Contacts of the strand formed by residues 353 - 362 (chain A) 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 GLU 353 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A CYS* 4.1 11.7 - - - -
296A LEU 3.4 11.7 - - - +
297A GLN* 3.5 25.0 - - - +
298A ILE* 4.1 0.9 - - - -
351A GLY 4.0 7.8 - - - +
352A GLU* 1.3 84.2 - - - +
354A ILE* 1.3 59.9 + - - +
355A TYR* 2.6 48.8 + - + -
378A PHE* 3.1 23.4 - - - -
379A LYS 4.8 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ALA* 4.1 26.2 - - + -
270A THR* 4.8 0.2 - - + -
294A PHE* 3.8 11.0 - - + +
295A CYS* 3.3 5.4 - - - -
296A LEU* 2.9 46.6 + - + +
298A ILE* 3.8 21.3 - - + -
304A VAL* 4.6 7.2 - - + -
307A LEU* 5.2 2.7 - - + -
346A LEU* 4.1 18.6 - - + -
348A VAL* 5.2 0.4 - - + -
353A GLU* 1.3 75.2 - - - +
355A TYR* 1.3 64.7 + - - +
376A LEU* 3.6 37.7 - - + -
377A ASP 3.9 3.1 - - - +
378A PHE* 3.8 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A PHE* 3.4 10.3 - - - -
295A CYS* 3.7 21.4 - - + -
353A GLU* 2.6 46.2 + - + -
354A ILE* 1.3 81.0 - - - +
356A GLY* 1.3 55.1 + - - +
376A LEU* 3.6 2.8 - - - +
377A ASP* 2.7 49.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ALA* 3.3 6.4 - - - +
294A PHE* 2.8 40.2 + - - +
355A TYR* 1.3 77.7 - - - +
357A THR* 1.3 64.2 + - - +
375A ASP* 3.0 16.4 - - - -
377A ASP* 4.6 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A THR* 4.1 22.0 - - + +
292A SER 3.4 8.3 - - - -
293A ALA* 4.2 12.6 - - + +
294A PHE* 3.5 6.2 - - - -
356A GLY* 1.3 81.0 - - - +
358A ILE* 1.3 61.8 + - - +
359A SER* 5.0 1.4 + - - -
373A THR* 4.8 2.1 + - - +
374A VAL* 3.4 2.6 - - - -
375A ASP* 2.9 52.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU* 5.8 1.1 - - + -
223A VAL* 4.9 11.9 - - + -
275A ILE* 3.8 38.6 - - + -
290A PHE* 4.1 4.3 - - + -
291A THR* 3.9 0.2 - - - -
292A SER* 3.0 33.9 + - - +
294A PHE* 3.5 24.7 - - + -
307A LEU* 6.3 1.1 - - + -
309A THR* 4.9 7.4 - - + -
340A PHE* 5.4 3.6 - - + -
357A THR* 1.3 75.7 - - - +
359A SER* 1.3 67.3 + - - +
360A MET* 5.2 4.0 - - + -
372A PHE* 4.3 22.4 - - + -
373A THR 3.4 6.1 - - - +
374A VAL* 4.3 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A PHE* 3.1 9.6 - - - -
291A THR* 3.0 33.3 + - - +
357A THR* 5.0 1.9 + - - -
358A ILE* 1.3 74.2 - - - +
360A MET* 1.3 62.9 - - - +
361A LYS* 6.3 1.8 - - - -
372A PHE* 3.2 7.1 - - - +
373A THR* 3.0 48.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A CYS* 5.1 2.2 - - - +
192A PHE* 3.5 42.0 - - + -
221A LEU* 4.8 8.7 - - - -
288A LEU 3.7 13.8 - - - +
289A SER* 3.3 3.8 - - - -
290A PHE* 3.1 62.2 + - + +
358A ILE* 5.2 3.4 - - + -
359A SER* 1.3 76.5 - - - +
361A LYS* 1.3 65.3 + - - +
362A PRO* 6.1 0.2 - - + -
370A LEU* 3.9 19.1 - - + -
371A ASP 3.1 16.4 - - - +
372A PHE* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LEU 5.3 0.2 - - - -
289A SER* 3.9 14.6 - - - +
290A PHE 5.7 0.2 - - - +
359A SER* 6.0 1.8 - - - -
360A MET* 1.3 79.4 - - - +
362A PRO* 1.3 80.9 - - + +
364A ALA* 5.6 5.6 - - - +
370A LEU* 3.6 11.1 - - - +
371A ASP* 3.0 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A SER* 4.0 13.7 - - - +
198A ASN* 5.1 7.2 - - - +
288A LEU* 4.6 10.5 - - + +
289A SER* 3.2 20.0 - - - +
360A MET* 6.1 0.4 - - + -
361A LYS* 1.3 101.0 - - + +
363A ASN* 1.3 67.4 + - - +
364A ALA* 3.5 2.4 + - - -
367A VAL* 3.7 31.2 - - + +
369A ASP 3.6 7.0 - - - +
370A LEU* 4.5 4.5 - - + -
371A ASP* 5.0 0.2 - - - -
----------------------------------------------------------
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