Contacts of the strand formed by residues 270 - 277 (chain A) in PDB entry 2JB3
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 GLY 270 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ASN* 3.7 7.4 + - - -
267A VAL* 2.9 30.1 + - - +
268A SER 3.4 1.8 + - - -
269A GLU* 1.3 81.0 - - - +
271A VAL* 1.3 67.4 + - - +
286A ALA 3.3 7.6 - - - -
287A ASP 3.5 13.0 - - - -
453A LYS* 4.1 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 4.6 3.4 - - + +
264A MET* 4.1 7.9 - - + -
265A LYS 3.3 15.3 - - - +
266A ASN* 3.9 2.0 - - - +
267A VAL* 3.9 1.5 - - - +
270A GLY* 1.3 80.0 - - - +
272A THR* 1.3 64.0 + - - +
273A VAL* 4.1 14.3 + - + -
284A ILE 3.8 0.9 - - - +
285A THR* 3.2 3.3 - - - +
286A ALA 2.8 35.5 + - - +
288A TYR 4.2 1.6 - - - +
289A ALA* 3.7 28.9 - - + +
453A LYS* 3.6 29.8 - - + +
454A ILE* 3.6 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A SER* 4.0 1.6 + - - +
264A MET* 3.6 1.7 + - - -
265A LYS* 2.9 34.4 + - - +
267A VAL* 3.3 28.5 - - - +
269A GLU* 4.5 2.6 + - - -
271A VAL* 1.3 71.7 - - - +
273A VAL* 1.3 65.5 + - - +
274A GLU* 4.3 10.8 + - + +
283A SER* 3.3 24.7 - - - +
284A ILE 3.3 5.4 - - - +
285A THR* 2.7 18.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 3.9 25.8 - - + -
18A LEU* 4.2 16.4 - - + -
41A LEU* 3.6 22.7 - - + -
261A VAL* 3.5 22.9 - - + -
263A SER 3.2 14.6 - - - +
264A MET* 4.4 5.2 - - + -
271A VAL* 4.1 11.7 - - + -
272A THR* 1.3 77.8 - - - +
274A GLU* 1.3 63.6 + - - +
275A TYR* 4.1 1.2 - - - -
283A SER* 3.4 1.7 - - - -
284A ILE* 2.9 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A VAL* 3.6 2.9 - - - +
262A THR* 2.9 30.7 + - - +
263A SER* 3.0 36.5 + - - +
272A THR* 4.7 9.1 - - + +
273A VAL* 1.3 76.8 - - - +
275A TYR* 1.3 60.6 + - - +
281A LYS* 5.7 6.7 - - + +
282A LYS 3.3 11.4 - - - +
283A SER* 4.4 12.7 + - - +
302A GLN* 4.7 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 3.7 31.7 - - + +
256A VAL* 4.1 17.1 - - + +
259A ALA* 3.6 22.4 - - + -
260A GLU 3.2 16.6 - - - +
261A VAL* 3.8 15.0 - - + +
262A THR* 4.2 3.3 + - - +
273A VAL 4.1 5.8 - - - -
274A GLU* 1.3 76.2 - - - +
276A THR* 1.3 60.2 + - - +
277A ALA* 3.6 25.1 - - + -
280A SER 3.7 0.2 - - - +
281A LYS* 3.7 3.7 - - - +
282A LYS* 2.8 66.1 + - + +
283A SER 4.3 2.9 + - - -
284A ILE* 4.1 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLY 3.3 4.2 - - - +
260A GLU* 2.9 40.1 + - - +
262A THR* 4.2 12.6 - - - +
275A TYR* 1.3 72.2 + - - +
277A ALA* 1.3 65.7 + - - +
279A GLY* 3.8 26.0 - - - +
280A SER 3.4 11.9 - - - +
281A LYS* 4.3 19.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A VAL* 4.2 11.4 - - + -
257A PHE 4.8 1.3 - - - +
258A GLY 3.5 14.8 - - - +
259A ALA* 4.1 3.1 - - - -
275A TYR* 3.6 27.3 + - + -
276A THR* 1.3 76.8 - - - +
278A GLY* 1.3 65.5 + - - +
279A GLY 3.2 0.9 - - - -
280A SER 3.1 18.1 + - - +
282A LYS* 3.4 21.9 - - + -
----------------------------------------------------------
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