Contacts of the helix formed by residues 314 - 330 (chain A) in PDB entry 1YOK
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 314 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A PRO* 1.3 69.5 - - - +
315A GLU* 1.3 63.7 + - - +
316A PRO* 2.9 16.4 - - - +
317A GLN* 2.8 55.0 + - + +
318A VAL* 3.0 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A PRO* 3.1 12.4 + - - +
314A ASP* 1.3 71.5 - - - +
316A PRO* 1.3 74.6 - - + +
318A VAL* 3.2 14.7 + - - +
319A GLN* 3.4 29.6 + - + +
392A TYR* 5.3 11.7 - - - -
393A ARG* 5.1 16.0 + - - +
396A VAL* 5.1 1.6 - - - +
397A HIS* 3.1 35.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ASP* 2.9 17.7 - - - +
315A GLU* 1.3 92.1 - - + +
317A GLN* 1.3 60.1 + - - +
319A GLN* 3.5 23.8 + - - +
320A ALA* 3.5 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ASP* 2.8 42.7 + - + +
316A PRO* 1.3 74.0 - - - +
318A VAL* 1.3 67.8 + - - +
320A ALA* 3.4 7.0 + - - +
321A LYS* 3.2 23.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A PRO* 4.2 19.5 - - + -
314A ASP 3.0 18.9 + - - +
315A GLU* 3.2 8.7 + - - +
317A GLN* 1.3 81.9 - - + +
319A GLN* 1.3 57.3 + - + +
321A LYS* 3.4 5.8 + - + +
322A ILE* 2.9 50.9 + - + +
355A SER* 4.1 21.5 - - - +
406A VAL* 4.8 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A GLU* 3.5 30.0 - - + +
316A PRO* 3.7 15.3 + - - +
317A GLN 3.3 0.2 - - - -
318A VAL* 1.3 78.9 - - + +
320A ALA* 1.3 58.4 + - - +
322A ILE* 4.2 1.4 - - - +
323A MET* 2.9 34.3 + - - +
393A ARG* 5.9 0.5 - - - -
397A HIS* 5.3 1.7 + - - -
404A PHE* 4.3 15.0 - - - -
406A VAL* 3.0 26.0 - - + +
407A THR* 3.5 15.1 + - - +
408A GLY* 3.9 19.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A PRO 3.5 8.1 + - - +
317A GLN* 3.4 10.3 + - - +
318A VAL 3.4 0.4 - - - -
319A GLN* 1.3 79.7 - - - +
321A LYS* 1.3 57.1 + - - +
323A MET* 3.7 4.6 - - - +
324A ALA* 2.8 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A GLN* 3.2 17.4 + - + +
318A VAL* 3.7 7.4 - - + +
320A ALA* 1.3 78.1 - - - +
322A ILE* 1.3 65.1 + - + +
324A ALA* 3.3 9.2 + - + +
325A TYR* 2.9 36.0 + - + +
351A GLN* 5.5 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A VAL* 2.9 38.4 + - + +
319A GLN* 4.2 2.9 - - - +
321A LYS* 1.3 76.9 - - + +
323A MET* 1.3 66.4 + - - +
325A TYR* 3.3 6.6 + - - +
326A LEU* 3.0 30.6 + - + +
348A MET* 4.3 9.9 - - + -
351A GLN* 3.8 46.9 - - + +
352A THR* 4.1 6.5 - - - +
355A SER* 4.9 1.6 - - - -
406A VAL* 4.0 20.6 - - + -
407A THR* 3.6 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A GLN 2.9 21.6 + - - +
320A ALA* 3.7 5.6 - - - +
322A ILE* 1.3 78.3 - - - +
324A ALA* 1.3 64.3 + - - +
326A LEU* 3.2 25.2 + - + +
327A GLN* 3.2 39.5 + - + +
407A THR* 3.9 19.3 - - + +
409A GLN* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ALA 2.8 20.8 + - - +
321A LYS* 3.4 14.4 - - + +
323A MET* 1.3 77.1 - - - +
325A TYR* 1.3 57.1 + - - +
327A GLN* 3.3 13.5 + - - +
328A GLN* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LYS* 2.9 29.0 + - - +
322A ILE 3.7 3.6 - - - +
323A MET 3.3 0.2 - - - -
324A ALA* 1.3 72.5 - - - +
326A LEU* 1.3 69.8 + - + +
328A GLN* 4.3 8.3 - - + -
329A GLU* 2.7 61.6 + - + +
347A LYS* 4.4 18.6 + - + +
350A ASP* 5.3 1.5 + - - -
351A GLN* 3.3 51.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ILE* 3.0 22.6 + - + +
323A MET* 3.2 17.7 + - + +
325A TYR* 1.3 87.8 - - + +
327A GLN* 1.3 59.5 + - - +
329A GLU* 3.7 5.2 - - - +
330A GLN* 3.3 24.8 + - - +
344A LEU* 4.4 22.0 - - + +
347A LYS* 3.9 30.3 - - + -
348A MET* 4.0 25.6 - - + +
407A THR* 3.5 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A MET* 3.2 38.2 + - + +
324A ALA* 3.6 12.0 + - - +
325A TYR 3.1 0.2 - - - -
326A LEU* 1.3 75.2 - - - +
328A GLN* 1.3 66.8 + - - +
329A GLU 3.1 1.3 - - - -
330A GLN* 2.8 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ALA 2.9 17.9 + - - +
325A TYR* 3.7 10.8 - - + +
327A GLN* 1.3 75.5 - - - +
329A GLU* 1.3 65.0 + - - +
330A GLN 3.8 4.3 - - - +
331A ALA* 3.9 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A TYR* 2.7 52.6 + - + +
326A LEU* 3.7 8.3 - - - +
328A GLN* 1.3 75.3 - - - +
330A GLN* 1.3 56.7 + - - +
331A ALA* 2.8 18.4 + - - +
332A ASN* 3.1 17.1 - - - +
333A ARG* 4.0 19.1 + - - -
339A LEU* 6.0 0.2 - - - -
347A LYS* 2.9 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LEU 3.3 14.3 + - - +
327A GLN* 2.8 22.1 + - - +
329A GLU* 1.3 79.9 + - - +
331A ALA* 1.3 65.7 + - - +
333A ARG* 4.4 9.7 - - - +
338A LYS* 4.2 23.6 + - - +
339A LEU* 3.2 33.3 - - - +
344A LEU* 5.9 6.8 - - + +
----------------------------------------------------------
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