Contacts of the strand formed by residues 223 - 228 (chain A) in PDB entry 4RTP
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 VAL 223 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PRO* 6.0 0.4 - - - -
169A MET* 4.5 1.1 - - + -
178A VAL* 3.3 13.2 - - + +
180A CYS* 4.3 13.2 - - - -
213A ALA* 3.7 28.3 - - + +
216A LEU* 3.8 31.2 - - + -
221A ILE 3.5 12.6 - - - +
222A PRO* 1.3 79.0 - - - +
224A LEU* 1.3 62.6 + - - +
225A ILE* 4.0 15.7 - - + -
266A ALA 3.7 1.4 - - - +
267A LEU* 3.7 4.4 - - - +
268A TYR* 2.7 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 3.8 32.3 - - + +
24A HIS* 3.8 23.8 - - + +
25A LEU* 3.8 26.5 - - + -
26A PRO* 5.0 0.2 - - + -
177A VAL* 5.9 0.2 - - - +
178A VAL 2.8 8.5 + - - +
179A TYR* 3.3 18.6 - - + -
180A CYS 2.7 31.9 + - - -
223A VAL* 1.3 74.3 - - - +
225A ILE* 1.3 59.5 + - - +
265A LEU* 4.4 9.4 - - + -
266A ALA 3.3 27.4 - - - +
267A LEU* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A CYS* 3.5 19.7 - - + +
182A PRO* 4.2 10.8 - - + -
209A LEU* 4.4 18.4 - - + +
210A ALA* 4.6 0.4 - - - -
213A ALA* 3.9 15.0 - - + -
223A VAL* 4.0 9.4 - - + -
224A LEU* 1.3 80.6 - - - +
226A SER* 1.3 68.7 + - - +
227A ASN* 4.2 0.4 + - - -
237A TYR* 3.6 39.2 - - + +
264A LEU 3.5 1.2 - - - +
265A LEU* 3.4 2.4 - - - -
266A ALA* 2.7 48.4 + - + +
268A TYR* 3.8 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.9 2.9 - - - -
21A ILE* 4.2 4.5 - - - -
179A TYR* 2.9 31.2 + - - -
180A CYS 3.2 8.7 + - - -
181A ASP* 3.5 16.3 + - - +
182A PRO* 3.6 19.6 - - - +
184A TYR* 5.6 1.2 - - - -
224A LEU 4.3 0.4 - - - -
225A ILE* 1.3 73.2 - - - +
227A ASN* 1.3 67.1 + - - +
263A GLU* 4.2 8.3 - - - -
264A LEU 3.3 6.3 - - - -
265A LEU* 4.1 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PRO* 4.1 9.0 - - - +
183A PRO 4.4 1.0 + - - -
184A TYR* 3.9 12.8 - - - -
185A ALA* 3.2 32.2 + - - +
206A GLN* 3.4 20.0 + - - +
226A SER* 1.3 75.6 - - - +
228A HIS* 1.3 76.8 + - - +
233A THR* 4.0 10.0 - - - +
236A TRP* 5.0 0.2 - - - -
237A TYR* 3.3 35.0 + - + +
263A GLU* 3.5 12.8 + - - +
264A LEU* 2.6 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A TYR* 3.3 49.7 - + + +
185A ALA* 3.5 25.1 - - + +
187A LEU* 5.6 7.4 - - + -
227A ASN* 1.3 87.5 + - - +
229A ASP* 1.3 59.9 + - - +
230A THR* 3.5 13.5 - - + -
233A THR* 2.8 25.8 + - - +
261A VAL* 3.9 31.7 - - + +
262A ASP 3.8 4.4 + - - -
263A GLU* 4.5 8.8 + - + +
264A LEU* 4.0 2.5 - - - +
----------------------------------------------------------
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