B TYR* 1.3 94.6 - - + +
50B ASP* 1.3 64.1 + - - +
501B MPD 2.9 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 4.1 6.8 - - - +
52A ARG 4.7 6.1 - - - +
53A VAL* 5.5 1.0 - - - +
27B PHE* 4.8 10.0 - - - -
31B TYR* 4.9 3.1 + - - -
46B GLY 3.0 16.0 + - - +
47B GLU 3.6 3.8 + - - +
48B TYR 3.4 5.7 - - - +
49B LEU* 1.3 80.8 - - - +
51B ARG* 1.3 70.0 + - - +
52B ARG* 2.7 44.6 + - - +
127B SER* 4.2 13.3 + - - -
131B SER* 2.7 28.5 + - - -
501B MPD 3.8 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