Contacts of the helix formed by residues 152 - 170 (chain E) in PDB entry 4Q9U
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 THR 152 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E PHE* 3.2 29.8 - - - +
151E LYS* 1.3 96.1 + - + +
153E GLY* 1.3 63.5 + - - +
154E GLN 3.2 3.5 + - - -
155E GLU* 3.4 20.9 + - + +
156E ILE* 3.7 26.9 + - + +
197E GLY* 6.1 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 153 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E LEU* 3.1 60.9 + - - +
147E LYS* 4.6 3.6 - - - -
149E PHE* 4.2 1.3 - - - -
150E HIS* 5.1 0.7 - - - -
151E LYS 3.2 6.5 - - - +
152E THR* 1.3 79.3 + - - +
154E GLN* 1.3 67.5 + - - +
156E ILE* 4.9 0.5 - - - +
157E TYR* 3.9 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 154 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E LYS* 5.4 13.2 - - - +
150E HIS* 5.4 8.3 + - - -
151E LYS 4.5 5.9 + - - +
152E THR 3.3 0.8 - - - -
153E GLY* 1.3 82.8 + - - +
155E GLU* 1.3 64.6 + - - +
156E ILE 3.4 0.4 - - - -
157E TYR* 3.1 10.3 + - + +
158E LYS* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 155 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E LYS 5.2 1.7 + - - +
152E THR* 3.4 18.5 + - + +
154E GLN* 1.3 77.6 - - - +
156E ILE* 1.3 71.7 + - + +
158E LYS* 4.2 1.8 - - - +
159E GLN* 3.1 42.6 + - - +
192E ARG* 3.5 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 156 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E LEU* 5.2 16.6 - - + -
149E PHE* 5.1 11.7 - - + -
152E THR* 3.7 26.2 + - + +
153E GLY* 4.9 2.7 - - - +
154E GLN 3.4 0.6 - - - -
155E GLU* 1.3 78.0 - - + +
157E TYR* 1.3 63.6 + - - +
159E GLN* 3.1 19.8 - - - +
160E THR* 2.3 42.7 + - - +
189E VAL* 6.2 2.0 - - + -
211E ILE* 6.4 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 157 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E PHE* 3.5 41.3 - + - -
146E LEU* 3.7 20.6 - - + +
153E GLY 3.9 5.4 + - - +
154E GLN* 3.1 13.7 + - + +
156E ILE* 1.3 82.0 - - - +
158E LYS* 1.3 70.5 + - + +
160E THR* 3.2 5.3 - - - -
161E LYS* 3.0 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 158 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E GLN 3.1 10.6 + - - +
155E GLU* 4.6 1.8 - - - +
157E TYR* 1.3 87.8 - - + +
159E GLN* 1.3 68.7 + - - +
161E LYS* 3.2 5.3 + - + +
162E LEU* 2.9 62.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 159 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E GLU* 3.1 34.2 + - - +
156E ILE* 3.1 36.5 + - - +
158E LYS* 1.3 75.7 - - - +
160E THR* 1.3 74.7 - - - +
162E LEU* 3.3 11.0 + - - +
163E PHE* 3.0 24.9 + - - +
185E PHE* 3.2 30.0 - - + -
189E VAL* 3.4 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 160 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E ILE* 2.3 36.8 + - - +
157E TYR* 3.2 6.7 - - - -
159E GLN* 1.3 79.7 - - - +
161E LYS* 1.3 64.6 + - - +
162E LEU 3.0 0.3 + - - -
163E PHE* 2.9 27.1 - - + -
164E LEU* 2.9 33.2 + - + +
185E PHE* 4.2 7.1 - - + -
214E TYR* 5.1 16.4 - - + -
215E ILE* 5.4 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 161 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157E TYR* 3.0 29.5 + - + +
158E LYS* 3.2 6.0 + - + +
160E THR* 1.3 80.2 - - + +
162E LEU* 1.3 58.7 + - + +
164E LEU* 3.6 22.9 - - + -
165E GLU* 2.9 57.5 + - - +
168E HIS* 5.7 5.2 - - - -
214E TYR* 6.0 0.9 - - - +
218E ARG* 4.2 22.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E LYS* 2.9 60.2 + - + +
159E GLN* 3.3 12.1 - - - +
160E THR 3.0 0.4 + - - -
161E LYS* 1.3 73.5 - - + +
163E PHE* 1.3 63.0 + - - +
164E LEU 2.9 4.0 - - - -
165E GLU* 3.0 40.1 - - + +
166E GLY* 3.0 5.9 + - - -
----------------------------------------------------------
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 GLN 3.0 12.5 + - - +
160E THR* 2.9 35.9 - - + -
162E LEU* 1.3 73.7 - - - +
164E LEU* 1.3 73.8 + - + +
166E GLY* 3.1 3.6 + - - +
167E MET* 2.8 82.1 + - + +
181E CYS* 4.8 9.2 - - - -
182E ALA* 4.5 6.1 - - + -
185E PHE* 3.5 65.5 - + + -
215E ILE* 4.4 14.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
160E THR* 2.9 24.4 + - + +
161E LYS* 3.2 30.3 - - + +
162E LEU 2.9 0.8 - - - -
163E PHE* 1.3 99.0 - - + +
165E GLU* 1.3 67.2 + - - +
166E GLY 3.0 0.9 - - - -
167E MET* 3.1 5.5 + - + +
168E HIS* 2.9 27.2 + - - +
214E TYR* 4.9 13.9 - - + +
215E ILE* 4.5 15.3 - - + -
218E ARG* 3.8 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E LYS* 2.9 40.6 + - - +
162E LEU* 3.0 39.9 - - + +
164E LEU* 1.3 73.3 - - - +
166E GLY* 1.3 62.6 + - - +
168E HIS* 3.4 19.7 + - + +
169E TYR* 2.9 47.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 166 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162E LEU 3.0 13.5 + - - -
163E PHE* 3.3 7.0 - - - -
164E LEU 3.0 0.6 - - - -
165E GLU* 1.3 79.5 - - - +
167E MET* 1.3 56.5 + - - +
169E TYR* 3.1 9.8 - - - +
170E LYS* 2.9 45.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 167 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E PHE* 2.8 68.9 + - + +
164E LEU* 3.1 5.8 + - + +
166E GLY* 1.3 71.0 - - - +
168E HIS* 1.3 60.8 + - - +
169E TYR 3.3 0.2 - - - -
170E LYS* 3.3 18.5 + - + +
171E ARG* 2.9 23.2 + - - +
178E GLN* 3.9 22.8 - - + +
181E CYS* 3.5 33.0 - - + -
182E ALA* 3.5 25.6 - - + -
222E TYR* 5.6 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 168 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E LYS* 5.7 5.0 - - - -
164E LEU 2.9 11.1 + - - +
165E GLU* 3.4 23.0 - - + -
167E MET* 1.3 73.6 - - - +
169E TYR* 1.3 89.8 + + - +
170E LYS 3.1 0.2 - - - -
171E ARG* 3.1 27.3 - - - +
222E TYR* 4.1 26.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 169 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E GLU* 2.9 38.7 + - + +
166E GLY* 3.1 12.1 - - - +
168E HIS* 1.3 100.9 - + - +
170E LYS* 1.3 60.5 + - + +
171E ARG 3.2 3.6 + - - -
172E ASP* 3.8 11.1 + - - +
173E LEU* 4.4 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 170 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166E GLY* 2.9 36.4 + - - +
167E MET* 3.3 24.7 - - + +
168E HIS 3.1 0.6 - - - -
169E TYR* 1.3 75.7 - - + +
171E ARG* 1.3 58.9 + - - +
172E ASP 3.0 2.9 - - - -
173E LEU* 2.7 56.4 + - + +
177E GLU 4.3 9.6 - - - +
178E GLN* 3.2 18.6 - - - +
181E CYS* 3.2 34.6 - - + +
----------------------------------------------------------
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