Contacts of the helix formed by residues 162 - 167 (chain E) in PDB entry 1NZB
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 ALA 162 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E ILE* 2.8 12.2 + - + +
159E ARG* 2.5 18.5 + - - +
161E LEU* 1.3 71.2 - - - +
163E PHE* 1.3 55.9 + - - -
165E GLY* 4.0 4.3 - - - +
166E ILE* 3.9 13.8 + - - +
217E VAL* 6.5 0.2 - - - -
220E LEU* 3.6 36.1 - - + +
221E VAL* 4.4 8.5 - - - +
224E TRP* 4.1 14.4 - - + -
239E PHE* 3.0 18.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 163 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E ARG 3.0 2.9 + - - +
160E ASN* 3.4 10.1 - - - +
162E ALA* 1.3 77.1 - - - +
164E LEU* 1.3 73.1 + - + +
165E GLY 2.7 13.5 + - - -
166E ILE* 4.0 2.2 - - - +
167E ALA* 3.1 28.3 + - + +
174E ILE* 5.0 5.8 - - + -
177E ILE* 4.3 23.6 - - + -
239E PHE* 3.7 23.8 - + + -
261E LEU* 3.2 64.8 - - + -
264E ILE* 4.0 14.8 - - + -
265E PHE* 3.7 31.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E PHE* 3.6 20.6 - - + -
142E PHE* 2.8 26.8 - - + -
145E VAL* 4.0 11.7 - - + -
149E MET* 5.4 1.3 - - - -
160E ASN* 2.9 21.6 + - + +
161E LEU* 3.4 9.2 + - + +
163E PHE* 1.3 89.6 - - + +
165E GLY* 1.3 58.4 + - - +
167E ALA* 4.7 2.9 - - - -
168E TYR* 4.0 7.1 - - - +
264E ILE* 4.4 5.2 - - + -
265E PHE* 3.4 39.9 - - + -
268E THR* 3.1 43.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 165 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E PHE* 3.4 23.2 - - - -
161E LEU 3.3 8.8 + - - -
162E ALA* 4.6 2.5 - - - -
163E PHE 2.7 3.2 - - - -
164E LEU* 1.3 79.3 - - - +
166E ILE* 1.3 68.2 + - - +
167E ALA 3.2 0.4 - - - -
168E TYR* 2.9 14.2 + - - +
169E ASN* 2.9 10.9 + - - +
217E VAL* 3.6 14.8 - - - +
220E LEU* 5.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 166 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162E ALA 3.9 16.6 + - - +
163E PHE* 3.4 7.9 + - + +
165E GLY* 1.3 70.7 - - - +
167E ALA* 1.3 57.0 + - - +
169E ASN 2.6 23.9 + - - -
170E THR* 3.0 23.0 + - + +
172E LEU* 4.3 2.5 - - + -
177E ILE* 3.3 34.1 - - + -
180E ILE* 4.8 3.8 - - + -
195E ILE* 3.3 26.7 - - + -
213E LEU* 3.1 37.7 - - + -
217E VAL* 3.7 3.2 - - - +
221E VAL* 4.3 15.3 - - + -
238E LEU* 5.7 2.7 - - + -
239E PHE* 4.5 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 167 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E PHE* 3.1 25.5 + - + +
164E LEU* 4.7 2.0 - - - -
166E ILE* 1.3 81.6 - - - +
168E TYR* 1.3 57.4 + - - +
170E THR* 4.3 3.4 - - - -
171E LEU* 3.1 28.6 + - - -
172E LEU 4.0 7.4 + - - +
177E ILE* 4.9 8.7 - - + -
265E PHE* 4.2 16.8 - - + -
288E GLY 5.9 0.2 - - - +
291E ALA* 3.6 21.0 - - + +
----------------------------------------------------------
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