Contacts of the helix formed by residues 146 - 152 (chain B) in PDB entry 3E1J
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 LEU 146 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ASP* 6.4 1.8 - - + -
83B VAL* 5.0 10.3 - - + -
84B GLU* 5.8 3.1 - - + +
141B ILE* 3.8 24.9 + - + +
145B GLY* 1.3 71.0 - - - -
147B GLN* 1.3 66.0 + - + +
149B TYR* 3.1 10.6 + - + +
150B LEU* 2.9 52.3 + - + +
250B SO4 3.2 17.8 + - - +
143J LYS 5.7 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLY 3.5 0.2 - - - -
146B LEU* 1.3 74.9 - - + +
148B ASN* 1.3 62.8 + - - +
150B LEU* 3.3 3.7 + - - +
151B GLN* 3.1 19.6 + - - +
250B SO4 3.1 26.8 + - - +
142J GLN 4.5 4.0 + - - -
143J LYS 3.5 18.6 + - - +
144J MET* 3.4 42.8 - - - +
145J GLY* 3.6 9.3 - - - +
148J ASN* 3.8 8.8 - - - +
250J SO4 4.7 8.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B MET* 3.4 33.1 + - + +
145B GLY 3.6 1.8 + - - -
146B LEU 3.4 0.2 - - - -
147B GLN* 1.3 75.7 - - - +
149B TYR* 1.3 66.3 + - - +
151B GLN* 3.4 1.0 + - - -
152B ALA* 3.2 19.6 + - - +
250B SO4 4.6 0.6 + - - -
147G GLN* 3.7 4.8 - - - +
148G ASN* 2.7 41.6 + - - +
151G GLN* 3.4 26.7 + - - +
148J ASN* 2.7 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 3.5 14.7 - - + +
83B VAL* 4.0 14.8 - - + -
87B LEU* 3.9 4.5 - - - +
137B GLU* 2.5 47.3 + - + +
140B LEU* 4.2 13.5 - - + -
141B ILE* 3.6 45.8 - - + -
144B MET* 3.8 15.0 - - + +
145B GLY 3.0 19.2 + - - +
146B LEU* 3.4 8.7 - - + +
148B ASN* 1.3 78.6 - - - +
150B LEU* 1.3 76.2 + - + +
152B ALA* 3.2 7.0 + - - +
153B GLN* 2.9 51.4 + - + -
154G ILE* 5.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.0 23.6 - - + +
83B VAL* 3.9 28.9 - - + -
146B LEU* 2.9 46.1 + - + +
147B GLN* 3.7 3.8 - - - +
149B TYR* 1.3 85.4 - - + +
151B GLN* 1.3 63.7 + - - +
153B GLN* 2.8 21.3 + - + +
154B ILE* 3.7 6.9 + - - +
140J LEU* 5.8 0.7 - - + -
143J LYS* 4.0 40.8 - - + +
144J MET* 4.4 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B GLN 3.1 14.6 + - - +
148B ASN* 3.9 0.7 + - - +
149B TYR 3.3 0.2 - - - -
150B LEU* 1.3 75.1 - - - +
152B ALA* 1.3 60.1 + - - +
153B GLN 3.1 1.4 + - - -
154B ILE* 3.4 17.1 + - - +
155B ARG* 4.9 0.7 + - - +
151G GLN* 2.8 29.1 + - - +
144J MET* 3.7 27.0 - - - +
148J ASN* 3.5 39.6 + - + +
151J GLN* 3.0 35.3 + - - +
152J ALA* 3.9 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG* 4.5 3.3 + - - -
148B ASN 3.2 12.1 + - - +
149B TYR* 3.4 11.2 - - - +
150B LEU 3.0 1.0 + - - -
151B GLN* 1.3 78.1 - - - +
153B GLN* 1.3 67.6 + - - +
154B ILE 3.5 0.4 - - - -
155B ARG 5.1 0.2 - - - -
151G GLN* 3.8 21.7 - - + +
154G ILE* 4.1 19.5 - - + +
155G ARG* 3.2 28.5 + - - +
----------------------------------------------------------
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