Contacts of the strand formed by residues 282 - 291 (chain G) in PDB entry 5YWB
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 282 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G PHE* 4.6 15.5 - - + +
219G VAL* 3.5 2.1 - - - -
220G VAL* 3.0 53.4 + - + +
280G ASP 4.2 0.8 - - - -
281G LEU* 1.3 72.3 - - - +
283G ILE* 1.3 62.9 + - - +
284G ILE* 3.9 9.3 + - + +
303G SER* 5.1 4.0 - - - -
304G TYR 3.4 5.8 - - - +
305G LEU* 4.5 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 283 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198G PHE* 4.3 27.1 - - + -
217G MET* 4.8 12.1 - - + -
218G GLN 3.6 12.8 - - - +
219G VAL* 3.6 31.6 - - + -
238G ILE* 5.1 5.6 - - + -
267G LEU* 3.7 24.2 - - + -
281G LEU* 4.8 11.4 - - + +
282G GLU* 1.3 75.5 - - - +
284G ILE* 1.3 62.7 + - - +
285G VAL* 5.4 2.2 - - + -
303G SER* 3.6 1.0 - - - -
304G TYR* 2.9 50.9 + - + +
305G LEU 5.9 0.4 - - - +
309G ILE* 5.7 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 284 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A PHE* 4.2 14.6 - - + -
35G PHE* 4.3 22.9 - - + -
36G VAL* 3.8 11.7 - - + -
217G MET* 3.7 1.6 - - - +
218G GLN* 2.9 66.9 + - + +
220G VAL* 4.9 7.2 - - + -
235G GLN* 5.0 0.9 - - - +
282G GLU* 3.9 9.4 + - + +
283G ILE* 1.3 76.9 - - - +
285G VAL* 1.3 64.8 + - - +
286G ILE* 4.0 19.3 - - + -
302G THR 3.0 7.6 - - - +
303G SER* 3.2 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 285 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183G PHE* 3.9 26.2 - - + -
198G PHE* 6.1 0.4 - - + -
200G LEU* 4.1 22.7 - - + -
202G VAL* 5.9 0.2 - - + -
215G ILE* 4.9 13.0 - - + -
216G HIS 3.8 4.3 - - - +
217G MET* 4.0 24.7 - - + +
257G ILE* 6.1 1.3 - - + -
283G ILE* 5.1 4.9 - - + +
284G ILE* 1.3 79.0 - - - +
286G ILE* 1.3 63.3 + - - +
287G LEU 5.1 0.2 - - - +
300G ALA 3.5 0.3 - - - +
301G ARG* 3.2 5.4 - - - -
302G THR* 2.9 53.4 + - + +
304G TYR* 4.9 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 286 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A PHE* 3.6 39.0 - - + -
36G VAL* 6.0 0.4 - - + -
214G THR 3.5 3.1 - - - +
215G ILE* 3.6 2.5 - - - -
216G HIS* 2.9 59.9 + - + +
218G GLN* 4.5 5.4 - - - +
284G ILE* 4.0 20.2 - - + -
285G VAL* 1.3 82.7 - - - +
287G LEU* 1.3 59.8 + - - +
288G GLU 3.7 0.9 + - - +
299G GLN* 3.4 37.5 - - - +
300G ALA 3.5 1.8 - - - -
301G ARG* 3.6 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 287 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G LEU* 3.9 26.2 - - + -
183G PHE* 3.2 35.9 - - + -
202G VAL* 5.1 3.8 - - + -
203G GLY 5.9 0.9 - - - +
210G ILE* 4.6 8.7 - - + +
213G ALA* 3.7 30.3 - - + -
214G THR 3.4 6.1 - - - +
215G ILE* 3.6 16.6 - - + -
249G ILE* 4.7 5.4 - - + -
251G LEU* 4.5 19.7 - - + -
285G VAL 4.0 0.8 - - - -
286G ILE* 1.3 71.1 - - - +
288G GLU* 1.3 61.1 + - - +
299G GLN* 3.0 5.1 - - - -
300G ALA* 2.8 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 288 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ILE* 4.7 7.6 - - + -
212A SER* 4.3 23.4 - - - +
210G ILE* 4.5 0.4 - - - -
212G SER* 4.5 5.6 + - - +
213G ALA* 2.8 26.9 - - - +
214G THR* 2.9 38.5 + - + +
216G HIS* 4.7 8.5 - - + +
286G ILE 3.7 0.8 + - - +
287G LEU* 1.3 76.3 - - - +
289G GLY* 1.3 80.5 + - - +
290G VAL* 4.2 2.1 + - - +
297G THR* 3.6 20.9 - - - +
298G THR 3.6 10.1 - - - +
299G GLN* 3.8 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 289 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210G ILE* 3.5 23.1 - - - +
211G ILE 3.8 8.1 - - - -
212G SER* 4.3 1.3 - - - -
213G ALA* 4.0 1.6 - - - -
288G GLU* 1.3 90.4 + - - +
290G VAL* 1.3 62.2 + - - -
291G VAL 3.9 0.5 + - - -
298G THR* 2.9 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 290 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288E GLU* 5.9 0.4 - - - +
297E THR* 3.5 34.3 - - + +
210G ILE* 4.1 1.6 - - - -
211G ILE* 2.7 52.2 + - + +
212G SER* 4.1 7.4 - - - +
288G GLU* 5.2 1.6 - - - +
289G GLY* 1.3 72.9 - - - -
291G VAL* 1.3 77.5 + - - +
295G GLY* 3.2 29.6 - - - +
296G ILE 3.2 8.7 - - - +
297G THR* 3.9 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 291 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297E THR 5.3 1.0 - - - +
177G ARG* 5.3 18.2 - - + +
178G ALA* 5.9 2.0 - - - -
208G SER* 6.4 2.0 - - - -
209G MET 4.1 10.3 - - - +
210G ILE* 4.6 11.4 - - + +
211G ILE* 5.6 0.2 - - - -
289G GLY 3.9 0.4 + - - -
290G VAL* 1.3 84.1 - - - +
292G GLU* 1.3 65.5 + - - +
293G THR* 4.8 2.9 - - + +
294G THR* 3.4 37.9 - - + +
295G GLY* 3.2 14.9 + - - -
296G ILE* 3.1 17.5 + - + +
298G THR* 4.1 14.4 - - - +
----------------------------------------------------------
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