Contacts of the strand formed by residues 289 - 296 (chain A) in PDB entry 1JRX
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 VAL 289 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A VAL* 3.9 13.2 - - + -
282A LEU 3.2 11.0 - - - +
283A LYS* 4.1 3.1 - - + +
284A ASP* 4.6 0.5 - - - +
288A THR* 1.3 82.1 + - - +
290A LYS* 1.3 60.9 + - - +
291A GLY 3.7 7.4 - - - +
306A ALA 3.8 6.5 - - - +
307A ASP* 3.7 24.7 - - - +
309A VAL* 3.6 32.3 - - + +
526A ILE* 4.9 3.6 - - + -
527A PRO 2.8 19.6 + - - +
528A GLY* 3.3 18.4 - - - +
529A LEU* 3.5 13.7 - - + +
567A TYR* 5.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LEU* 2.7 30.8 + - + +
283A LYS 3.5 21.5 + - - +
284A ASP* 3.7 24.3 - - + +
289A VAL* 1.3 75.8 - - - +
291A GLY* 1.4 61.1 + - - +
303A TRP* 4.1 15.6 - - + -
305A LYS* 3.4 26.9 + - - +
306A ALA 3.0 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A VAL* 3.7 0.7 - - - -
282A LEU* 2.7 36.0 + - - +
289A VAL* 3.7 3.2 - - - +
290A LYS* 1.4 82.4 - - - +
292A ILE* 1.3 60.9 + - - +
303A TRP* 4.5 0.4 - - - -
304A VAL 2.9 15.3 - - - -
305A LYS* 4.1 0.2 - - - -
306A ALA* 3.6 12.3 + - - -
309A VAL* 3.7 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL* 3.9 35.9 - - + -
132A VAL* 3.5 31.0 - - + -
155A ILE* 4.5 2.0 - - + -
278A GLY* 3.9 17.7 - - - -
279A ILE 4.6 0.7 - - - +
280A GLU 3.4 16.6 - - - +
281A VAL* 4.4 6.5 - - + +
282A LEU* 3.6 6.3 - - - +
291A GLY* 1.3 76.8 - - - +
293A LEU* 1.3 75.7 + - - +
294A VAL* 3.8 9.2 + - + +
303A TRP* 3.2 1.0 - - - -
304A VAL* 3.0 27.4 + - + +
309A VAL* 4.0 14.8 - - + -
311A LEU* 4.9 2.7 - - + -
348A VAL* 5.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ARG* 3.7 42.8 - - + +
118A ALA* 5.4 2.7 - - + -
119A LEU* 3.9 29.6 - - + -
279A ILE* 2.9 25.6 + - + -
280A GLU* 2.8 70.0 + - + +
282A LEU* 3.6 2.9 - - + +
292A ILE* 1.3 78.2 - - - +
294A VAL* 1.3 60.7 - - - +
301A TYR* 4.4 9.6 - - + -
302A TYR 3.5 9.0 - - - +
303A TRP* 3.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL* 5.5 0.4 - - + -
155A ILE* 3.7 30.7 - - + -
276A THR* 3.8 13.9 - - + -
277A ARG 3.1 10.8 - - - +
278A GLY* 4.2 1.3 - - - -
279A ILE* 4.0 3.4 - - - -
292A ILE* 4.2 17.7 - - + +
293A LEU* 1.3 78.7 - - - +
295A LYS* 1.3 61.7 + - - +
296A GLY 3.9 0.2 - - - -
301A TYR* 3.2 9.4 - - - -
302A TYR* 2.8 77.2 + - + +
304A VAL* 5.2 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 4.5 16.2 - - + -
111A ASP* 3.7 10.1 - - - -
114A GLU* 5.4 3.1 - - - -
275A ASN 3.9 0.2 - - - +
276A THR* 3.5 1.4 - - - -
277A ARG* 2.7 43.6 + - + +
279A ILE* 3.6 18.4 - - + +
294A VAL* 1.3 74.5 - - - +
296A GLY* 1.3 73.1 + - - +
297A MET* 3.7 7.8 + - - +
300A GLY* 3.8 6.0 - - - -
301A TYR* 3.5 44.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASP* 3.3 26.7 - - - -
275A ASN 3.5 3.8 - - - -
276A THR* 4.2 6.1 - - - -
294A VAL 3.9 1.0 - - - -
295A LYS* 1.3 80.7 + - - +
297A MET* 1.3 63.2 + - - +
298A TYR 3.2 3.1 - - - -
300A GLY* 2.7 38.0 + - - -
302A TYR* 4.7 2.3 - - - -
----------------------------------------------------------
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