Contacts of the strand formed by residues 316 - 326 (chain G) in PDB entry 4PKY
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 TYR 316 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280G PHE 4.4 0.7 - - - -
281G TYR 5.2 0.2 - - - -
282G HIS* 3.7 44.9 - + - -
283G ALA 5.8 0.3 + - - -
308G ARG* 4.0 26.0 - - + -
309G MET 3.5 5.6 - - - -
310G LEU* 3.5 53.2 - - + +
311G ALA* 4.7 0.4 - - - +
315G GLY* 1.3 79.3 - - - -
317G VAL* 1.3 65.0 + - - +
318G TRP* 4.3 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 317 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264G LEU 4.1 14.6 - - - +
265G ILE* 3.4 33.0 - - + -
308G ARG* 3.6 2.5 - - - -
309G MET 3.1 34.5 + - - +
311G ALA* 5.1 10.3 - - + +
316G TYR* 1.3 76.9 - - - +
318G TRP* 1.3 64.4 + - - +
319G LEU* 3.3 18.3 + - + +
343G VAL* 4.6 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 318 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285G ASP* 4.8 2.7 - - - -
306G GLN* 3.9 42.2 - - + -
307G TYR* 3.4 22.2 - - - -
308G ARG* 3.5 48.2 - - + +
316G TYR 5.0 5.4 - - - -
317G VAL* 1.3 71.0 - - - +
319G LEU* 1.3 64.0 - - - +
343G VAL* 3.8 1.3 - - - +
344G LEU* 2.9 48.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G PHE* 4.3 14.1 - - + -
265G ILE* 4.4 2.0 - - + -
306G GLN* 3.5 5.9 - - - -
307G TYR* 2.8 55.9 + - + +
309G MET* 3.4 42.6 - - + -
317G VAL* 3.6 22.9 - - + +
318G TRP* 1.3 81.1 - - - +
320G GLU* 1.3 61.8 + - - +
321G THR* 4.9 0.2 - - - +
341G ASN* 4.9 2.0 - - + -
342G TYR 3.1 10.8 - - - +
343G VAL* 3.6 30.5 - - + +
344G LEU* 4.3 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 320 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303G VAL* 5.1 12.4 - - + +
304G SER* 3.9 5.2 - - - -
305G GLY* 3.9 17.0 - - - +
306G GLN* 4.8 5.8 + - - +
319G LEU* 1.3 75.8 - - - +
321G THR* 1.3 63.0 + - - +
341G ASN* 3.5 1.0 - - - -
342G TYR* 2.8 66.6 + - + +
344G LEU* 4.1 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 321 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252G MET* 5.9 1.8 - - + -
281G TYR* 5.6 1.9 + - - +
289G MET* 5.1 2.5 - - - -
302G VAL* 3.4 4.0 - - - +
303G VAL* 3.5 3.2 - - - +
304G SER* 2.8 49.1 + - - +
307G TYR* 2.7 29.9 + - - -
320G GLU* 1.3 74.1 - - - +
322G GLN* 1.3 63.9 + - - +
323G GLY* 3.6 1.9 + - - +
339G CYS* 3.6 32.1 - - + -
340G VAL 3.6 2.7 - - - +
341G ASN* 2.8 21.4 + - - +
342G TYR* 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 322 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B MET* 6.3 0.2 - - - -
301G GLN* 5.8 6.9 + - - +
302G VAL 3.5 8.3 - - - +
303G VAL* 4.6 13.6 - - + +
320G GLU 4.3 0.2 - - - -
321G THR* 1.3 71.5 - - - +
323G GLY* 1.3 66.4 + - - +
324G THR* 4.3 10.6 + - - +
338G MET 3.5 2.3 - - - +
339G CYS* 3.5 1.7 - - - -
340G VAL* 3.0 51.7 + - + +
342G TYR* 3.6 24.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 323 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296G LEU* 3.6 19.3 - - - -
301G GLN* 3.4 16.6 - - - +
302G VAL* 3.0 17.5 + - - +
321G THR* 3.6 4.9 + - - +
322G GLN* 1.3 75.6 - - - +
324G THR* 1.3 67.4 + - - -
338G MET 3.6 4.0 - - - -
339G CYS* 4.1 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 324 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296G LEU* 3.7 2.6 - - - +
300G GLY 3.6 8.7 - - - +
301G GLN* 4.1 15.1 + - + +
322G GLN* 4.3 14.7 + - - +
323G GLY* 1.3 79.7 + - - -
325G VAL* 1.3 75.0 + - - +
326G ILE* 3.7 14.7 + - + +
337G ILE* 3.5 3.7 - - - +
338G MET* 2.8 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 325 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250G MET* 4.6 16.6 - - + -
296G LEU* 3.6 33.2 - - + +
297G CYS* 4.6 6.5 - - - +
300G GLY* 2.8 29.9 + - - +
324G THR* 1.3 76.7 - - - +
326G ILE* 1.3 70.5 + - - +
327G TYR* 3.9 39.9 + - + +
335G GLN 5.3 1.6 - - - +
336G CYS 3.8 9.4 - - - +
337G ILE* 4.5 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 326 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B ALA* 5.0 18.8 - - + +
592B SER* 3.9 17.5 - - - +
595B LYS* 4.1 26.7 - - + +
324G THR* 4.0 16.8 - - + +
325G VAL* 1.3 80.9 - - - +
327G TYR* 1.3 70.8 + - - +
335G GLN* 2.9 43.7 + - - +
336G CYS* 3.0 23.0 + - - +
338G MET* 4.1 23.1 - - + -
----------------------------------------------------------
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