Contacts of the helix formed by residues 151 - 165 (chain E) in PDB entry 5AQP
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 ASN 151 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E GLY 4.9 2.4 + - - -
76E ARG* 6.3 0.2 - - - +
149E TYR 3.5 2.2 + - - +
150E PHE* 1.3 76.0 - - - +
152E ASP* 1.3 66.3 + - - +
153E SER* 3.1 12.3 + - - -
154E GLN* 2.7 58.0 + - - +
155E ARG* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 152 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E ASN* 1.3 76.6 - - - +
153E SER* 1.3 57.9 + - - +
155E ARG* 3.9 8.2 - - - +
156E GLN* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 153 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E GLY* 2.7 28.7 + - - -
151E ASN* 3.1 10.2 + - - -
152E ASP* 1.3 79.9 - - - +
154E GLN* 1.4 56.9 + - - +
156E GLN* 3.9 4.6 - - - +
157E ALA* 3.0 30.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
71E LYS 5.3 0.8 + - - -
74E ILE* 3.3 18.2 + - - +
75E GLY* 3.8 15.9 - - - +
76E ARG* 3.4 41.8 + - + +
149E TYR* 4.1 5.2 - - - +
150E PHE* 3.2 47.1 - - + -
151E ASN* 2.7 50.0 + - - +
153E SER* 1.4 71.7 - - - +
155E ARG* 1.3 59.3 + - - +
157E ALA* 4.0 2.1 - - - +
158E THR* 2.9 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 155 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E VAL* 3.5 27.2 - - + +
147E PRO 3.3 9.0 + - - -
148E ALA 3.1 26.3 + - - -
150E PHE* 3.0 25.9 + - + -
151E ASN 3.0 17.2 + - - +
152E ASP* 3.9 8.1 - - - +
154E GLN* 1.3 75.6 - - - +
156E GLN* 1.4 60.0 + - - +
158E THR* 3.3 6.3 + - - -
159E LYS* 3.1 27.4 + - - +
172E ILE* 4.6 19.0 + - + +
174E ASN* 2.9 29.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
152E ASP 3.0 19.8 + - - +
153E SER* 3.9 6.3 - - - +
155E ARG* 1.4 74.4 - - - +
157E ALA* 1.3 56.4 + - - +
159E LYS* 3.2 12.7 + - - +
160E ASP* 2.9 65.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 157 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E ILE* 3.6 23.6 - - + -
75E GLY* 3.7 14.1 - - - +
117E GLU* 3.5 26.7 - - + +
153E SER 3.0 19.8 + - - +
154E GLN 4.0 1.6 - - - +
156E GLN* 1.3 74.2 - - - +
158E THR* 1.4 56.7 + - - +
160E ASP* 3.4 10.0 + - - +
161E ALA* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 158 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E LEU* 4.1 15.7 - - + +
74E ILE* 4.0 16.7 - - - +
124E LEU* 4.5 2.3 - - - +
144E VAL* 4.1 24.4 - - + +
145E THR 4.6 0.9 - - - +
146E VAL* 3.6 22.9 - - + -
150E PHE* 3.7 13.7 - - - -
154E GLN 2.9 20.0 + - - -
155E ARG 3.6 5.2 - - - -
156E GLN 3.3 0.4 - - - -
157E ALA* 1.4 73.5 - - - +
159E LYS* 1.4 64.8 + - - +
161E ALA* 3.2 5.3 + - - +
162E GLY* 3.2 17.3 + - - -
169E VAL* 5.5 0.2 - - - +
172E ILE* 4.3 4.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 159 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E ARG 3.1 14.0 + - - +
156E GLN* 3.6 19.3 - - - +
158E THR* 1.4 73.9 - - - +
160E ASP* 1.4 57.7 + - - +
162E GLY* 3.1 4.9 + - - -
163E THR* 3.0 29.9 + - - +
169E VAL* 4.2 13.8 - - + +
172E ILE* 4.5 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 160 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E GLU* 4.7 14.2 - - + +
156E GLN* 2.9 51.5 + - - +
157E ALA* 3.5 10.3 - - - +
158E THR 3.3 0.2 - - - -
159E LYS* 1.4 73.0 - - - +
161E ALA* 1.4 58.4 + - - +
163E THR* 3.3 7.5 + - - -
164E ILE* 2.9 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E LEU* 5.3 0.9 - - + -
74E ILE* 4.5 0.4 - - + -
117E GLU* 3.3 28.2 - - - +
120E SER* 3.9 14.1 - - - -
121E SER* 3.2 32.6 - - - +
124E LEU* 3.7 9.2 - - + -
157E ALA 3.0 13.9 + - - +
158E THR* 3.4 12.6 - - - +
160E ASP* 1.4 74.5 - - - +
162E GLY* 1.3 61.1 - - - +
164E ILE* 4.6 0.4 - - - -
165E ALA* 3.2 10.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
124E LEU* 3.5 15.6 - - - +
144E VAL* 5.6 0.4 - - - -
158E THR 3.2 7.8 + - - -
159E LYS 3.1 8.9 + - - -
161E ALA* 1.3 76.5 - - - +
163E THR* 1.3 58.4 + - - +
165E ALA* 3.4 6.5 + - - +
166E GLY 3.5 0.2 + - - -
167E LEU* 3.0 37.2 + - - +
169E VAL* 3.8 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 163 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E LYS 3.0 14.1 + - - -
160E ASP* 3.3 10.8 + - - -
162E GLY* 1.3 73.0 - - - +
164E ILE* 1.3 68.9 + - + +
166E GLY* 3.1 14.2 + - - -
167E LEU 3.7 11.5 + - - +
169E VAL* 4.5 3.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 164 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E GLU* 4.5 18.2 - - + +
118E GLU* 4.5 22.7 - - + -
121E SER* 3.7 21.8 - - - +
160E ASP* 2.9 28.8 + - + +
162E GLY 3.4 0.2 - - - -
163E THR* 1.3 77.3 - - + +
165E ALA* 1.3 61.0 + - - +
166E GLY* 3.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 165 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E SER* 3.3 16.4 - - - +
124E LEU* 4.1 8.3 - - + -
125E THR* 3.2 37.1 + - - +
128E LYS* 3.6 20.3 + - - +
161E ALA 3.2 12.1 + - - +
162E GLY 3.7 6.3 - - - +
163E THR 3.2 0.6 - - - -
164E ILE* 1.3 78.1 - - - +
166E GLY* 1.3 56.8 + - - +
167E LEU* 3.5 5.6 - - + +
----------------------------------------------------------
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