Contacts of the strand formed by residues 153 - 159 (chain E) in PDB entry 2WNU
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 153 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E LEU* 5.7 2.2 - - + -
113E ILE* 5.7 3.6 - - + -
145E TYR* 5.6 1.1 - - + -
147E ALA* 3.6 31.0 - - + -
149E SER* 4.2 10.3 - - - +
151E GLY 3.5 0.2 + - - -
152E ASN* 1.3 75.5 - - - +
154E CYS* 1.3 71.9 + - - +
155E VAL* 4.9 10.1 - - + +
170E PHE 3.8 1.3 - - - +
171E CYS* 3.4 1.7 - - - -
172E ASP* 3.0 38.3 + - - +
173E TYR* 4.4 1.0 - - - -
179E GLN* 4.3 0.9 - - - +
181E THR* 4.2 14.3 - - + +
199E ALA* 6.4 1.1 - - + -
202E LYS* 3.5 15.0 - - - +
203E ASN* 4.2 4.5 - - - -
204E SER 3.6 28.7 - - - +
205E LEU* 4.0 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 154 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E LEU* 1.3 80.2 - - - +
155E VAL* 1.3 60.2 + - - +
169E THR* 4.2 7.6 - - + -
170E PHE 3.2 4.5 - - - +
171E CYS* 2.0 48.7 - - - -
173E TYR* 3.8 15.5 - - - -
199E ALA* 4.4 1.4 - - - -
200E THR* 2.8 40.2 + - + +
202E LYS* 3.1 24.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E ILE* 3.6 29.6 - - + -
145E TYR* 2.9 41.7 - - + +
153E LEU* 5.2 11.0 - - + -
154E CYS* 1.3 74.5 - - - +
156E ASN* 1.3 67.7 + - - +
157E LEU 4.1 0.7 + - - +
169E THR* 3.2 3.3 - - - -
170E PHE* 2.9 40.2 + - + +
197E LEU* 3.6 27.4 - - + -
198E GLN 3.7 3.8 - - - +
205E LEU* 6.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 156 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E ASP* 5.5 1.6 + - - -
155E VAL* 1.3 74.9 - - - +
157E LEU* 1.3 61.5 + - - +
158E MET* 3.7 19.7 + - - +
166E LYS* 3.9 15.6 - - + +
168E VAL 3.5 4.9 - - - +
169E THR* 2.4 36.4 + - - +
197E LEU* 3.4 4.5 - - - -
198E GLN* 2.8 59.1 + - - +
199E ALA 4.6 0.6 + - - -
200E THR* 3.7 20.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
143E PHE* 4.7 11.7 - - + +
145E TYR* 6.1 0.7 - - + -
155E VAL* 4.1 1.8 + - + +
156E ASN* 1.3 70.1 - - - +
158E MET* 1.3 56.0 + - - +
166E LYS* 3.5 2.1 - - - -
167E VAL* 2.8 38.5 + - + +
168E VAL* 3.0 31.6 + - + -
170E PHE* 4.9 10.5 - - + -
184E GLY* 5.2 1.1 - - - -
185E MET* 3.5 35.4 - - + +
187E LEU* 4.5 8.7 - - + -
195E VAL* 3.7 29.2 - - + -
196E PHE 3.8 2.5 - - - +
197E LEU* 3.8 25.1 - - + +
215E PHE* 5.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 158 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E ASN* 3.7 9.6 - - - +
157E LEU* 1.3 74.1 - - - +
159E ARG* 1.3 60.0 + - - +
164E ALA* 3.9 21.5 - - + +
165E GLN 3.7 6.3 - - - -
166E LYS* 3.5 37.9 - - + +
167E VAL* 4.6 1.1 - - - -
187E LEU* 6.1 0.2 - - - -
194E ASN 4.3 0.9 - - - -
195E VAL* 3.1 31.2 - - - +
196E PHE* 2.8 51.1 + - + +
198E GLN* 3.4 42.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 159 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D ILE* 4.7 9.9 + - - +
116D THR* 5.3 2.0 + - - -
158E MET* 1.3 74.1 - - - +
160E GLY* 1.3 62.9 + - - +
163E ARG 4.0 0.2 - - - +
164E ALA* 3.3 4.9 - - - -
165E GLN* 2.8 40.4 + - - +
167E VAL* 3.9 26.5 - - + +
187E LEU* 3.4 30.8 - - + +
188E LYS* 3.5 20.4 + - - +
189E LEU* 3.7 25.8 - - + -
193E GLU* 4.1 18.2 - - + +
194E ASN 3.2 9.9 - - - +
195E VAL* 4.4 5.2 - - + -
----------------------------------------------------------
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