Contacts of the helix formed by residues 177 - 183 (chain E) in PDB entry 1M54
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 177 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E SER 4.3 16.8 - - - +
148E GLY* 5.5 4.7 - - - -
152E ILE* 4.8 8.1 - - + -
169E MET* 5.2 4.7 - - + -
173E MET* 3.8 30.0 + - - -
174E SER* 6.3 0.7 - - - -
175E SER* 3.3 6.0 - - - +
176E GLU* 1.3 109.0 + - - +
178E VAL* 1.3 65.4 + - + +
179E ASP 3.3 1.3 - - - -
180E VAL* 3.1 11.2 - - + +
181E LEU* 3.0 35.2 + - + +
304E GLU* 2.7 43.5 + - - +
379E ARG* 4.9 0.7 - - - +
380E ASN* 3.9 23.6 - - - +
384E LYS* 4.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E MET* 3.6 30.3 - - + -
173E MET* 5.9 0.9 - - + -
174E SER 5.0 0.4 - - - -
175E SER* 3.6 32.1 - - - +
176E GLU 3.6 0.2 - - - +
177E LYS* 1.3 81.5 - - + +
179E ASP* 1.3 66.6 + - - +
181E LEU* 3.1 1.9 + - - +
182E ARG* 3.0 50.6 + - + +
188E ILE* 4.2 15.9 - - + +
190E ARG* 4.8 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 179 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175E SER* 4.0 6.1 + - - -
176E GLU 4.6 0.2 - - - +
177E LYS 3.3 1.0 - - - +
178E VAL* 1.3 78.1 - - - +
180E VAL* 1.3 67.2 + - - +
182E ARG* 3.9 10.7 - - - +
183E ALA* 3.1 23.9 + - - +
396E PHE* 2.9 39.0 - - + -
386F LEU* 4.1 13.3 - - + +
387F SER* 3.0 38.5 - - - +
388F ASP* 5.9 2.5 - - - +
389F ARG* 3.2 13.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 180 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E ILE* 4.4 11.9 - - + -
176E GLU 2.6 31.4 - - - +
177E LYS* 3.1 15.5 - - + +
179E ASP* 1.3 80.6 - - - +
181E LEU* 1.3 61.9 + - + +
183E ALA* 3.5 11.8 - - - +
184E LEU* 3.4 20.1 - - + +
379E ARG* 3.4 37.2 - - - +
339F ILE* 5.1 0.5 - - - +
345F LEU* 5.5 9.3 - - + +
382F MET* 3.8 15.7 - - + -
386F LEU* 4.8 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E SER* 4.7 10.3 - - - +
151E GLY 4.0 2.2 - - - +
152E ILE* 3.7 44.0 - - + +
155E ALA* 4.0 12.1 - - + -
167E ILE* 4.5 17.0 - - + -
169E MET* 4.5 10.1 - - + -
177E LYS* 3.0 20.5 + - + +
178E VAL 3.6 4.0 - - - +
180E VAL* 1.3 71.1 - - - +
182E ARG* 1.3 56.9 + - - +
183E ALA 2.9 2.0 - - - -
184E LEU* 2.5 38.8 + - + +
185E GLY 3.4 2.8 + - - -
186E ALA* 3.5 18.6 + - + +
188E ILE* 3.7 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 182 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E VAL* 3.0 46.4 + - + +
179E ASP* 3.9 10.1 - - - +
181E LEU* 1.3 72.5 - - - +
183E ALA* 1.3 61.0 + - - +
185E GLY* 3.3 13.2 + - - -
186E ALA 3.8 17.2 + - - +
187E GLU* 6.2 0.8 - - - +
188E ILE* 4.5 23.9 + - + +
388F ASP* 4.8 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E ASP 3.1 11.2 + - - +
180E VAL 3.5 11.0 - - - +
181E LEU 2.8 0.6 + - - -
182E ARG* 1.3 77.3 - - - +
184E LEU* 1.3 56.2 + - - +
185E GLY 3.2 1.1 - - - -
336F ARG* 4.6 8.4 - - + +
339F ILE* 3.3 26.3 - - + +
340F ALA* 3.0 30.8 + - - +
386F LEU* 3.6 17.3 - - + -
388F ASP* 5.7 1.5 + - - -
----------------------------------------------------------
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