Contacts of the helix formed by residues 168 - 180 (chain A) in PDB entry 2RRB
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 ASN 168 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A CYS* 3.9 7.7 - - - +
143A PRO* 4.9 3.2 - - - +
166A PHE* 3.3 9.1 - - - +
167A GLU* 1.3 104.8 + - - +
169A VAL* 1.3 64.5 + - - +
170A ASP* 4.2 9.2 - - + +
171A ASP* 2.9 36.2 + - - +
172A ALA 3.4 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PRO* 3.9 16.8 - - + +
117A ASN* 3.5 32.8 - - - +
118A CYS* 3.9 17.6 - - + +
168A ASN* 1.3 71.4 - - + +
170A ASP* 1.3 61.9 + - + +
172A ALA* 3.4 2.1 + - - +
173A LYS* 2.9 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASN* 3.3 7.7 - - + +
169A VAL* 1.3 79.4 - - + +
171A ASP* 1.3 62.7 + - - +
173A LYS* 3.6 21.8 + - - +
174A GLU* 3.2 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TYR* 3.6 22.4 - - - +
142A GLY* 3.8 13.7 - - - -
143A PRO* 3.6 13.0 - - - +
166A PHE* 3.5 22.7 - - + -
168A ASN* 2.9 42.5 + - - +
170A ASP* 1.3 77.6 - - - +
172A ALA* 1.3 60.6 + - - +
174A GLU* 3.4 4.1 + - - +
175A ALA* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN 3.2 26.5 - - - +
118A CYS* 3.8 13.9 - - - +
120A LEU* 3.6 9.7 - - + +
166A PHE* 3.7 26.2 - - + -
168A ASN 3.4 2.5 + - - +
169A VAL 3.4 6.0 + - - +
171A ASP* 1.3 77.3 - - - +
173A LYS* 1.3 57.9 + - - +
175A ALA* 3.6 1.0 - - - +
176A LYS* 2.9 31.9 + - - +
193A PHE* 3.9 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PRO* 4.0 25.2 - - + +
169A VAL* 2.9 32.2 + - + +
170A ASP* 3.7 21.3 - - - +
172A ALA* 1.3 73.8 - - - +
174A GLU* 1.3 64.8 + - - +
176A LYS* 3.9 1.4 - - - +
177A GLU* 3.1 41.5 + - - +
193A PHE* 3.9 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LYS 4.5 2.9 - - - +
141A TYR* 4.1 25.6 - - + +
170A ASP* 3.2 15.3 + - - +
171A ASP* 3.7 8.0 - - - +
173A LYS* 1.3 75.4 - - - +
175A ALA* 1.3 61.6 + - - +
177A GLU* 3.3 10.2 + - - +
178A ARG* 2.8 69.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 3.8 7.2 - - + -
138A PHE* 4.0 4.9 - - + -
141A TYR* 3.4 31.1 - - + +
166A PHE* 3.5 22.9 - - + -
171A ASP 3.0 17.5 + - - +
172A ALA 3.6 4.7 - - - +
174A GLU* 1.3 75.1 - - - +
176A LYS* 1.3 57.3 + - - +
178A ARG 3.1 0.5 + - - -
179A ALA* 2.9 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ALA* 5.2 6.1 - - - +
113A ASN 5.1 2.8 + - - -
114A PRO* 6.0 1.8 - - - +
120A LEU* 4.0 10.0 - - + +
172A ALA 2.9 21.9 + - - +
173A LYS 3.9 1.6 - - - +
175A ALA* 1.3 71.1 - - - +
177A GLU* 1.3 62.1 + - + +
178A ARG 3.6 0.2 + - - -
180A ASN* 3.2 37.3 - - + +
191A VAL* 3.4 26.8 + - + +
192A ASP* 3.3 37.2 + - - +
193A PHE* 3.8 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LYS* 3.1 32.9 + - - +
174A GLU* 3.3 7.2 + - - +
176A LYS* 1.3 79.5 - - + +
178A ARG* 1.3 61.7 + - + +
180A ASN* 4.9 2.3 - - - +
193A PHE* 6.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LYS 5.3 1.0 + - - -
141A TYR* 3.3 39.3 + - + +
174A GLU* 2.8 55.4 + - + +
175A ALA 3.1 1.2 + - - -
177A GLU* 1.3 82.6 - - + +
179A ALA* 1.3 63.7 + - - +
180A ASN 3.6 2.9 - - - +
182A MET* 4.6 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 4.6 3.4 - - + -
138A PHE* 3.9 30.7 - - + -
141A TYR* 4.2 13.0 - - + -
175A ALA 2.9 17.4 + - - +
178A ARG* 1.3 71.9 - - - +
180A ASN* 1.3 64.4 + - - +
181A GLY 3.0 4.3 + - - -
182A MET* 3.3 34.8 + - - +
189A ILE* 3.5 8.7 - - + +
191A VAL* 4.0 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LYS* 3.2 32.0 + - - +
177A GLU 4.9 1.9 - - - +
178A ARG 3.6 4.8 - - - +
179A ALA* 1.3 73.1 - - - +
181A GLY* 1.3 61.0 + - - +
182A MET 3.7 0.5 + - - -
190A ARG* 3.5 17.3 - - - +
191A VAL* 2.8 49.1 + - + +
192A ASP* 5.7 0.8 + - - -
----------------------------------------------------------
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