Contacts of the strand formed by residues 381 - 387 (chain A) in PDB entry 4JDJ
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 MET 381 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A GLU* 4.0 36.1 - - - +
369A ILE* 3.9 23.8 - - + -
370A MET* 3.6 39.5 - - + +
374A GLN* 3.3 19.0 + - - +
378A VAL* 4.9 0.4 - - + -
379A VAL* 3.4 24.2 + - + +
380A GLU* 1.3 79.3 - - - +
382A TYR* 1.3 64.7 + - - +
393A VAL* 4.1 14.6 - - + -
395A MET* 3.8 16.4 - - + -
457A SER* 6.0 0.2 - - - -
458A ASP 5.9 2.0 - - - +
459A PHE* 4.2 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ASP* 4.7 0.2 - - - +
347A VAL* 4.2 15.3 - - + -
370A MET* 4.1 6.7 - - - +
380A GLU* 3.8 31.3 + - + -
381A MET* 1.3 78.7 - - - +
383A ASN* 1.3 78.5 + - - +
394A VAL* 2.8 24.6 + - + +
395A MET* 3.4 19.5 - - - -
396A GLU* 3.3 40.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ASP* 2.8 29.5 + - - +
320A TYR* 4.5 3.5 + - - -
370A MET* 3.9 7.4 - - - -
381A MET 4.0 0.2 - - - -
382A TYR* 1.3 95.1 + - + +
384A SER* 1.3 60.3 - - - +
385A TYR* 3.3 31.5 + - + +
392A TRP 3.9 0.2 - - - +
393A VAL* 3.5 4.7 - - - +
394A VAL* 2.8 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A VAL 4.5 1.2 + - - -
312A VAL* 3.6 27.1 - - - +
313A ASP* 2.7 40.9 + - - +
367A VAL* 4.1 14.0 - - - +
370A MET* 4.0 21.1 - - - +
383A ASN* 1.3 74.5 - - - +
385A TYR* 1.3 62.1 + - - +
391A LEU* 4.4 7.9 - - - -
392A TRP 3.2 7.6 - - - -
393A VAL* 4.4 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A VAL* 4.0 9.4 - - - -
313A ASP* 3.7 15.9 - - + -
314A PRO 3.6 14.4 - - - -
315A GLY* 3.4 28.0 - - - +
316A ASP 4.5 0.9 - - - -
317A PRO* 3.5 33.4 - - + -
320A TYR* 2.8 34.0 + + - -
383A ASN* 3.3 36.2 + - + +
384A SER* 1.3 78.4 - - - +
386A LEU* 1.3 60.5 + - - +
387A VAL* 3.7 6.5 + - + -
391A LEU* 3.5 5.2 - - - +
392A TRP* 2.7 45.0 + - + +
394A VAL* 3.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ARG* 3.5 48.0 + - + +
308A LEU* 4.2 24.5 - - + -
309A GLN* 3.4 33.0 + - + +
312A VAL* 3.8 18.0 - - + +
313A ASP 4.8 1.0 + - - -
315A GLY 4.3 9.3 + - - +
316A ASP* 6.0 0.2 - - - +
354A LEU* 4.3 13.0 - - + -
385A TYR* 1.3 71.5 - - - +
387A VAL* 1.3 61.1 + - - +
388A GLY 3.8 15.8 + - - +
390A GLU 3.5 15.7 - - - +
391A LEU* 4.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ASP* 4.1 6.7 - - - +
317A PRO* 3.8 24.2 - - + -
318A ARG* 3.2 38.8 - - - +
385A TYR* 3.7 5.6 + - + -
386A LEU* 1.3 76.1 - - - +
388A GLY* 1.3 64.2 + - - +
389A ASP 3.1 0.7 + - - -
390A GLU* 2.8 30.2 + - - +
392A TRP* 3.7 44.6 - - + +
----------------------------------------------------------
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