Contacts of the helix formed by residues 157 - 168 (chain A) in PDB entry 1R3R
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 ALA 157 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A GLY* 1.3 75.2 - - - -
158A PRO* 1.3 78.9 - - + +
159A TRP 3.4 0.7 - - - -
160A THR* 3.2 1.9 + - - -
161A LEU* 2.9 20.7 + - - +
216A LEU* 3.7 21.5 - - + +
217A PHE 3.0 16.4 + - - +
218A GLU* 3.4 35.0 - - + +
237A ILE* 4.5 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ALA* 1.3 89.7 - - + +
159A TRP* 1.3 64.6 + - - +
161A LEU* 3.2 1.1 + - + -
162A MET* 2.9 20.3 + - - +
192A LEU* 3.7 17.9 - - + +
195A LEU* 3.5 19.6 - - + +
196A THR* 3.6 21.3 - - - +
199A LEU* 3.7 21.1 - - + -
216A LEU* 4.4 8.7 - - + -
218A GLU* 5.0 0.2 - - - +
232A PHE 5.9 0.2 - - - +
233A ALA 5.7 0.7 - - - +
236A TYR* 3.7 25.8 - - + -
237A ILE* 5.0 3.1 - - + +
240A VAL* 4.4 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ALA 3.4 0.6 - - - -
158A PRO* 1.3 77.6 - - - +
160A THR* 1.3 64.0 + - - +
162A MET* 3.1 20.3 + - - +
163A THR* 2.9 35.9 + - + +
174A MET* 4.6 7.4 - - + -
177A ALA* 3.6 33.7 - - + -
178A LYS* 4.0 9.2 - - + -
181A LEU* 3.4 38.4 - - + -
192A LEU* 3.7 10.7 - - + +
218A GLU* 3.7 27.6 + - - +
220A HIS 2.9 32.4 + - - -
221A ALA* 4.3 1.8 - - - -
223A HIS* 4.9 1.3 - - + -
224A LEU* 3.6 35.9 - - + +
232A PHE* 4.6 3.3 + - + +
233A ALA* 4.0 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ILE* 4.2 9.9 - - + -
157A ALA 3.2 6.2 + - - +
159A TRP* 1.3 78.6 - - - +
161A LEU* 1.3 61.3 + - - +
163A THR* 2.6 26.6 + - - -
164A TYR* 3.3 24.1 + - + -
217A PHE 3.9 11.4 - - - +
218A GLU* 2.6 25.2 + - - -
219A SER* 3.1 22.6 + - - +
220A HIS* 3.0 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ILE* 3.5 36.1 - - + +
88A LEU* 4.6 3.8 - - + -
90A VAL* 3.9 31.4 - - + -
91A PRO* 4.1 11.7 - - + +
156A GLY* 3.4 31.9 - - - +
157A ALA 2.9 18.0 + - - +
158A PRO* 3.7 4.0 - - + +
160A THR* 1.3 74.8 - - - +
162A MET* 1.3 63.3 + - - +
164A TYR* 3.2 7.0 + - - +
165A MET* 3.0 29.4 + - - +
195A LEU* 4.1 17.9 - - + -
199A LEU* 4.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PRO 2.9 14.4 + - - +
159A TRP* 3.1 22.6 + - + +
161A LEU* 1.3 76.8 - - - +
163A THR* 1.3 63.6 + - - +
165A MET* 3.1 6.4 + - - -
166A VAL* 3.0 29.0 + - + +
177A ALA* 3.9 7.4 - - + +
180A TRP* 3.7 30.1 - - + -
181A LEU* 3.9 10.3 - - + -
188A SER* 3.7 25.6 - - - +
191A LEU* 3.7 15.9 - - + -
192A LEU* 3.9 31.2 - - + -
195A LEU* 3.8 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TRP* 2.9 60.5 + - + +
160A THR 2.6 17.5 + - - -
162A MET* 1.3 76.5 - - - +
164A TYR* 1.3 55.7 + - - +
167A GLU* 2.8 36.1 + - - +
169A GLY 4.7 1.3 - - - -
174A MET* 3.7 25.1 - - - -
177A ALA* 4.1 9.2 - - + -
220A HIS* 2.8 24.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ILE* 4.0 23.6 - - + +
88A LEU* 3.6 36.1 - - + -
106A PRO* 4.4 17.8 - - + +
108A PHE* 3.4 14.6 - + + -
160A THR* 3.3 25.3 + - + -
161A LEU* 3.2 8.8 + - - +
163A THR* 1.3 82.8 + - - +
165A MET* 1.3 58.4 + - + +
168A GLY* 2.8 29.8 + - - -
169A GLY* 3.8 30.7 - - - -
170A GLY* 4.3 4.8 - - - -
219A SER* 5.6 2.3 - - - -
220A HIS* 3.6 31.6 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PRO* 3.7 28.7 - - + -
94A LEU* 4.3 11.2 - - + -
96A MET* 3.6 29.6 - - + +
108A PHE* 4.8 2.7 - - + -
111A PRO* 3.3 10.4 - - - +
112A LEU* 2.9 45.3 + - + -
121A LEU* 4.3 15.0 - - + -
161A LEU 3.0 15.8 + - - +
162A MET* 3.1 6.7 + - - +
164A TYR* 1.3 78.8 - - - +
166A VAL* 1.3 57.6 + - + +
168A GLY* 4.8 0.2 - - - -
191A LEU* 4.1 12.3 - - + -
195A LEU* 3.8 30.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A PRO* 3.4 3.6 - - - +
112A LEU* 3.5 20.9 - - + +
113A ARG* 2.5 35.3 + - - +
162A MET* 3.0 31.8 + - + +
165A MET* 1.3 78.8 - - - +
167A GLU* 1.3 60.8 + - - +
168A GLY 3.3 0.2 - - - -
176A GLN* 3.9 8.1 - - + -
177A ALA* 3.7 30.1 - - + +
180A TRP* 3.8 32.5 - - + -
191A LEU* 4.4 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A PRO* 4.7 0.3 - - - +
113A ARG* 3.1 16.4 + - - +
163A THR 2.8 21.7 + - - +
166A VAL* 1.3 76.4 - - - +
168A GLY* 1.3 60.6 + - - +
169A GLY 3.3 14.9 + - - +
170A GLY 5.0 1.7 - - - +
171A SER* 3.9 15.2 + - - -
174A MET* 3.1 35.8 - - - -
175A ALA 4.5 0.5 + - - -
176A GLN* 2.9 28.6 + - - +
177A ALA* 2.8 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A SER* 3.2 12.3 + - - -
108A PHE* 2.9 46.0 + - - +
111A PRO* 4.0 9.9 - - - -
164A TYR 2.8 15.9 + - - -
166A VAL 3.3 2.0 - - - -
167A GLU* 1.3 78.1 - - - +
169A GLY* 1.3 56.4 + - - +
----------------------------------------------------------
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