Contacts of the strand formed by residues 223 - 228 (chain B) in PDB entry 4MXR
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 THR 223 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B MET* 3.9 2.6 - - - +
133B GLY 3.3 6.3 - - - +
135B ILE* 4.2 4.9 - - + -
216B PHE* 3.9 22.8 - - + -
219B THR* 2.8 33.5 + - - +
220B GLY 2.8 24.0 + - - -
222B ASN* 1.3 73.4 - - - +
224B PHE* 1.3 73.9 + - - +
225B PHE 3.7 3.0 + - - +
265B THR* 2.7 16.7 + - - -
266B VAL* 3.5 11.5 - - + -
267B MET 2.9 23.6 + - - -
268B MET 3.8 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER* 3.6 22.9 - - - -
120B ASN* 3.7 10.5 - - + -
121B GLY* 3.9 20.9 - - - -
124B MET* 4.1 17.5 - - + -
133B GLY 2.8 14.7 + - - +
134B VAL* 4.0 20.6 - - + -
135B ILE* 3.1 26.2 + - - +
158B PHE* 4.8 1.8 - + - -
161B LEU* 4.8 3.1 - - + -
222B ASN 3.8 1.0 + - - -
223B THR* 1.3 71.0 - - - +
225B PHE* 1.3 61.2 + - - +
226B SER* 3.4 19.8 + - - -
268B MET* 3.6 25.4 - - + -
270B ASP* 3.3 48.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ILE* 3.7 17.9 - - + -
137B VAL* 4.0 18.6 - - + -
212B LEU* 4.1 22.0 - - + -
216B PHE* 3.9 11.4 - + + -
223B THR* 3.7 1.6 + - - -
224B PHE* 1.3 68.8 - - - +
226B SER* 1.3 60.4 + - - +
227B PHE* 3.6 26.7 - + + -
256B MET* 4.2 11.4 - - + -
257B CYS* 4.2 5.8 - - - -
260B ALA* 3.6 24.7 - - + -
266B VAL* 3.8 17.7 - - + -
268B MET 3.0 16.0 + - - +
269B MET* 3.1 62.0 - - + +
270B ASP 3.2 2.9 + - - -
294B PHE* 5.4 0.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASN* 4.5 2.1 + - - -
117B SER* 3.2 16.8 + - - -
135B ILE 3.0 17.3 + - - +
136B ASN* 3.5 3.6 + - - +
137B VAL* 2.8 30.1 + - - +
158B PHE* 3.6 19.9 - - - -
224B PHE* 3.4 17.4 + - - -
225B PHE* 1.3 72.6 - - - +
227B PHE* 1.3 60.6 + - - +
228B ASP 4.0 0.4 + - - -
270B ASP* 2.6 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASN* 6.0 0.4 - - - -
137B VAL* 3.6 17.0 - - + -
225B PHE* 3.6 28.7 - + + -
226B SER* 1.3 72.3 - - - +
228B ASP* 1.3 71.1 + - - +
229B VAL* 3.4 3.4 + - - -
231B SER* 3.2 20.9 - - - -
232B LEU* 3.5 22.4 - - + -
248B LEU* 4.3 2.2 - - + -
253B ALA* 4.0 11.4 - - + -
256B MET* 3.9 22.4 - - + -
257B CYS* 4.1 9.2 - - - -
269B MET* 4.2 9.2 - - + -
270B ASP* 3.0 19.5 + - - +
271B MET* 3.2 7.5 - - + +
272B SER* 3.1 22.9 + - - -
290B MET* 3.5 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASN* 3.3 17.6 + - - +
136B ASN* 4.5 1.7 + - - +
137B VAL 2.8 16.4 + - - +
138B ASP* 3.4 9.6 - - + +
226B SER 3.9 1.0 + - - -
227B PHE* 1.3 69.6 - - - +
229B VAL* 1.3 59.9 + - - +
230B ASP* 2.9 25.1 + - - +
231B SER* 2.8 24.6 + - - -
272B SER 3.8 6.1 - - - +
273B GLU* 3.2 17.6 - - - +
400B MN 2.1 31.7 + - - -
401B MN 2.3 19.1 + - - -
----------------------------------------------------------
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