Contacts of the helix formed by residues 165 - 175 (chain A) in PDB entry 1R1M
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 MET 165 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLN* 1.3 89.3 - - - +
166A THR* 1.3 63.7 + - - +
167A GLN 3.5 2.0 - - - -
168A VAL* 3.8 23.1 - - + -
169A CYS* 3.0 28.6 + - - +
192A CYS* 3.5 20.0 - - - +
193A ILE* 3.7 18.2 - - + -
195A PRO* 3.9 33.7 - - + -
196A ASP* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 3.7 57.2 - - + +
163A ALA* 4.4 14.5 + - - +
164A GLN 3.6 2.2 - - - -
165A MET* 1.3 75.6 - - - +
167A GLN* 1.3 58.5 + - - +
169A CYS* 4.1 0.5 - - - +
170A GLU* 2.9 40.5 + - + +
189A LEU* 5.1 0.2 - - - +
193A ILE* 4.7 2.2 - - - +
196A ASP* 4.2 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLN 5.0 1.6 + - - +
165A MET 3.5 0.6 - - - -
166A THR* 1.3 76.8 - - - +
168A VAL* 1.3 73.8 + - + +
169A CYS 3.1 0.2 + - - -
170A GLU* 3.2 6.2 + - - +
171A ALA* 2.9 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLN 4.5 8.5 + - - +
165A MET* 3.2 44.2 - - + +
167A GLN* 1.3 81.1 - - + +
169A CYS* 1.3 72.5 + - - +
171A ALA* 3.7 4.7 - - - +
172A GLU* 2.9 31.9 + - - +
192A CYS* 4.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A MET* 3.0 24.3 + - - +
166A THR 4.1 0.4 - - - +
168A VAL* 1.3 87.0 - - - +
170A GLU* 1.3 65.1 + - - +
172A GLU* 3.6 1.3 - - - +
173A VAL* 2.9 28.4 + - - +
189A LEU* 3.9 6.7 - - + +
192A CYS* 2.0 67.7 - - + +
193A ILE* 3.6 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 3.5 22.9 - - + -
166A THR* 2.9 36.1 + - + +
167A GLN* 3.9 8.1 - - - +
169A CYS* 1.3 76.6 - - - +
171A ALA* 1.3 59.8 + - - +
173A VAL* 2.9 27.2 - - - +
174A ALA* 3.1 14.0 + - - +
189A LEU* 4.0 19.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLN* 2.9 32.0 + - - +
168A VAL* 3.7 5.2 - - - +
170A GLU* 1.3 75.9 - - - +
172A GLU* 1.3 66.4 + - - +
174A ALA* 3.9 4.4 - - - +
175A LYS* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A VAL* 2.9 20.9 + - - +
169A CYS* 3.6 5.2 - - - +
171A ALA* 1.3 76.5 - - - +
173A VAL* 1.3 61.5 + - - +
175A LYS* 3.2 25.2 - - + +
176A LEU* 4.3 9.4 - - + +
188A ALA* 6.2 0.2 - - - +
192A CYS* 3.8 28.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A CYS 2.9 15.5 + - - +
170A GLU* 2.9 35.9 - - - +
172A GLU* 1.3 73.8 - - - +
174A ALA* 1.3 63.9 + - - +
175A LYS 2.9 4.9 - - - -
176A LEU* 2.9 29.2 + - - +
185A LYS* 3.3 48.9 - - + +
188A ALA* 4.7 10.8 - - + -
189A LEU* 4.6 10.8 - - + +
192A CYS* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLU 3.1 15.3 + - - +
171A ALA* 3.9 4.7 - - - +
173A VAL* 1.3 78.3 - - + +
175A LYS* 1.3 52.5 + - - +
176A LEU* 2.7 17.0 + - - -
177A GLY* 3.9 9.5 + - - -
185A LYS* 6.0 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ALA 3.1 13.6 + - - +
172A GLU* 3.2 19.7 - - + +
173A VAL 2.9 1.0 - - - -
174A ALA* 1.3 74.2 - - - +
176A LEU* 1.3 74.5 + - + +
177A GLY 4.2 0.2 - - - -
----------------------------------------------------------
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