Contacts of the helix formed by residues 144 - 153 (chain A) in PDB entry 1R2Y
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 SER 144 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PRO 4.3 9.2 - - - -
142A ALA 3.8 2.4 + - - -
143A PHE* 1.3 77.8 - - - +
145A PRO* 1.3 78.4 - - - +
146A ALA* 3.4 20.4 + - - +
147A VAL* 3.1 20.8 + - - +
148A LEU* 3.3 9.9 + - - +
204A HIS* 3.3 11.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A SER* 1.3 89.8 - - - +
146A ALA* 1.3 51.4 + - - +
148A LEU* 3.0 5.2 + - + +
149A ALA* 2.8 36.1 + - - +
200A ILE* 3.7 8.2 - - + +
201A GLU* 4.3 25.6 - - + +
204A HIS* 3.6 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A SER* 3.1 11.1 + - - +
145A PRO* 1.3 78.6 - - - +
147A VAL* 1.3 59.6 + - + +
149A ALA* 3.2 7.6 + - - +
150A GLU* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PRO* 4.2 15.3 - - + -
142A ALA 3.4 22.0 - - - +
143A PHE* 4.5 5.6 - - + -
144A SER* 3.1 21.8 + - - +
146A ALA* 1.3 77.1 - - + +
148A LEU* 1.3 61.8 + - - +
150A GLU* 3.7 7.1 + - - +
151A ARG* 3.5 24.3 + - + +
168A VAL* 4.1 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A PHE* 4.2 17.9 - - + -
144A SER 3.3 7.6 + - - +
145A PRO* 3.0 9.3 + - + +
147A VAL* 1.3 76.9 - - - +
149A ALA* 1.3 55.5 + - - +
151A ARG* 3.3 4.3 + - - +
152A ALA* 2.7 38.6 + - + +
162A LEU* 4.4 7.4 - - + +
163A LEU* 4.0 20.9 - - + -
168A VAL* 4.1 20.4 - - + -
169A VAL* 5.3 0.7 - - + -
200A ILE* 4.1 21.8 - - + +
203A LEU* 3.9 29.8 - - + -
204A HIS* 4.2 8.1 - - + +
207A MET* 4.0 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PRO 2.8 16.1 + - - +
146A ALA* 3.6 8.1 - - - +
148A LEU* 1.3 74.4 - - - +
150A GLU* 1.3 66.5 + - - +
152A ALA* 4.1 0.2 - - - -
153A VAL* 2.8 36.8 + - + +
200A ILE* 3.9 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ALA 2.8 21.0 + - - +
147A VAL* 3.7 10.1 - - - +
148A LEU 3.3 0.2 - - - -
149A ALA* 1.3 74.2 - - - +
151A ARG* 1.3 62.4 + - + +
153A VAL* 4.1 8.8 - - - +
154A LYS* 3.6 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A VAL* 3.5 13.8 + - + +
148A LEU 3.3 6.7 + - - +
149A ALA 3.1 0.2 - - - -
150A GLU* 1.3 81.9 - - + +
152A ALA* 1.3 66.7 + - - +
154A LYS* 3.6 12.2 + - - +
155A THR* 3.5 16.6 - - - +
157A ARG* 3.6 18.6 - - - +
162A LEU* 4.0 13.7 - - + +
165A ASP* 3.7 1.8 + - - -
167A THR* 3.2 39.8 + - - -
168A VAL* 3.4 32.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LEU* 2.7 24.4 + - + +
149A ALA* 3.0 8.0 + - - +
151A ARG* 1.3 68.9 - - - +
153A VAL* 1.3 53.1 + - - +
154A LYS 2.8 16.7 + - - -
155A THR* 3.3 19.9 + - - +
159A VAL* 6.5 0.2 - - + -
162A LEU* 3.9 20.6 - - + +
192A ALA* 3.6 22.7 - - + +
193A ALA 3.5 8.3 + - - -
195A LEU* 5.5 2.2 - - + -
200A ILE* 4.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ALA* 2.8 37.1 + - + +
150A GLU* 4.1 8.5 - - - +
152A ALA* 1.3 68.3 - - + +
154A LYS* 1.3 57.7 + - - +
192A ALA 5.4 0.2 - - - +
193A ALA* 4.5 16.6 - - - +
195A LEU 5.1 5.6 - - - +
200A ILE* 4.6 15.5 - - + -
----------------------------------------------------------
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