Contacts of the strand formed by residues 302 - 314 (chain G) 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 ASP 302 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227G GLU* 3.7 14.0 - - - +
269G VAL* 3.9 22.2 - - + -
300G ARG* 3.0 41.5 + - - +
301G ASN* 1.3 76.6 - - - +
303G TYR* 1.3 79.3 + - - +
347G THR* 4.0 0.3 - - - -
348G VAL* 2.9 34.0 + - - +
319I HIS* 3.3 11.2 + - - -
320I LYS* 3.1 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 303 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227G GLU* 3.2 28.1 + - + +
269G VAL* 3.9 2.1 - - - +
302G ASP* 1.3 87.9 + - - +
304G VAL* 1.3 65.8 + - - +
305G HIS* 3.8 22.9 - + + -
345G TYR* 3.6 28.0 - + + -
346G LEU 3.3 5.6 - - - +
347G THR* 3.8 29.2 - - + -
105I HIS* 2.4 46.2 + + + +
106I ASN* 3.2 14.4 + - - -
319I HIS* 3.7 15.8 - - - +
320I LYS* 4.5 22.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 304 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225G ALA* 3.8 17.9 - - + -
226G ILE 3.3 4.5 - - - +
269G VAL* 3.9 31.0 - - + -
298G ILE* 5.2 0.2 - - + -
303G TYR* 1.3 79.2 - - - +
305G HIS* 1.3 61.5 + - - +
306G ALA 3.8 21.5 - - - +
307G LEU* 5.2 0.9 - - + -
342G LEU* 4.2 14.4 - - + +
345G TYR* 3.3 3.7 - - - -
346G LEU* 2.8 55.2 + - + +
348G VAL* 4.0 13.9 - - + -
354G ILE* 4.6 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 305 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226G ILE 2.8 4.9 + - - -
227G GLU* 3.8 8.9 - - + +
228G ASP* 3.1 34.8 + - + +
229G ARG* 3.1 41.9 - - + +
232G LYS* 4.1 23.1 - - + +
303G TYR* 3.8 26.7 - + + +
304G VAL* 1.3 73.5 - - - +
306G ALA* 1.3 62.5 + - + +
341G TYR* 3.8 5.4 - - + -
342G LEU* 3.0 32.3 + - - +
345G TYR* 3.6 33.6 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 306 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225G ALA* 3.4 6.6 - - - +
226G ILE* 2.9 37.3 + - + +
304G VAL* 3.6 4.5 - - - +
305G HIS* 1.3 83.4 - - + +
307G LEU* 1.3 70.2 + - - +
339G VAL* 3.9 16.8 - - + -
340G PHE 3.1 22.2 - - - +
341G TYR* 3.9 9.4 - - + -
342G LEU* 4.0 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223G VAL* 4.5 15.7 - - + -
224G VAL 3.4 7.2 - - - +
225G ALA* 3.9 18.6 - - + -
294G PHE* 4.0 18.4 - - + -
296G LEU* 4.1 12.3 - - + -
304G VAL* 5.2 2.7 - - + -
306G ALA* 1.3 81.2 - - - +
308G VAL* 1.3 64.0 + - - +
340G PHE* 2.7 47.4 + - + +
342G LEU* 4.8 8.1 - - + -
354G ILE* 5.1 4.0 - - + -
358G ILE* 6.3 1.3 - - + -
374G VAL* 3.8 32.3 - - + -
376G LEU* 4.3 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 308 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223G VAL* 3.3 3.3 - - - -
224G VAL* 2.9 38.5 + - + +
226G ILE* 3.6 42.8 - - + -
263G VAL* 4.2 7.2 - - + -
307G LEU* 1.3 80.9 - - - +
309G THR* 1.3 68.1 + - - +
310G TYR* 4.3 2.7 + - + -
328G PRO* 4.8 9.4 - - + -
337G GLN* 3.7 33.2 - - + -
338G THR 3.2 7.4 - - - +
339G VAL* 4.1 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 309 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G CYS* 3.4 17.2 - - - +
221G LEU* 4.2 11.9 - - + -
222G TYR 3.0 16.8 - - - +
223G VAL* 3.6 20.6 - - + -
275G ILE* 4.7 8.3 - - + -
308G VAL* 1.3 75.8 - - - +
310G TYR* 1.3 61.6 + - - +
337G GLN* 3.9 3.8 - - - -
338G THR* 2.9 48.0 + - - -
340G PHE* 3.7 19.4 - - + -
358G ILE* 4.8 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 310 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G CYS* 6.4 0.7 - - - +
221G LEU* 3.5 6.0 - - - +
222G TYR* 2.8 63.3 + + + -
224G VAL* 4.3 22.0 - - + -
272G ALA* 3.3 20.3 - - - +
308G VAL* 5.0 4.7 - - + -
309G THR* 1.3 76.6 - - - +
311G PHE* 1.3 67.6 + - - +
312G ASN* 3.7 20.5 + - - -
326G THR* 3.4 24.9 - - - +
327G ALA* 3.6 28.5 - - + -
328G PRO* 3.9 15.5 - - + -
329G ASP* 5.7 0.9 - - - -
336G LYS 5.4 1.1 - - - -
337G GLN* 4.4 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 311 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187G MET* 4.1 7.9 - - + -
188G GLY 3.5 8.5 - - - -
190G CYS* 4.3 5.4 - - - -
191G LEU* 3.4 48.9 - - + -
220G ALA 3.0 20.2 - - - +
221G LEU* 4.1 7.9 - - + -
222G TYR* 4.9 0.2 - - - -
310G TYR* 1.3 77.3 - - - +
312G ASN* 1.3 62.8 + - - +
313G ILE* 3.7 31.4 - - + -
324G PHE* 4.6 2.5 - + - -
325G SER* 3.9 0.2 - - - -
326G THR* 2.8 50.1 + - + +
335G TRP* 3.6 43.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 312 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218G ARG* 5.8 4.3 + - - +
219G ALA* 3.4 4.2 - - - -
220G ALA* 2.8 35.6 + - + +
222G TYR* 3.2 28.5 + - + -
310G TYR* 3.7 11.9 + - - -
311G PHE* 1.3 78.8 + - - +
313G ILE* 1.3 66.8 + - - +
324G PHE 3.5 6.3 - - - +
325G SER* 2.7 36.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 313 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186G TRP* 5.0 0.4 - - + -
187G MET* 3.8 28.5 - - + -
191G LEU* 4.3 0.2 - - + -
216G PRO* 3.5 31.2 - - + -
218G ARG* 3.7 2.7 - - - +
219G ALA* 3.7 21.8 - - + -
311G PHE* 3.7 22.4 - - + -
312G ASN* 1.3 82.8 - - - +
314G GLU* 1.3 66.6 + - - +
315G PHE* 4.1 5.4 - - + -
321G LYS* 4.6 2.6 + - - -
323G GLY* 3.0 3.7 - - - -
324G PHE* 2.8 66.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 314 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216G PRO* 3.3 2.5 - - - +
217G ASP* 3.2 8.1 + - - +
218G ARG* 2.8 69.0 + - + +
313G ILE* 1.3 75.1 - - - +
315G PHE* 1.3 72.2 + - - +
316G THR* 3.7 20.9 - - + +
321G LYS* 3.9 26.8 + - + +
322G MET 3.4 14.0 + - - +
323G GLY* 4.1 0.7 - - - -
----------------------------------------------------------
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