Contacts of the strand formed by residues 380 - 389 (chain B) in PDB entry 2JED
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 PHE 380 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B LYS* 3.6 29.4 - - - -
377B ILE* 3.4 26.9 + - + +
378B GLU* 3.1 6.1 - - - +
379B ASP* 1.3 83.3 - - + +
381B GLU* 1.3 59.7 + - - +
382B LEU* 3.8 9.8 + - + +
397B ALA* 3.9 17.0 - - + -
398B GLU 3.2 5.8 - - - +
399B PHE* 3.7 44.9 - + + -
400B LYS* 4.2 4.9 - - - -
406B PHE* 4.0 16.8 - + + -
408B ILE* 3.8 30.3 - - + -
448B PHE* 4.5 7.0 - + - -
457B VAL* 4.1 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B PHE* 1.3 70.8 - - - +
382B LEU* 1.3 69.1 + - - +
383B HIS* 3.1 49.6 + - + +
397B ALA* 3.3 2.1 - - - -
398B GLU* 2.8 38.8 + - + +
400B LYS* 3.2 38.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ILE* 5.2 8.7 - - + +
380B PHE* 3.8 12.6 + - + +
381B GLU* 1.3 78.4 + - - +
383B HIS* 1.3 59.8 + - - +
384B LYS 3.6 1.3 - - - -
395B PHE* 3.9 30.5 - - + -
396B LEU 3.6 1.8 - - - +
397B ALA* 3.6 26.7 - - + -
408B ILE* 4.8 9.2 - - + -
674B ARG 4.7 4.0 + - - +
675B LEU* 3.3 42.1 - - + +
677B PHE* 3.4 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B GLU* 3.1 48.2 + - - +
382B LEU* 1.3 73.2 - - - +
384B LYS* 1.3 66.1 + - + +
396B LEU* 2.9 21.3 + - + +
398B GLU* 2.8 43.8 + - + +
405B PHE* 4.3 16.2 - + - -
675B LEU* 3.7 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B HIS* 1.3 83.3 - - + +
385B MET* 1.3 72.7 + - - +
386B LEU* 3.8 21.1 - - + +
395B PHE* 3.3 6.2 - - - +
396B LEU* 2.7 49.6 + - + -
675B LEU* 3.5 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B LYS* 1.3 86.4 + - - +
386B LEU* 1.3 66.9 + - - +
387B GLY* 3.9 27.1 - - - +
388B LYS* 4.0 22.9 - - + +
393B LYS* 4.3 18.6 - - + -
394B VAL 3.6 11.7 - - - +
395B PHE* 3.9 24.5 - - + -
675B LEU* 4.2 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B LYS* 3.6 19.7 + - + +
385B MET* 1.3 73.4 - - - +
387B GLY* 1.3 56.5 + - - +
394B VAL* 2.7 28.5 + - + +
395B PHE 3.9 7.6 - - - +
396B LEU* 3.7 35.9 - - + +
407B ALA* 4.1 12.6 - - + -
460B TYR* 4.1 30.7 - - + +
1712B LG8 3.6 42.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B MET* 3.4 15.2 - - - +
386B LEU* 1.3 81.8 - - - +
388B LYS* 1.3 61.3 + - - +
391B PHE* 3.7 9.1 - - - -
393B LYS* 3.6 1.9 - - - -
394B VAL 3.0 27.1 + - - +
1712B LG8 3.6 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B MET* 4.0 18.5 - - + +
387B GLY* 1.3 75.0 - - - +
389B GLY* 1.3 63.9 + - - +
391B PHE* 3.6 8.4 - - - -
392B GLY 3.2 12.3 - - - +
393B LYS* 3.8 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B LYS* 1.3 79.3 - - - +
390B SER* 1.3 61.5 + - - -
391B PHE* 3.1 13.8 - - - -
392B GLY* 2.9 23.9 + - - +
----------------------------------------------------------
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