Contacts of the strand formed by residues 153 - 163 (chain E) in PDB entry 4QRR
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 LYS 153 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D MET* 3.8 19.7 - - + -
184D MET* 5.7 5.8 - - - -
186D PHE* 3.8 41.8 - - + -
147E GLU* 3.0 32.2 + - - +
148E ILE* 3.7 4.1 + - - +
151E THR* 3.2 22.7 + - - +
152E GLN* 1.3 80.1 - - - +
154E ALA* 1.3 60.9 + - - +
208E ARG* 3.5 32.1 - - - +
209E VAL 3.5 11.2 - - - +
210E SER* 4.9 4.3 - - - -
211E ALA* 4.0 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E PRO* 3.7 23.3 - - + -
147E GLU* 3.4 6.5 - - - -
148E ILE* 4.0 13.0 - - + -
153E LYS* 1.3 73.7 - - - +
155E THR* 1.4 60.0 + - - +
156E LEU 4.1 0.4 - - - -
207E LEU 3.6 0.5 - - - +
208E ARG* 3.4 2.6 - - - -
209E VAL* 2.8 43.2 + - + +
210E SER 4.5 2.6 - - - +
211E ALA* 5.0 0.9 - - - -
214E TRP* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 155 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D LEU* 3.6 10.9 - - - +
153D LEU* 3.8 26.2 - - + +
155D THR* 5.0 0.8 - - + +
179D LEU* 5.2 2.0 - - + -
190D SER* 5.9 1.8 - - - -
143E PRO* 3.4 20.7 - - - +
147E GLU* 2.7 33.6 + - - +
154E ALA* 1.4 70.0 - - - +
156E LEU* 1.3 61.9 + - - +
157E VAL* 4.3 4.0 - - + -
206E ARG* 4.1 24.7 - - + -
207E LEU 3.3 10.3 - - - +
208E ARG* 3.3 25.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E VAL* 4.2 17.7 - - + -
141E PHE 3.7 7.2 - - - +
142E GLU* 5.1 0.7 - - - -
143E PRO* 3.8 22.9 - - + -
155E THR* 1.3 72.2 - - - +
157E VAL* 1.3 60.5 + - - +
172E TRP* 3.9 16.7 - - + -
205E SER 3.9 0.5 - - - +
206E ARG* 3.4 3.8 - - - -
207E LEU* 2.8 56.7 + - + +
209E VAL* 4.1 19.3 - - + -
214E TRP* 4.2 21.1 - - + -
221E PHE* 3.9 28.7 - - + -
252E ALA* 4.7 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 157 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D LEU* 4.0 24.9 - - + +
151D VAL* 4.4 15.3 - - + -
153D LEU* 4.1 26.0 - - + -
192D VAL* 3.9 30.3 - - + -
141E PHE* 2.8 45.2 + - + -
155E THR* 3.9 9.4 + - + -
156E LEU* 1.3 77.3 - - - +
158E CYS* 1.3 69.4 + - - +
159E LEU* 5.1 0.9 - - + -
172E TRP* 4.4 2.5 - - - -
204E SER* 5.0 0.2 - - - -
205E SER 3.4 7.4 - - - +
206E ARG* 4.4 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 158 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E VAL* 3.9 15.7 - - - -
139E ALA 3.5 6.3 - - - +
140E VAL* 4.4 2.5 - - - +
141E PHE* 4.9 0.2 - - - -
157E VAL* 1.3 75.5 - - - +
159E LEU* 1.3 73.1 + - - +
160E ALA 4.3 0.4 - - - -
170E LEU* 4.0 21.1 - - - -
172E TRP* 3.5 17.6 - - + -
204E SER* 3.4 7.7 - - - -
205E SER* 2.9 29.4 + - - +
223E CYS* 3.1 37.2 - - + -
225E VAL* 4.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D LYS* 5.5 6.7 - - + -
151D VAL* 3.8 19.5 - - + -
192D VAL* 5.1 0.4 - - + -
194D TRP* 3.6 63.9 - - + -
137E GLU 2.9 17.3 - - - +
138E VAL* 3.4 0.3 - - - -
139E ALA* 3.1 21.4 + - + +
141E PHE* 3.8 29.4 - - + -
157E VAL* 5.1 0.9 - - + -
158E CYS* 1.3 82.2 - - - +
160E ALA* 1.3 59.6 + - - +
161E THR* 3.8 13.3 + - + +
203E LEU 3.6 12.6 - - - +
204E SER* 4.0 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E PRO* 4.3 12.6 - - + -
137E GLU 3.8 6.1 - - - -
138E VAL* 4.4 4.9 - - + -
158E CYS* 4.3 1.2 - - - -
159E LEU* 1.3 70.3 - - - +
161E THR* 1.3 60.3 + - - +
163E PHE* 3.3 20.4 - - + -
168E VAL* 5.7 0.9 - - + -
170E LEU* 4.7 4.9 - - + -
202E ALA* 3.4 0.5 - - - -
203E LEU* 2.8 48.5 + - + +
225E VAL* 4.3 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 161 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D LYS* 3.7 28.3 + - + +
194D TRP* 4.3 13.0 - - - +
136E PRO* 3.6 1.0 - - - +
137E GLU* 2.8 55.9 + - - +
159E LEU* 4.1 26.3 + - + +
160E ALA* 1.3 78.2 - - - +
162E GLY* 1.3 65.2 + - - +
163E PHE* 3.6 2.7 - - - -
192E GLU* 4.6 4.3 - - - +
201E TYR 4.3 2.9 - - - -
202E ALA* 4.1 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 162 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E PHE* 3.5 5.9 - - - +
135E PRO 3.0 13.9 - - - +
137E GLU* 5.1 5.1 - - - +
161E THR* 1.3 75.1 - - - +
163E PHE* 1.4 56.7 + - - +
192E GLU* 3.3 21.2 + - - -
200E ARG* 3.1 41.5 + - - -
201E TYR 3.4 2.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
134E PHE 3.3 11.0 - - - +
136E PRO* 3.7 32.8 - - + -
160E ALA* 3.3 34.1 - - + -
162E GLY* 1.4 78.1 - - - +
164E TYR* 1.3 60.5 + - - +
165E PRO 3.6 13.5 - - - -
166E ASP* 4.1 13.7 - - - -
168E VAL* 3.7 36.6 - - + -
189E PRO* 4.5 4.7 - - + -
200E ARG* 4.5 1.8 - - - -
201E TYR* 2.9 67.4 + - + +
202E ALA* 3.8 8.1 - - - -
203E LEU* 3.9 7.0 - - + -
227E PHE* 4.1 3.6 - + + -
----------------------------------------------------------
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