Contacts of the strand formed by residues 283 - 287 (chain A) in PDB entry 5E6J
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 LEU 283 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU* 4.1 34.8 - - + +
255A GLN 4.5 1.6 - - - +
256A GLN* 4.0 27.6 - - + +
259A PHE* 4.3 13.7 - - + -
277A ILE* 4.5 10.8 - - + -
278A THR 3.8 3.6 - - - +
279A ALA* 4.3 11.0 - - + -
282A THR* 1.3 88.1 + - - +
284A TYR* 1.3 61.4 + - - +
293A LYS* 3.4 0.9 - - - -
294A MET* 2.6 49.2 + - + +
295A SER 3.4 20.6 - - - +
296A GLU* 4.2 8.3 - - - -
297A TYR* 4.4 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLY* 5.6 8.1 - - - -
276A HIS 3.8 0.2 - - - +
277A ILE* 3.4 5.3 - - - +
278A THR* 2.8 61.6 + - + +
280A LYS* 4.7 13.7 - - + -
281A GLU* 3.7 27.0 + - + -
282A THR* 3.8 32.6 - - + +
283A LEU* 1.3 72.9 - - - +
285A ARG* 1.3 59.8 + - - +
286A ILE* 3.9 0.6 + - + -
291A LEU* 3.9 30.3 - - + -
292A THR 3.8 1.8 - - - -
293A LYS* 3.8 35.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A GLU* 2.9 31.0 + - - -
266A THR* 5.1 3.8 - - - +
275A THR* 3.7 26.1 + - - +
276A HIS 3.3 5.4 - - - +
277A ILE* 3.5 22.2 - - + -
283A LEU 3.9 0.4 + - - -
284A TYR* 1.3 72.2 - - - +
286A ILE* 1.3 64.3 + - - +
287A ASP* 3.8 5.6 + - + +
290A HIS 3.8 0.7 - - - +
291A LEU* 3.5 4.1 - - - -
292A THR* 2.8 53.2 + - - +
294A MET* 3.8 28.4 - - + +
297A TYR* 3.2 25.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL* 3.8 38.8 - - + +
100A GLY* 5.5 1.1 - - - -
102A LEU* 4.5 4.7 - - + -
104A SER* 4.0 3.6 - - - +
119A LEU* 3.6 44.5 - - + +
275A THR* 3.8 1.2 - - - -
276A HIS* 2.7 47.2 + - + +
278A THR* 4.2 23.6 - - + -
284A TYR* 5.6 0.2 - - + -
285A ARG* 1.3 74.6 - - - +
287A ASP* 1.3 62.3 + - - +
288A GLY 3.6 22.1 + - - +
290A HIS 3.6 2.7 - - - +
291A LEU* 4.0 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TRP* 3.0 39.6 + - - -
274A TYR 4.3 0.6 - - - +
275A THR* 4.1 19.8 - - + +
285A ARG* 3.8 7.7 + - + +
286A ILE* 1.3 71.5 - - - +
288A GLY* 1.3 58.9 + - - +
289A ALA 3.1 0.7 + - - -
290A HIS* 2.8 50.9 + - + +
401A ACT 3.4 8.2 - - - +
----------------------------------------------------------
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