Contacts of the helix formed by residues 149 - 161 (chain E) in PDB entry 1S3Q
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 ASP 149 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ASP* 4.5 2.8 - - - +
150C LYS* 3.6 29.8 + - + +
151C ARG* 3.7 8.8 + - - +
146E ILE* 3.3 21.7 + - - +
147E GLY 3.4 0.4 - - - +
148E GLU* 1.3 73.5 - - - +
150E LYS* 1.3 59.2 + - - +
151E ARG* 2.9 26.2 + - - +
152E ALA* 2.9 22.2 + - + +
153E LEU* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 150 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148E GLU 3.1 14.5 + - - +
149E ASP* 1.3 72.0 + - - +
151E ARG* 1.3 66.0 + - + +
153E LEU* 3.4 17.3 + - + +
154E LEU* 3.0 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 151 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ASP* 3.8 25.1 + - - -
151C ARG* 3.3 41.8 + - - +
152C ALA 5.4 0.2 - - - +
149E ASP* 2.9 11.4 + - - +
150E LYS* 1.3 78.3 - - + +
152E ALA* 1.3 56.1 + - - +
154E LEU* 3.4 9.7 + - - +
155E PHE* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C LYS* 4.1 5.6 - - + -
151C ARG* 3.9 24.0 - - - +
154C LEU* 4.5 3.5 - - + +
146E ILE* 3.6 30.5 - - + +
149E ASP* 2.9 30.4 + - + +
151E ARG* 1.3 73.1 - - - +
153E LEU* 1.3 67.4 + - - +
155E PHE* 3.2 7.0 + - - +
156E LEU 3.0 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E LEU* 4.1 26.0 - - + -
41E PHE* 4.0 13.9 - - + -
85E PRO* 4.2 17.5 - - + -
143E LEU* 3.8 27.6 - - + -
146E ILE* 4.0 13.8 - - + +
149E ASP 3.1 15.5 + - - +
150E LYS* 3.4 22.0 - - + +
152E ALA* 1.3 76.5 - - - +
154E LEU* 1.3 59.1 + - + +
156E LEU* 3.2 6.2 + - - +
157E ASP* 2.8 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E GLY 5.2 3.6 - - - +
38E LEU* 3.7 27.6 - - + -
150E LYS* 3.0 24.9 + - + +
151E ARG* 3.7 8.7 - - - +
152E ALA 3.3 0.2 - - - -
153E LEU* 1.3 76.3 - - + +
155E PHE* 1.3 60.9 + - - +
157E ASP* 3.3 10.1 + - + +
158E LYS* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 155 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C ARG* 4.1 32.5 - - + +
154C LEU* 3.5 45.8 - - + -
155C PHE* 3.8 26.9 - + - -
158C LYS* 4.1 16.4 - - + -
142E LYS* 6.2 0.9 - - - -
151E ARG 3.1 13.1 + - - +
152E ALA* 3.2 9.8 + - - +
154E LEU* 1.3 75.0 - - - +
156E LEU* 1.3 61.2 + - - +
158E LYS* 3.1 38.5 + - - +
159E GLU* 3.0 40.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
154C LEU* 5.3 2.2 - - + -
41E PHE* 3.8 12.8 - - + -
139E ILE* 4.6 10.1 - - + -
142E LYS* 4.1 22.7 - - + -
143E LEU* 3.6 35.7 - - + -
146E ILE* 3.7 17.3 - - + -
152E ALA 3.0 12.5 + - - +
153E LEU 3.3 8.3 - - - +
155E PHE* 1.3 76.3 - - + +
157E ASP* 1.3 65.6 + - - +
159E GLU* 3.1 10.6 + - + -
160E LEU* 2.8 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 157 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E GLY 4.9 1.4 - - - +
38E LEU* 3.2 26.4 - - + +
39E LYS* 4.0 4.5 + - - +
40E GLY* 2.7 39.3 + - - -
41E PHE* 3.0 27.6 + - + -
153E LEU 2.8 16.6 + - - +
154E LEU* 3.4 16.9 - - - +
156E LEU* 1.3 73.9 - - - +
158E LYS* 1.3 65.0 + - - +
160E LEU* 3.3 0.9 + - - -
161E SER* 3.1 18.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
151C ARG* 5.3 3.7 - - - +
155C PHE* 5.0 9.3 - - - -
158C LYS* 4.0 18.1 - - - +
154E LEU 2.9 14.3 + - - +
155E PHE* 3.1 38.9 + - + +
157E ASP* 1.3 78.2 + - - +
159E GLU* 1.3 77.1 + - - +
161E SER* 2.6 29.2 + - - +
162E LEU* 3.6 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 159 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C LYS* 3.2 47.4 + - - +
155E PHE* 3.0 24.3 + - + +
156E LEU* 3.1 18.4 + - + +
158E LYS* 1.3 85.4 - - - +
160E LEU* 1.3 60.4 + - + +
162E LEU* 3.0 40.9 + - + +
163E ARG 4.1 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E GLY 3.5 15.6 - - - +
41E PHE* 3.7 45.8 - - + -
43E ASN* 3.1 8.7 - - - +
44E TRP* 3.6 31.6 + - + +
89E PHE* 4.7 1.6 - - + -
139E ILE* 4.1 20.9 - - + -
156E LEU* 2.8 36.1 + - + +
157E ASP 3.8 2.2 - - - +
159E GLU* 1.3 70.7 - - + +
161E SER* 1.3 60.9 + - - +
162E LEU 3.0 6.6 + - - -
163E ARG* 3.1 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 161 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E LYS 5.1 0.7 - - - -
40E GLY* 3.6 23.5 - - - -
43E ASN* 3.4 17.2 + - - +
157E ASP* 3.1 8.1 + - - -
158E LYS* 2.6 26.4 + - - +
160E LEU* 1.3 75.9 - - - +
162E LEU* 1.3 66.2 + - - +
163E ARG 3.3 0.9 - - - +
164E GLN* 5.6 0.9 + - - -
----------------------------------------------------------
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