Contacts of the helix formed by residues 150 - 160 (chain E) in PDB entry 2NYM
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 ASP 150 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E LYS 4.9 6.4 - - - +
147E LYS* 5.2 8.1 - - - +
148E TYR 3.8 1.8 + - - -
149E ILE* 1.3 77.3 - - - +
151E GLN* 1.3 88.9 + - - +
152E LYS* 3.1 13.2 + - + +
153E PHE* 2.6 36.3 + - - +
154E VAL* 3.2 6.5 + - - -
186E LEU* 4.8 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 151 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E ASP* 1.3 92.5 + - - +
152E LYS* 1.3 52.9 + - - +
154E VAL* 2.7 12.4 + - - +
155E LEU* 2.7 34.8 + - - +
186E LEU* 4.3 12.2 - - + +
188E ALA* 6.3 0.6 - - - +
189E TYR* 3.2 64.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 152 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D GLU* 5.1 10.7 + - - +
150E ASP* 2.9 11.0 + - + +
151E GLN* 1.3 79.1 - - - +
153E PHE* 1.3 58.6 + - - +
155E LEU* 3.9 9.9 - - + +
156E GLN* 3.0 53.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 153 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E VAL* 4.1 23.1 - - + -
89E PHE* 3.5 34.5 - + - -
90E ALA* 4.0 9.0 - - + -
94E PHE* 3.5 30.9 - + - -
131E PHE* 3.6 24.5 - + - -
148E TYR 4.9 1.3 - - - +
149E ILE* 4.1 22.4 - - + -
150E ASP 2.6 28.8 + - - +
152E LYS* 1.3 71.4 - - - +
154E VAL* 1.3 62.8 + - + -
156E GLN* 3.2 1.9 + - - +
157E LEU* 2.8 36.5 + - + +
179E ILE* 4.1 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 154 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E ILE* 5.1 0.7 - - + -
150E ASP 3.2 4.2 + - - +
151E GLN* 2.7 15.6 + - - +
153E PHE* 1.3 81.6 - - + +
155E LEU* 1.3 52.9 + - - +
157E LEU* 3.0 10.3 + - - +
158E LEU* 2.8 48.8 + - + +
176E LEU* 4.8 5.1 - - + +
179E ILE* 4.7 10.8 - - + -
186E LEU* 3.9 22.9 - - + -
189E TYR* 4.0 12.3 - - + -
190E ILE* 3.5 42.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D GLU* 3.2 43.1 - - + +
217D GLN* 4.1 22.2 - - - +
151E GLN 2.7 18.8 + - - +
152E LYS* 3.9 8.5 - - + +
154E VAL* 1.3 77.0 - - - +
156E GLN* 1.3 66.8 + - + +
158E LEU* 3.2 18.8 + - + +
159E GLU* 3.4 17.9 + - + +
189E TYR* 3.4 20.9 - - + +
193E GLN* 3.9 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 156 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E PHE* 3.1 52.7 - - + +
152E LYS* 3.0 46.5 + - + +
153E PHE* 5.4 0.4 - - - +
155E LEU* 1.3 80.9 - - + +
157E LEU* 1.3 63.0 + - - +
159E GLU* 3.4 25.5 + - - +
160E LEU* 3.7 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E PHE* 3.9 28.0 - - + -
94E PHE* 3.8 9.4 - - + -
153E PHE* 2.8 18.9 + - + +
154E VAL* 3.2 10.8 - - - +
156E GLN* 1.3 77.3 - - - +
158E LEU* 1.3 64.6 + - - +
160E LEU* 3.4 20.0 - - + +
161E PHE* 3.9 7.7 - - + -
172E LEU* 3.3 30.6 - - + +
175E THR* 4.3 10.8 - - + -
176E LEU* 4.3 29.6 - - + +
179E ILE* 3.9 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E VAL* 2.8 26.9 + - + +
155E LEU* 3.2 13.6 + - + +
157E LEU* 1.3 75.0 - - + +
159E GLU* 1.3 67.9 + - - +
161E PHE* 2.7 32.2 + - + +
176E LEU* 3.8 21.1 - - + -
190E ILE* 4.6 2.0 - - - +
193E GLN* 3.9 35.9 - - + +
194E ILE* 4.2 11.2 - - + -
197E ILE* 4.4 18.4 - - + +
214E LEU* 3.6 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 159 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D GLU 5.1 6.1 - - - +
217D GLN* 4.9 17.2 + - - +
218D ASP* 5.2 9.7 + - - +
95E ARG 5.2 3.1 - - - +
96E THR* 4.8 14.9 - - - +
97E LEU* 4.1 21.5 - - + +
155E LEU* 3.4 16.1 + - + +
156E GLN* 3.7 16.0 - - - +
157E LEU 3.4 0.6 - - - -
158E LEU* 1.3 76.1 - - - +
160E LEU* 1.3 56.1 + - + +
161E PHE* 2.4 20.1 + - - +
162E ASP* 3.4 15.8 + - - +
197E ILE* 5.2 4.7 - - - +
208E HIS* 5.5 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E MSE 3.2 31.0 - - + +
94E PHE* 3.6 34.8 - - + -
95E ARG* 4.0 34.5 - - - +
97E LEU* 4.2 14.7 - - + +
128E TYR* 4.1 9.6 - - - +
156E GLN 3.8 6.5 - - - +
157E LEU* 3.4 14.8 - - + +
159E GLU* 1.3 77.4 - - + +
161E PHE* 1.3 51.5 + - - +
162E ASP* 2.3 19.1 + - - -
163E SER 4.3 2.4 + - - -
168E GLU* 4.3 6.2 - - - +
169E ARG* 5.3 0.3 - - - +
172E LEU* 3.2 26.9 - - + +
----------------------------------------------------------
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