Contacts of the helix formed by residues 160 - 167 (chain A) in PDB entry 6RLR
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 GLU 160 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 4.8 3.1 - - - +
158A GLY 3.9 4.2 + - - +
159A VAL* 1.3 81.2 - - - +
161A GLN* 1.3 66.6 + - - +
162A PHE* 3.3 13.2 - - + -
163A ILE* 3.3 13.0 + - + +
164A SER* 3.4 8.9 + - - -
129D TYR* 2.6 37.0 + - - +
133D LYS* 2.7 39.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLU* 1.3 71.5 - - - +
162A PHE* 1.3 59.9 + - - +
164A SER* 2.4 54.8 + - - -
165A ASP* 4.6 0.3 - - - +
173B LEU* 5.2 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 5.6 1.7 + - - -
160A GLU* 3.9 13.9 - - + -
161A GLN* 1.3 77.9 - - - +
163A ILE* 1.3 66.9 + - + +
165A ASP* 3.4 13.6 - - - +
166A ILE* 5.6 0.5 - - - +
129D TYR* 3.5 52.5 - + - -
132D LEU* 3.8 30.0 - - + +
133D LYS* 3.5 55.4 - - + -
137D GLU* 3.6 43.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 4.0 14.8 - - + -
147A HIS* 3.8 16.8 - - + -
153A CYS* 4.1 7.9 - - - -
154A GLY* 4.7 3.4 - - - -
159A VAL* 3.4 25.6 - - + -
160A GLU* 3.3 10.4 + - - +
161A GLN 3.1 0.8 - - - -
162A PHE* 1.3 89.3 - - + +
164A SER* 1.3 64.9 + - - +
165A ASP* 3.0 6.3 + - - -
166A ILE* 3.1 26.3 + - + +
167A CYS* 3.6 5.7 - - - -
125D TYR* 3.6 14.1 - - - +
129D TYR* 3.1 41.1 - - + -
132D LEU* 4.6 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A VAL* 4.1 12.6 - - - -
160A GLU 3.4 8.4 + - - -
161A GLN* 2.4 46.9 + - - -
163A ILE* 1.3 77.8 - - - +
165A ASP* 1.3 63.6 + - - +
166A ILE 3.5 0.9 + - - -
167A CYS* 3.7 5.2 + - - +
171B ASP* 4.3 6.9 - - - +
172B VAL* 3.3 28.4 - - - +
173B LEU* 5.2 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 2.7 31.1 + - - -
144A LYS* 5.8 1.0 - - - -
148A TYR* 5.8 0.2 + - - -
161A GLN 4.6 0.2 - - - +
162A PHE 3.4 21.0 - - - +
163A ILE* 3.9 1.2 - - - -
164A SER* 1.3 77.1 + - - +
166A ILE* 1.3 61.4 + - - +
167A CYS 3.6 3.9 - - - +
171B ASP* 5.1 6.6 - - - +
140D ARG* 4.5 8.8 + - - -
165D ASP* 5.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 3.2 66.2 - - + +
143A LEU* 3.9 10.1 - - + -
144A LYS* 4.1 25.8 - - + +
147A HIS* 2.9 43.9 + - + +
148A TYR* 3.9 12.0 - - - -
162A PHE 5.6 0.4 - - - +
163A ILE* 3.1 24.0 + - + +
165A ASP* 1.3 80.7 - - - +
167A CYS* 1.3 62.4 + - - +
132D LEU* 4.5 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TYR* 3.7 9.1 + - - -
153A CYS* 2.0 48.5 - - + -
159A VAL* 3.7 12.1 - - - -
163A ILE 3.6 10.3 - - - -
164A SER 3.7 1.9 + - - +
165A ASP 3.6 4.2 - - - +
166A ILE* 1.3 81.0 + - - +
168A PRO* 1.4 70.2 - - + +
169A LYS* 3.7 3.3 + - - +
178A VAL* 5.4 0.2 - - + -
171B ASP* 5.3 4.5 - - - +
172B VAL* 3.7 40.8 + - + +
----------------------------------------------------------
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