Contacts of the helix formed by residues 150 - 157 (chain D) in PDB entry 1J1D
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 TYR 150 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D GLU* 3.2 30.1 + - - +
98D SER* 3.4 39.9 + - - -
101D PHE* 3.6 34.6 - + + -
110D GLY 4.5 1.4 + - - -
149D ASP* 1.3 73.0 - - - +
151D ASP* 1.3 64.5 + - - +
153D PHE* 3.0 13.3 + - - +
154D LEU* 3.2 37.8 + - + +
263E VAL* 4.1 20.9 - - + -
267E ARG* 3.1 56.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D ASP* 2.9 11.9 + - - +
150D TYR* 1.3 79.4 - - - +
152D GLU* 1.3 62.6 + - + +
153D PHE 3.4 0.3 + - - -
154D LEU* 3.4 9.9 + - - +
155D GLU* 3.4 20.1 + - - +
267E ARG* 2.8 45.6 + - - +
271E ASN* 3.3 17.0 - - - +
136F ARG* 3.5 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D GLY 3.2 23.7 - - - +
141D ASP* 3.6 0.7 - - - -
142D LYS* 4.2 12.3 - - + +
143D ASN* 2.9 28.3 + - - +
147D ARG 3.2 1.0 - - - +
148D ILE* 3.0 25.8 - - + +
149D ASP* 2.6 35.5 + - - +
151D ASP* 1.3 71.4 - - + +
153D PHE* 1.3 58.2 + - - -
155D GLU* 4.1 4.9 - - - +
156D PHE* 3.1 28.4 + - - +
203D CA 2.2 32.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D LEU* 3.4 42.4 - - + -
100D LEU* 4.4 0.9 - - + -
101D PHE* 3.4 44.6 - + + -
104D PHE* 3.6 51.1 - + - -
112D ILE* 4.9 8.3 - - + -
148D ILE* 3.8 7.4 - - + +
149D ASP 2.9 4.6 + - - +
150D TYR* 3.0 10.5 + + - +
152D GLU* 1.3 78.2 - - - +
154D LEU* 1.3 67.6 + - + +
156D PHE* 3.6 8.9 + + - +
157D MET* 3.1 36.7 + - + +
54F LEU* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D GLU* 3.5 44.9 - - + +
97D LEU* 3.5 43.1 - - + +
150D TYR* 3.2 34.2 + - + +
151D ASP* 3.8 9.9 - - - +
152D GLU 3.4 0.2 - - - -
153D PHE* 1.3 81.0 - - + +
155D GLU* 1.3 64.1 + - - +
157D MET 3.6 1.6 + - - -
158D LYS* 3.3 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D LYS* 3.1 32.4 + - + +
151D ASP 3.4 12.5 + - - +
152D GLU* 4.2 4.5 - - - +
153D PHE 3.3 0.2 - - - -
154D LEU* 1.3 75.4 - - - +
156D PHE* 1.3 59.3 + - - +
157D MET 2.9 9.8 + - - -
158D LYS* 2.9 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D PHE* 5.8 1.3 - + - -
117D LEU* 5.4 6.5 - - + -
136D LEU* 3.3 44.0 - - + -
139D ASP* 3.6 13.2 - - + -
140D GLY* 3.4 26.7 - - - -
142D LYS* 5.4 0.8 - - - +
148D ILE* 5.4 11.0 - - + -
152D GLU 3.1 18.6 + - - +
153D PHE* 3.8 11.7 - + - +
155D GLU* 1.3 78.4 - - - +
157D MET* 1.3 88.7 + - + +
158D LYS 3.6 0.6 + - - -
160D VAL* 4.4 0.7 - - - +
50F LYS* 2.9 60.9 + - + +
53F LEU* 4.8 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D LYS* 5.5 0.7 - - - +
97D LEU* 4.3 24.3 - - + +
104D PHE* 4.5 6.1 - - + -
153D PHE* 3.1 29.5 + - + +
154D LEU 3.8 2.2 - - - -
155D GLU 3.0 1.4 - - - -
156D PHE* 1.3 108.0 - - + +
158D LYS* 1.3 63.2 + - - +
159D GLY 3.2 3.3 + - - -
160D VAL* 3.2 33.1 + - - +
50F LYS* 3.9 22.0 - - + +
53F LEU* 4.1 10.8 - - + -
54F LEU* 3.6 42.4 - - + -
----------------------------------------------------------
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