Contacts of the strand formed by residues 225 - 235 (chain A) in PDB entry 3RBQ
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 ARG 225 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE 3.5 5.2 - - - +
84A TYR* 4.0 15.4 + - - -
221A PHE* 3.2 4.3 - - - -
222A VAL 2.9 29.6 + - - +
223A ASP* 3.2 38.9 + - - +
224A ASP* 1.3 84.8 - - + +
226A LEU* 1.3 67.7 + - - +
227A VAL* 3.3 7.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 3.0 37.0 + - + +
76A LEU* 3.7 33.7 - - + +
77A CYS* 3.9 24.3 - - + +
81A GLU* 4.5 13.7 - - - +
219A PHE* 3.7 19.7 - - + -
220A TYR 3.3 24.2 - - - +
221A PHE* 3.4 14.8 - - + -
225A ARG* 1.3 71.9 - - - +
227A VAL* 1.3 63.8 + - - +
228A MET 3.4 16.6 - - - +
229A HIS* 4.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A CYS* 3.9 8.7 - - - -
78A SER 4.6 1.7 - - - +
81A GLU 3.6 19.3 - - - +
82A ASN* 3.4 24.7 + - - +
83A ILE* 5.3 1.1 - - + -
84A TYR* 4.0 25.1 - - + -
86A ILE* 4.6 9.2 - - + -
159A PHE* 5.0 0.2 - - + -
220A TYR* 2.8 26.6 + - + +
222A VAL* 3.7 26.9 - - + +
225A ARG* 3.5 16.6 - - + +
226A LEU* 1.3 76.4 - - - +
228A MET* 1.3 71.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A CYS* 3.7 7.5 - - - -
82A ASN* 3.4 33.2 - - + +
86A ILE* 3.8 28.3 - - - +
88A PHE* 3.7 30.5 - - + -
127A ARG* 5.6 0.2 - - - +
220A TYR* 2.8 46.9 + - + -
226A LEU* 3.4 7.4 - - - +
227A VAL* 1.3 86.2 - - + +
229A HIS* 1.3 62.0 + - - +
230A ASN* 4.2 18.4 - - - +
505G SER* 4.9 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A THR* 3.2 25.4 - - - -
74A ASP 3.6 9.0 - - - -
75A TYR* 3.4 15.0 - + - -
76A LEU* 2.9 25.7 + - + +
77A CYS* 3.7 18.3 - - - -
127A ARG* 3.4 22.2 + - - +
217A ASP* 2.8 24.6 + - - -
218A SER 3.3 11.0 - - - +
219A PHE* 3.4 25.0 - + + -
226A LEU* 4.7 2.5 - - + -
228A MET* 1.3 77.1 - - - +
230A ASN* 1.3 80.9 + - - +
231A LYS* 3.9 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE* 4.6 0.6 - - - -
126A GLY 4.7 1.0 - - - +
127A ARG* 3.3 30.2 + - - +
217A ASP* 3.6 0.9 - - - -
218A SER* 2.7 43.1 + - - -
220A TYR* 4.1 13.2 + - - -
228A MET* 4.2 18.8 - - - +
229A HIS* 1.3 84.1 + - - +
231A LYS* 1.3 62.7 + - - +
501G GLY* 3.0 38.3 + - - +
502G ALA* 4.2 3.6 - - - +
504G ALA* 4.1 4.6 - - - +
505G SER* 4.4 9.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 3.6 13.3 - - + +
72A THR* 2.9 40.5 + - - -
73A GLY 5.2 0.4 - - - -
74A ASP* 3.8 17.5 - - - +
75A TYR* 3.8 31.8 - - + +
127A ARG 2.8 6.4 + - - +
128A PHE* 3.2 15.7 - - + -
129A VAL* 3.0 25.1 + - - +
216A SER 3.5 5.4 - - - +
217A ASP* 2.8 29.5 + - - +
229A HIS* 3.9 6.3 - - - +
230A ASN* 1.3 76.0 - - - +
232A ALA* 1.3 63.5 + - - +
501G GLY* 5.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PHE* 4.0 5.5 - - - -
129A VAL* 3.0 24.5 - - + +
131A TYR* 4.1 4.3 - - + -
215A GLN* 3.3 4.3 - - - +
216A SER* 3.0 45.1 + - - +
231A LYS* 1.3 78.7 - - - +
233A ASP* 1.3 64.4 + - - +
234A TYR* 3.5 16.4 - - + +
500G DAO 4.7 3.4 - - - +
501G GLY* 4.7 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PHE* 3.4 15.9 - - + -
129A VAL 3.0 8.2 + - - +
130A ARG* 2.8 50.2 + - - +
131A TYR* 2.8 27.3 + - - +
212A TYR* 3.5 20.1 - - - +
214A THR 3.3 13.7 - - - +
215A GLN* 4.0 8.5 - - + +
232A ALA* 1.3 75.5 - - - +
234A TYR* 1.3 66.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A TYR* 3.3 26.9 - + + -
133A PHE* 3.8 24.7 - + - -
137A PHE* 5.7 0.7 - + - -
165A HIS* 3.2 22.4 - + - -
207A MET 5.6 0.2 - - - +
210A HIS 5.0 0.2 - - - +
211A PRO* 3.9 0.9 - - - +
212A TYR* 2.8 26.6 + - - +
214A THR* 3.0 32.4 + - + +
215A GLN 4.0 1.1 - - - -
216A SER* 2.9 43.1 + - - -
232A ALA* 3.5 17.5 - - + +
233A ASP* 1.3 76.3 - - - +
235A SER* 1.3 59.5 + - - +
236A TYR* 3.2 35.7 - + + +
500G DAO 3.6 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A TYR 2.7 11.2 + - - +
132A GLN* 4.3 8.8 + - - +
133A PHE* 2.8 32.1 + - - +
211A PRO* 3.6 12.0 - - - +
212A TYR* 3.3 32.6 + - - -
234A TYR* 1.3 74.9 - - - +
236A TYR* 1.3 63.8 + - - +
237A SER* 3.2 25.3 + - - -
238A GLY 4.6 0.9 + - - -
----------------------------------------------------------
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