Contacts of the strand formed by residues 221 - 226 (chain A) in PDB entry 1CJY
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 ALA 221 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ARG* 2.3 36.0 + - - -
165A ILE* 3.6 2.4 - - - +
190A VAL* 3.5 9.4 - - + +
192A ILE* 3.3 34.3 - - + -
217A ILE 3.5 3.6 + - - +
218A LEU* 2.8 16.4 + - + +
220A CYS* 1.3 80.3 - - - +
222A THR* 1.3 60.5 + - - +
223A TYR 4.0 6.1 - - - +
224A VAL* 5.3 0.2 - - + -
325A PRO* 3.8 8.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PHE* 3.4 15.0 - - + -
158A ARG* 4.8 16.2 - - + +
161A ARG* 4.5 8.0 - - + +
165A ILE* 4.6 10.0 - - - +
188A PRO 4.7 1.2 + - - -
189A VAL* 3.7 33.2 - - + +
190A VAL 2.8 7.4 + - - -
220A CYS 3.9 3.0 + - - -
221A ALA* 1.3 75.1 - - - +
223A TYR* 1.3 89.9 + - + +
325A PRO* 4.0 0.7 - - - -
326A LEU 3.0 21.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLU* 2.8 28.5 + - + +
157A PHE* 5.1 1.8 - + - -
158A ARG* 3.5 25.1 + - - +
189A VAL* 3.9 12.8 - - + -
190A VAL 3.3 2.4 + - - -
191A ALA* 3.6 13.9 - - + -
192A ILE* 2.9 28.2 + - - +
221A ALA* 3.5 1.6 - - - +
222A THR* 1.3 108.2 - - + +
224A VAL* 1.3 69.0 + - - +
225A ALA 4.1 0.4 - - - +
325A PRO* 4.1 1.1 - - - -
326A LEU* 3.5 27.6 - - + +
328A LEU* 3.8 22.2 - - + -
561A ILE* 4.8 3.1 - - + -
566A ARG* 3.4 30.7 - - + +
568A VAL* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ILE* 3.5 15.7 - - + +
205A PHE* 4.3 18.6 - - + -
209A MET* 4.3 18.8 - - + -
218A LEU* 4.4 3.6 - - + -
223A TYR* 1.3 78.5 - - - +
225A ALA* 1.3 54.0 + - - +
234A MET* 3.1 34.0 - - + +
238A TYR* 3.9 16.6 - - + +
325A PRO* 3.7 22.2 - - + -
326A LEU 3.1 7.4 + - - +
327A PRO* 3.4 1.2 - - + +
328A LEU* 2.7 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ILE 2.9 13.5 + - - +
193A LEU* 3.6 14.5 - - + -
194A GLY* 3.0 23.9 + - - -
205A PHE* 4.7 0.3 - - - -
223A TYR 4.1 0.2 - - - -
224A VAL* 1.3 77.4 - - - +
226A GLY* 1.3 59.3 + - - +
234A MET* 3.8 6.4 - - - +
328A LEU* 3.2 13.2 - - + -
557A PRO* 4.2 6.2 - - + +
560A LEU* 3.9 21.1 - - + -
561A ILE* 4.3 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A GLY 3.7 10.3 - - - -
225A ALA* 1.3 76.2 - - - +
227A LEU* 1.3 62.4 + - - +
230A SER* 4.2 6.1 - - - -
231A THR* 3.6 6.9 + - - -
234A MET* 3.6 14.1 - - - -
328A LEU 3.0 9.1 + - - -
329A PHE* 3.6 4.3 - - - -
330A THR* 3.5 23.7 + - - +
557A PRO* 4.0 4.7 - - - +
560A LEU* 3.9 1.2 - - - +
----------------------------------------------------------
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