Contacts of the strand formed by residues 222 - 226 (chain B) in PDB entry 2JAJ
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 222 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B TYR* 3.1 37.0 - - + +
53B LEU* 4.9 3.6 - - + -
221B CYS* 1.3 76.1 - - - +
223B TYR* 1.3 63.7 + - - +
224B LEU* 3.9 18.7 + - + +
232B VAL 3.6 0.5 - - - +
233B LEU* 3.2 7.1 - - - -
234B LEU* 2.7 55.3 + - + +
271B LEU* 3.8 11.6 - - + +
272B THR* 4.2 17.9 - - + +
275B SER* 3.7 11.9 - - - +
277B LEU* 3.9 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 3.5 45.7 + + - -
10B GLY* 3.8 8.9 - - - +
179B MET* 3.3 26.0 + - + +
180B ALA 3.6 15.3 - - - -
181B GLY* 3.7 7.9 - - - +
182B PRO* 3.8 6.8 - - + +
222B ILE* 1.3 76.2 - - - +
224B LEU* 1.3 80.8 + - - +
225B ASN* 3.4 26.9 + - - +
231B HIS* 2.6 40.9 + - - -
232B VAL 3.5 6.5 - - - -
233B LEU* 3.5 8.5 - - + +
254B HIS* 3.8 12.8 - - - -
277B LEU* 4.9 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLY 3.4 15.5 - - - +
12B ALA* 4.1 10.3 - - + +
53B LEU* 3.9 23.6 - - + -
57B LEU* 3.7 24.9 - - + -
59B LEU* 3.8 27.1 - - + -
222B ILE* 3.9 13.4 + - + +
223B TYR* 1.3 82.4 - - - +
225B ASN* 1.3 58.9 + - - +
226B ILE* 3.9 16.8 - - + -
230B GLY 3.5 1.0 - - - +
232B VAL* 2.6 45.7 + - + +
234B LEU* 5.0 2.9 - - + -
277B LEU* 3.9 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU 2.8 30.4 + - - +
4B GLY* 3.6 6.3 - - - -
8B ALA* 4.0 14.6 - - + +
9B PHE 3.5 19.4 + - - +
10B GLY 2.9 14.6 + - - +
11B ARG* 2.8 58.2 + - - +
12B ALA 4.6 0.5 + - - -
182B PRO* 5.7 1.4 - - - +
223B TYR* 3.4 17.4 + - - +
224B LEU* 1.3 71.1 - - - +
226B ILE* 1.3 68.7 + - - +
230B GLY 3.5 6.8 - - - -
231B HIS* 4.5 4.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU 6.0 0.2 - - - -
11B ARG* 4.0 2.2 + - - -
12B ALA 5.3 0.4 - - - +
57B LEU* 3.9 39.5 - - + +
59B LEU* 3.8 28.7 - - + -
224B LEU* 3.9 21.1 - - + -
225B ASN* 1.3 81.5 + - - +
227B PRO* 1.3 85.1 - - + +
228B ASN 3.2 0.9 + - - -
229B LYS* 3.1 23.5 + - + -
230B GLY* 3.0 15.8 + - - -
232B VAL* 3.8 26.2 - - + -
----------------------------------------------------------
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