Contacts of the strand formed by residues 370 - 379 (chain B) in PDB entry 5DST
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 LEU 370 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B TYR 4.7 1.6 - - - +
190B CYS* 5.0 1.8 - - + -
192B PHE* 4.0 15.0 - - + +
193B TYR* 3.6 40.6 - - + +
195B SER* 4.6 9.2 - - - +
360B MET* 3.9 26.0 - - + -
361B LYS 3.7 13.2 - - - +
362B PRO* 4.7 2.9 - - + -
368B ARG 4.5 1.1 - - - +
369B ASP* 1.3 78.6 - - - +
371B ASP* 1.3 65.7 + - - +
372B PHE* 3.8 33.0 - - + -
392B LYS* 3.2 5.4 - - - +
393B MET* 2.9 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B MET* 3.1 27.4 - - - +
361B LYS* 3.1 33.9 + - - +
363B ASN* 3.0 44.4 + - - +
364B ALA 4.6 0.7 + - - -
369B ASP* 5.1 0.7 - - - +
370B LEU* 1.3 76.7 - - - +
372B PHE* 1.3 63.4 + - - +
391B TYR 3.6 4.9 - - - +
392B LYS* 3.4 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B CYS* 3.7 26.5 - - + -
340B PHE* 3.8 28.5 - + + -
358B ILE* 4.3 16.2 - - + -
359B SER 3.3 8.1 - - - +
360B MET* 3.7 31.0 - - + -
370B LEU* 3.8 37.0 - - + -
371B ASP* 1.3 80.0 - - - +
373B THR* 1.3 69.6 + - - +
374B VAL* 5.0 1.6 - - + -
390B ASP* 3.6 4.7 - - - +
391B TYR* 2.9 50.8 + - + +
393B MET* 3.8 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B THR* 3.8 1.6 + - - +
358B ILE* 3.4 1.9 - - - -
359B SER* 3.0 42.7 + - - +
372B PHE* 1.3 74.4 + - - +
374B VAL* 1.3 62.0 + - - +
375B ASP* 3.4 25.7 + - - +
388B SER* 4.0 7.2 - - - +
389B ASN 3.4 6.3 - - - +
390B ASP* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B PHE* 4.4 6.1 - - + -
307B LEU* 3.7 30.5 - - + -
340B PHE* 4.8 9.9 - - + -
342B LEU* 5.8 2.9 - - + -
357B THR 3.5 6.5 - - - +
358B ILE* 4.2 21.3 - - + -
372B PHE* 5.0 3.8 - - + -
373B THR* 1.3 75.1 - - - +
375B ASP* 1.3 73.6 + - - +
376B LEU* 4.0 8.0 + - + +
387B VAL 3.9 0.9 - - - +
388B SER* 3.6 0.5 - - - -
389B ASN* 2.9 36.2 + - + +
391B TYR* 3.8 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B PHE* 3.8 3.5 - - - -
356B GLY* 3.1 5.5 - - - -
357B THR* 2.8 49.8 + - + +
373B THR* 3.4 15.9 + - - +
374B VAL* 1.3 72.8 - - - +
376B LEU* 1.3 61.1 + - - +
377B ASP* 5.1 3.6 - - - +
387B VAL 3.2 5.8 - - - +
388B SER* 2.6 32.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B PHE* 4.6 2.0 - - + -
307B LEU* 4.3 23.8 - - + -
342B LEU* 4.3 29.8 - - + -
346B LEU* 4.1 23.1 - - + -
354B ILE* 3.7 27.4 - - + -
355B TYR 3.7 3.1 - - - -
374B VAL* 4.6 6.7 - - + +
375B ASP* 1.3 75.2 - - - +
377B ASP* 1.3 70.8 + - - +
378B PHE* 4.4 4.3 - - + +
385B THR* 4.5 11.7 - - - +
386B SER* 3.2 2.1 - - - -
387B VAL* 2.7 49.8 + - + +
389B ASN* 6.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B GLU 4.4 0.7 - - - +
354B ILE* 4.0 0.3 - - - -
355B TYR* 2.9 48.3 + - + +
356B GLY* 4.7 1.3 - - - -
375B ASP* 5.1 3.1 - - - +
376B LEU* 1.3 83.9 + - - +
378B PHE* 1.3 60.8 + - - +
385B THR 3.5 3.1 - - - -
386B SER* 3.3 25.7 + - - -
387B VAL 4.3 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ILE* 4.0 9.9 - - + -
346B LEU* 4.3 21.8 - - + -
347B THR 3.8 15.3 - - - -
348B VAL* 3.6 16.2 - - + -
352B GLU* 3.4 37.2 - - + -
353B GLU 3.0 35.0 - - - -
354B ILE* 3.9 9.4 - - + -
376B LEU* 4.3 4.9 - - + +
377B ASP* 1.3 73.8 - - - +
379B LYS* 1.3 60.4 + - - +
380B GLY* 3.5 20.9 - - - -
383B CYS* 3.8 22.4 - - - -
384B GLU* 3.2 6.1 - - - +
385B THR* 2.9 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B GLU* 5.6 1.0 - - - +
353B GLU 4.7 2.6 + - - -
378B PHE* 1.3 77.0 - - - +
380B GLY* 1.3 63.5 + - - +
383B CYS 4.1 2.7 - - - -
384B GLU* 3.3 35.7 - - + +
291G THR 5.3 6.5 + - - -
----------------------------------------------------------
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