Contacts of the strand formed by residues 284 - 289 (chain D) in PDB entry 4JF7
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 TRP 284 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D ALA 4.4 2.6 - - - +
256D PRO* 3.5 19.3 - - + +
279D GLY 3.5 22.5 + - - -
280D VAL* 2.8 35.8 + - + +
282D ASP 4.9 0.5 + - - -
283D VAL* 1.3 79.0 + - + +
285D ALA* 1.3 63.9 + - - +
286D THR 3.3 23.8 - - - +
287D LEU* 3.7 21.3 - - + -
305D ILE* 4.4 7.4 - - + -
306D TYR 4.0 0.2 - - - -
307D GLY* 3.6 27.8 - - - -
308D GLY 3.4 10.3 - - - -
309D VAL* 4.0 5.6 - - + +
310D ILE* 4.2 2.5 - - - +
315D LEU* 3.7 21.7 - - + +
359D GLN* 3.5 36.3 - - + -
360D SER 5.0 2.9 - - - -
361D GLY* 5.6 0.2 - - - -
377D VAL* 3.9 29.0 - - + +
379D PRO* 4.8 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 285 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D ASP 3.4 8.1 - - - +
251D TYR* 3.6 6.7 - - - +
253D SER 3.5 17.7 - - - +
254D ALA 4.6 2.5 - - - -
255D ALA 3.7 4.7 - - - +
256D PRO* 3.2 19.6 - - - +
257D PRO* 4.1 0.5 - - - +
284D TRP* 1.3 72.1 - - - +
286D THR* 1.3 60.6 + - - +
308D GLY 2.6 15.7 + - - +
310D ILE* 3.7 18.0 - - + +
356D ARG* 3.4 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 286 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D ASP* 3.4 23.5 + - + +
251D TYR* 3.4 49.6 - - + +
256D PRO* 4.5 0.9 - - - -
257D PRO* 3.3 24.5 - - - +
284D TRP* 3.3 15.5 - - - +
285D ALA* 1.3 79.2 - - - +
287D LEU* 1.3 66.0 + - - +
288D ASN* 4.2 8.9 + - - +
307D GLY* 4.1 2.5 - - - -
308D GLY 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 287 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D TYR* 3.7 17.7 - - - +
241D PHE* 4.0 5.4 - - - +
256D PRO* 5.4 1.1 - - + -
257D PRO* 3.9 4.6 - - + +
259D GLN* 3.0 40.0 + - + +
277D PRO* 5.0 4.5 - - + -
280D VAL* 4.2 20.9 - - + -
284D TRP* 3.7 29.8 - - + -
286D THR* 1.3 80.7 + - - +
288D ASN* 1.3 69.6 + - - +
305D ILE* 3.7 30.5 - - + -
306D TYR 3.6 9.0 - - - +
307D GLY* 4.4 0.2 - - - -
363D LEU* 5.7 0.4 - - + -
377D VAL* 4.2 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 288 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D SER* 4.1 4.3 + - - +
239D TYR* 4.1 5.2 - - - -
241D PHE* 3.5 35.5 - - - -
247D GLU* 4.6 10.3 + - - +
250D ASP* 5.3 0.3 - - - +
251D TYR* 5.1 4.8 + - - -
286D THR* 4.2 10.7 + - - +
287D LEU* 1.3 86.0 - - - +
289D PRO* 1.3 78.2 - - + +
305D ILE* 3.1 5.9 - - - +
306D TYR* 2.8 64.4 + - + +
307D GLY* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 289 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D SER* 3.0 45.6 + - - +
228D SER* 3.9 10.3 - - - +
239D TYR* 3.3 62.8 - - + +
240D CYS* 3.9 4.0 - - - -
241D PHE* 4.1 12.6 - - + +
288D ASN* 1.3 93.7 - - + +
290D GLY* 1.3 58.8 + - - +
291D THR 3.3 2.2 - - - -
304D PRO 3.4 7.6 - - - +
306D TYR* 3.6 2.4 - - - -
----------------------------------------------------------
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