Contacts of the strand formed by residues 389 - 396 (chain B) in PDB entry 1JEY
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 389 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A VAL* 4.0 13.5 - - + -
467A GLU* 5.7 0.9 - - - -
470A ARG* 3.3 57.2 - - + +
345B PHE* 3.8 21.1 - - + +
346B CYS* 3.1 22.2 - - - +
347B LYS* 4.2 4.5 - - + -
348B SER* 4.0 1.5 - - - +
384B LEU* 2.8 34.8 + - + +
387B LEU* 3.1 33.7 - - + +
388B ASP* 1.3 79.3 - - - +
390B VAL* 1.3 71.5 + - - +
410B PRO* 3.8 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A LYS* 5.0 3.1 - - - +
345B PHE* 3.1 5.4 - - - +
346B CYS* 2.8 54.4 + - - +
348B SER* 3.9 23.1 - - - -
351B VAL* 4.1 10.5 - - + -
384B LEU* 4.2 9.6 - - - -
389B MET* 1.3 80.5 - - - +
391B ALA* 1.3 61.0 + - - +
392B ILE* 4.6 0.4 - - + -
407B VAL* 3.8 24.0 - - + -
408B ALA 3.8 4.7 - - - +
409B PHE* 3.5 26.9 - - + -
410B PRO* 4.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B VAL* 4.7 4.7 - - + -
344B GLY 3.6 5.6 - - - +
345B PHE* 3.6 24.5 - - + -
380B LEU* 5.7 2.9 - - + -
384B LEU* 4.4 6.2 - - + +
390B VAL* 1.3 74.8 - - - +
392B ILE* 1.3 61.1 + - - +
393B VAL* 3.9 17.0 + - + -
407B VAL* 3.3 7.6 - - - +
408B ALA* 2.9 42.7 + - + +
419B LEU* 6.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A PHE* 3.7 33.9 - - + -
473A TYR* 4.1 9.0 - - + -
478A PHE* 4.2 13.5 - - + -
343B LEU* 2.8 29.7 + - + +
344B GLY 2.9 10.3 + - - +
346B CYS* 3.7 28.3 - - - -
351B VAL* 4.0 10.1 - - + -
390B VAL 5.0 0.2 - - - +
391B ALA* 1.3 76.8 - - - +
393B VAL* 1.3 62.9 + - - +
405B VAL* 4.0 20.9 - - + -
406B GLY 3.3 6.1 - - - +
407B VAL* 4.4 4.0 - - + -
424B LEU* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LEU* 6.1 0.4 - - + -
340B PHE* 4.1 22.2 - - + -
341B SER 3.2 17.3 - - - +
342B VAL* 3.8 21.3 - - + -
343B LEU* 4.0 6.5 - - - -
391B ALA* 4.0 15.5 - - + +
392B ILE* 1.3 80.5 - - - +
394B ARG* 1.3 63.4 + - - +
395B TYR 3.9 0.2 + - - -
405B VAL* 3.3 5.4 - - - +
406B GLY 2.7 42.7 + - - +
408B ALA* 4.5 9.2 - - + -
421B TYR* 3.8 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A ASP* 3.5 4.9 + - - -
507A THR* 2.6 47.5 + - - +
508A LEU* 3.4 26.8 - - - +
509A PRO* 4.4 3.8 - - - -
333B TYR* 3.0 27.3 + - - -
335B SER* 3.8 13.5 - - - +
336B GLU* 5.2 4.0 + - - +
337B GLY 4.4 4.9 + - - +
339B CYS* 3.1 31.2 - - - -
340B PHE* 3.3 6.2 - - - -
341B SER* 2.8 37.3 + - - +
343B LEU* 4.1 3.7 - - + +
393B VAL* 1.3 72.4 - - - +
395B TYR* 1.3 61.3 + - - +
396B ALA* 4.3 4.6 - - - +
403B PRO* 3.6 21.3 - - + +
404B GLN 3.2 10.3 - - - +
405B VAL* 4.6 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B TRP* 3.4 34.1 - + - -
265B LYS* 5.7 1.4 - - - -
339B CYS* 3.7 1.6 - - - -
340B PHE* 3.6 24.5 - + + -
360B GLN* 4.1 18.1 + - - -
362B LEU* 3.8 22.4 - - + +
393B VAL 3.9 0.6 + - - -
394B ARG* 1.3 75.0 - - - +
396B ALA* 1.3 63.1 - - - +
397B TYR* 3.5 39.5 - - + +
403B PRO* 3.6 0.6 - - - -
404B GLN* 2.7 67.3 + - + +
421B TYR* 3.5 30.3 - + + +
24D A 4.7 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B TRP* 3.7 2.9 - - - -
335B SER* 5.5 3.1 - - - +
337B GLY 3.7 20.4 - - - +
338B LYS* 3.4 0.7 - - - -
339B CYS* 3.2 34.4 + - - +
394B ARG* 4.3 7.6 - - - +
395B TYR* 1.3 78.9 - - - +
397B TYR* 1.3 68.8 + - - +
398B ASP 3.3 8.9 + - - +
401B ALA* 4.8 4.0 - - - +
402B ASN 4.8 2.7 - - - -
403B PRO* 4.3 14.1 - - + -
----------------------------------------------------------
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