Contacts of the strand formed by residues 382 - 392 (chain B) in PDB entry 1Z3S
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 382 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B HIS* 2.8 33.4 + - + +
375B LEU 3.1 9.0 - - - +
376B LYS* 3.0 33.7 - - + -
380B GLY 4.5 6.3 - - - +
381B ASN* 1.3 83.3 - - - +
383B ALA* 1.3 64.6 + - - +
409B THR* 4.7 0.9 + - - -
477B TRP* 4.0 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B HIS* 3.5 8.1 - - - -
375B LEU* 2.7 33.9 + - + +
382B GLU* 1.3 77.3 - - - +
384B TYR* 1.3 63.2 + - - +
409B THR* 3.4 26.2 - - - +
410B ALA* 4.2 5.2 - - + -
477B TRP* 3.7 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LYS* 4.0 29.6 - - - -
373B ILE 3.0 13.7 - - - +
374B HIS* 4.3 7.9 - + + -
375B LEU 4.7 0.2 - - - +
383B ALA* 1.3 80.4 - - - +
385B SER* 1.3 70.5 + - - +
386B LEU* 3.9 23.5 - - + +
407B THR* 4.8 2.0 + - - -
408B GLY* 3.5 26.9 + - - -
409B THR* 2.9 49.5 + - + +
410B ALA* 3.0 8.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LEU 3.9 0.8 - - - +
372B LYS* 3.5 2.4 - - - -
373B ILE* 2.9 36.9 + - - +
384B TYR* 1.3 76.6 - - - +
386B LEU* 1.3 60.3 + - - +
387B TYR* 4.2 7.6 - - - -
406B LEU* 4.2 16.0 - - - +
407B THR 3.5 6.4 + - - -
408B GLY* 4.6 0.2 - - - -
410B ALA* 3.0 29.7 + - - +
411B GLY 5.1 0.7 + - - -
474B TRP* 3.5 27.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
322B TRP* 4.6 4.3 - - + -
370B VAL* 3.3 32.1 - - + -
371B LEU 3.3 10.3 - - - +
372B LYS* 3.5 25.8 - - + -
384B TYR* 3.9 18.6 - - + +
385B SER* 1.3 74.7 - - - +
387B TYR* 1.3 64.1 + - - +
388B GLU* 4.1 1.8 - - + +
405B GLY 3.4 1.7 - - - +
406B LEU* 3.3 6.8 - - - +
407B THR* 2.9 50.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B VAL* 3.1 6.5 - - - +
371B LEU* 2.9 59.3 + - + +
373B ILE* 4.0 22.0 - - + -
385B SER* 4.2 6.7 - - - -
386B LEU* 1.3 75.1 - - - +
388B GLU* 1.3 66.2 + - - +
389B HIS* 3.1 14.7 + - - +
403B LEU* 3.6 42.8 - - + +
404B LYS 4.0 5.8 - - - +
405B GLY 3.7 2.7 - - - -
406B LEU* 3.5 38.6 - - + +
414B SER* 2.6 31.8 + - - -
416B ILE* 4.8 0.7 - - + -
418B GLN* 5.5 1.8 - - - -
474B TRP* 3.9 15.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ARG* 6.0 0.9 - - - +
369B TYR 3.7 1.9 - - - +
370B VAL* 3.2 27.2 - - - +
386B LEU* 4.1 2.5 - - + +
387B TYR* 1.3 70.5 - - - +
389B HIS* 1.3 62.5 + - + +
404B LYS 3.2 9.0 + - - +
405B GLY* 3.2 29.0 + - - +
407B THR* 4.7 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B THR 5.4 0.9 - - - -
367B GLN 5.1 1.1 - - - -
368B ARG* 3.1 60.7 + - + +
369B TYR 3.5 7.5 + - - -
387B TYR* 3.1 5.0 + - - +
388B GLU* 1.3 82.2 + - + +
390B PHE* 1.3 70.3 + - - +
391B TYR* 3.5 28.7 - + + -
402B HIS 3.5 4.4 - - - +
403B LEU* 3.7 1.0 - - - -
404B LYS* 3.3 66.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ILE* 4.4 10.3 - - + -
360B VAL* 4.2 11.2 - - + -
364B THR* 3.6 30.4 - - + +
369B TYR* 2.8 26.1 + - + +
371B LEU* 3.5 40.6 - - + -
387B TYR* 4.8 0.2 - - + -
389B HIS* 1.3 80.2 + - - +
391B TYR* 1.3 67.3 + - - +
392B LEU* 3.4 34.8 - - + -
401B ILE* 3.6 15.5 - - + -
402B HIS 3.3 7.0 - - - +
403B LEU* 3.7 14.6 - - + -
446B TRP* 5.2 2.7 - + - -
491B ILE* 3.6 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B THR* 3.3 31.4 - - - +
365B ASN* 3.9 21.3 - - - -
389B HIS* 3.5 32.5 - + + +
390B PHE* 1.3 78.0 - - - +
392B LEU* 1.3 69.6 + - - +
393B SER* 4.4 5.6 - - - -
401B ILE* 3.8 0.5 - - - -
402B HIS* 3.1 76.7 + + + +
404B LYS* 4.6 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ILE* 6.2 0.9 - - + -
354B TRP* 5.8 0.9 - - + -
357B ASN* 3.7 31.4 - - + +
360B VAL* 3.6 28.5 - - + -
361B SER* 2.9 28.3 + - - -
364B THR* 3.1 6.6 + - - +
365B ASN* 3.0 14.6 - - - +
390B PHE* 3.4 33.7 - - + -
391B TYR* 1.3 76.5 - - - +
393B SER* 1.3 63.6 + - - +
399B TYR* 3.8 13.7 - - + +
400B ARG 3.4 2.2 - - - -
401B ILE* 4.0 12.3 - - + -
446B TRP* 3.8 21.1 - - + -
----------------------------------------------------------
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