Contacts of the strand formed by residues 187 - 193 (chain B) in PDB entry 2CX9
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 ILE 187 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ALA* 3.6 35.4 - - + +
139B LEU* 3.9 29.2 - - + -
171B MET* 4.3 8.7 - - + -
172B ALA 4.0 5.6 - - - +
173B ARG* 3.6 22.2 - - - +
183B LYS 3.6 12.3 - - - +
184B HIS 4.4 0.4 - - - +
186B GLY* 1.3 80.1 - - - +
188B SER* 1.3 67.5 + - - +
235B GLY 3.0 9.4 + - - -
237B GLY 2.8 28.2 + - - -
238B PHE* 3.7 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B VAL 3.9 0.2 - - - +
171B MET* 3.3 3.7 - - - -
172B ALA 2.8 32.2 + - - +
174B THR* 2.8 32.4 + - - +
186B GLY 4.1 0.4 + - - -
187B ILE* 1.3 74.5 - - - +
189B ALA* 1.3 60.4 + - - +
190B PHE* 3.7 11.9 - - - -
230B LEU* 4.1 9.6 - - - -
233B GLU 5.1 1.1 - - - -
234B ARG* 3.4 6.6 - - - +
235B GLY 2.7 28.3 + - - +
237B GLY* 4.3 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B HIS* 3.6 31.9 - - + +
169B VAL* 4.6 1.1 - - + -
170B VAL 3.5 3.8 - - - -
171B MET* 3.7 11.7 - - + -
188B SER* 1.3 73.2 - - - +
190B PHE* 1.3 68.7 + - - +
230B LEU* 3.7 4.3 - - - +
231B LEU* 2.8 47.5 + - + +
237B GLY* 4.5 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ALA* 3.5 31.4 - - + -
150B TRP* 3.5 35.4 - + + -
152B LEU* 4.4 18.6 - - + -
168B TYR 3.5 1.6 - - - +
169B VAL* 3.1 5.3 - - - -
170B VAL 2.7 48.1 + - - +
172B ALA* 4.4 3.4 - - + -
174B THR* 3.7 11.7 - - + -
188B SER* 3.7 26.2 - - - -
189B ALA* 1.3 78.0 - - - +
191B ALA* 1.3 60.0 + - - +
192B PHE* 3.7 14.5 - - + -
225B VAL* 4.1 16.4 - - + -
229B ALA* 3.3 6.5 - - + +
230B LEU* 4.0 20.9 - - + -
231B LEU* 4.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ILE* 4.1 20.2 - - + -
108B GLN* 5.7 1.3 - - - +
112B PHE* 3.5 21.5 - - + -
167B VAL* 5.4 0.2 - - + -
168B TYR 3.1 8.3 - - - +
169B VAL* 4.0 15.0 - - + +
190B PHE* 1.3 72.9 - - - +
192B PHE* 1.3 65.2 + - - +
229B ALA* 2.9 29.5 + - - +
231B LEU* 4.3 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 3.9 15.2 - - - -
152B LEU* 4.1 10.8 - - + -
167B VAL* 3.6 0.9 - - - -
168B TYR* 2.8 55.7 + + + -
170B VAL* 3.9 20.0 - - + -
190B PHE* 3.7 19.3 - - + -
191B ALA* 1.3 80.2 - - - +
193B PHE* 1.3 79.2 + - - +
195B PRO* 3.8 17.3 - - + -
199B LEU* 5.0 2.0 - - + -
220B LEU* 5.2 3.4 - - + -
223B LEU* 3.6 27.8 - - + -
225B VAL* 3.5 32.3 - - + -
226B PRO* 5.2 6.3 - - + -
229B ALA* 4.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ALA* 3.4 29.8 - - + -
112B PHE* 3.3 25.4 - + - -
115B LYS* 3.7 38.4 - - + -
166B GLY 3.4 18.4 - - - +
167B VAL* 3.9 13.9 - - + +
192B PHE* 1.3 82.9 - - - +
194B ARG* 1.3 71.1 + - - +
195B PRO* 2.9 11.5 - - - +
----------------------------------------------------------
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