Contacts of the strand formed by residues 282 - 288 (chain A) in PDB entry 4JHN
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 GLU 282 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ASN* 4.9 6.7 - - - +
267A GLY 3.2 13.9 - - - +
268A LEU* 4.1 15.9 - - + -
274A LEU* 3.9 4.2 - - - +
280A LEU* 3.5 16.8 - - - +
281A PHE* 1.3 89.8 + - - +
283A THR* 1.3 69.4 + - - +
284A SER 5.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ASN 4.8 0.7 - - - -
220A GLY* 4.1 2.4 - - - -
265A THR 3.9 6.1 - - - +
266A PHE* 3.6 18.1 - - - +
267A GLY* 2.8 37.5 + - - +
274A LEU* 4.2 2.9 - - + -
276A LEU* 4.0 13.7 - - + -
280A LEU* 4.6 6.7 - - - -
282A GLU* 1.3 82.0 - - - +
284A SER* 1.3 61.3 + - - +
285A GLU* 2.7 30.3 + - - +
287A LYS* 3.7 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLY* 3.7 22.7 - - - +
223A GLY* 3.3 28.5 - - - -
224A LEU 4.0 10.8 + - - +
225A PRO* 6.4 0.4 - - - -
226A ASN* 5.5 8.1 + - - -
240A GLU* 4.9 0.3 - - - +
282A GLU* 5.3 1.2 - - - +
283A THR* 1.3 73.7 + - - +
285A GLU* 1.3 68.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A PRO* 6.6 0.4 - - + -
240A GLU* 3.4 22.9 - - - +
266A PHE* 4.1 2.2 - - - -
283A THR* 2.7 34.1 + - - +
284A SER* 1.3 87.4 - - - +
286A PRO* 1.3 73.2 - - + +
287A LYS* 3.3 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A GLY* 3.7 13.2 - - - +
238A VAL* 3.9 25.1 - - + -
240A GLU* 3.4 25.0 - - + +
241A ILE* 3.8 10.1 - - + -
264A TYR* 3.6 25.7 - - + -
265A THR 3.7 0.2 - - - +
266A PHE* 3.7 30.5 - - + -
284A SER 4.1 1.3 - - - +
285A GLU* 1.3 86.5 - - - +
287A LYS* 1.3 65.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A TYR* 3.3 5.9 - - - -
265A THR 2.9 30.5 + - - +
276A LEU* 3.7 27.8 - - + +
280A LEU* 4.5 11.2 - - + -
283A THR* 3.7 23.1 - - + +
285A GLU* 3.5 33.1 + - - +
286A PRO* 1.3 77.0 - - - +
288A VAL* 1.3 63.1 + - - +
289A ILE 3.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ALA* 3.9 20.0 - - + -
263A VAL 3.4 10.5 - - - +
264A TYR* 3.6 36.6 - - + +
276A LEU* 3.5 11.0 - - - +
287A LYS* 1.3 72.8 - - - +
289A ILE* 1.3 76.4 + - - +
290A GLU* 3.4 30.8 + - - +
293A ARG* 5.2 6.1 - - + -
----------------------------------------------------------
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