Contacts of the strand formed by residues 130 - 136 (chain B) in PDB entry 1R47
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 LYS 130 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLU* 3.1 35.1 + - + +
88B TYR* 3.5 36.5 - - + +
89B LEU* 2.9 28.1 + - - +
124B VAL* 3.8 3.1 - - - -
125B HIS* 5.4 4.4 + - + -
128B GLY 5.0 4.2 + - - +
129B LEU* 1.3 81.3 + - - +
131B LEU* 1.3 60.3 + - - +
165B ASP* 3.0 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PHE* 5.9 2.0 - - + -
88B TYR* 5.2 0.2 - - - -
89B LEU* 3.3 12.3 - - + +
90B CYS* 4.8 0.4 - - - -
91B ILE* 4.0 22.0 - - + -
117B ILE* 4.0 27.4 - - + -
120B LEU* 5.7 5.2 - - + -
121B ALA* 4.0 22.7 - - + +
124B VAL* 3.8 25.6 - - + +
125B HIS* 4.8 1.1 - - - +
130B LYS* 1.3 74.0 - - - +
132B GLY* 1.3 85.6 + - - +
133B ILE* 4.9 2.9 - - + +
163B GLY 5.0 2.7 - - - +
164B VAL* 3.7 13.8 - - + +
165B ASP* 2.8 40.1 + - - +
166B LEU* 3.0 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU 2.9 9.7 + - - -
90B CYS* 3.7 20.6 - - - -
91B ILE* 2.6 31.8 + - - +
131B LEU* 1.3 86.6 - - - +
133B ILE* 1.3 56.9 + - - -
164B VAL* 4.3 0.4 - - - -
166B LEU* 2.9 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B CYS* 6.0 0.2 - - - -
91B ILE* 3.4 31.2 - - + -
95B TRP* 3.3 55.9 - - + -
117B ILE* 5.1 5.6 - - + -
131B LEU* 5.6 3.4 - - + -
132B GLY* 1.3 74.8 - - - -
134B TYR* 1.3 67.1 + - - +
159B PHE* 3.6 32.5 - - + -
162B TRP* 5.5 2.0 - - + -
164B VAL* 4.0 19.3 - - + +
166B LEU* 2.8 6.9 + - - +
167B LEU* 3.2 13.6 - - + +
168B LYS* 2.9 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ILE 3.1 16.5 + - - +
92B ASP* 3.2 23.6 - - - +
93B ASP* 2.8 48.1 + - - -
95B TRP* 2.8 28.5 + - + -
133B ILE* 1.3 83.2 - - - +
135B ALA* 1.3 73.6 + - - +
136B ASP* 3.7 0.5 + - - -
141B THR* 3.5 16.6 - - + -
142B CYS 3.3 8.5 + - - -
159B PHE* 5.0 0.3 - - - -
168B LYS* 3.5 18.4 - - + -
170B ASP* 2.4 38.8 + - + +
1103B GAL 3.1 28.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B MET* 4.8 7.4 - - + -
106B LEU* 6.1 0.9 - - + -
134B TYR* 1.3 85.2 - - - +
136B ASP* 1.3 62.5 + - - +
148B SER* 4.4 6.7 - - - +
159B PHE* 4.2 15.7 - - + -
167B LEU* 3.7 14.1 - - + -
168B LYS 3.0 6.3 + - - +
169B PHE* 3.6 24.7 - - + -
170B ASP* 2.8 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B TYR* 4.6 0.2 - - + -
135B ALA* 1.3 79.0 - - - +
137B VAL* 1.3 71.1 + - - +
138B GLY 2.9 6.2 + - - -
140B LYS 2.9 17.8 - - - +
141B THR* 3.1 33.3 - - + +
142B CYS 3.4 6.2 + - - -
147B GLY* 3.2 9.9 + - - -
148B SER* 2.8 31.3 + - - -
169B PHE* 3.8 4.3 - - - -
170B ASP* 3.2 18.7 - - - +
172B CYS* 2.9 36.7 + - - +
----------------------------------------------------------
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