Contacts of the helix formed by residues 314 - 325 (chain A) in PDB entry 1Y24
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 ALA 314 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A TRP 3.5 4.0 + - - -
313A ARG* 1.3 68.3 - - + +
315A ASP* 1.3 64.3 + - - +
317A THR* 3.1 28.1 - - - -
318A TYR* 3.8 6.5 + - - -
368A ARG* 3.0 45.5 + - - +
439A LEU* 3.9 17.0 - - + -
443A SER* 4.5 8.0 + - - +
445A ASP* 4.9 0.2 + - - -
446A THR* 5.8 0.2 - - + -
494A VAL* 3.5 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ARG* 2.8 59.2 + - - +
314A ALA* 1.3 77.2 - - - +
316A VAL* 1.3 62.8 + - - -
317A THR 3.1 2.4 + - - -
318A TYR* 2.7 40.0 + - + -
319A ALA* 2.9 26.6 + - - +
408A ALA* 3.9 6.6 - - - +
439A LEU* 5.4 1.6 - - - +
494A VAL* 3.8 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ARG* 6.2 0.9 - - - +
302A PRO* 3.7 29.2 - - + -
310A GLN* 2.9 16.0 + - - +
311A PRO* 3.1 37.5 - - + +
312A TRP 4.7 0.9 - - - +
313A ARG* 3.1 16.0 + - - +
315A ASP* 1.3 72.6 - - - +
317A THR* 1.3 62.9 + - - +
319A ALA* 3.7 4.9 - - - +
320A ALA* 2.7 39.0 + - + +
369A PHE* 3.6 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ALA 3.1 14.2 + - - -
316A VAL* 1.3 84.2 - - - +
318A TYR* 1.3 58.3 + - - +
321A MET 2.8 22.2 + - - -
368A ARG* 3.1 58.3 - - + +
369A PHE* 3.2 3.5 + - - -
371A VAL* 4.5 4.9 - - + -
372A ASN* 2.9 38.0 + - + +
496A PRO* 3.6 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ARG* 5.0 1.8 + - - -
314A ALA 3.8 1.2 + - - -
315A ASP* 2.7 57.0 + - + +
317A THR* 1.3 80.7 - - - +
319A ALA* 1.3 83.3 + - + +
321A MET* 3.3 13.7 + - - +
322A VAL 3.9 0.7 + - - -
405A VAL* 3.3 29.8 - - + +
406A SER 4.1 7.6 - - - +
407A GLN* 3.3 40.9 + - + -
408A ALA 2.9 36.0 + - - -
409A GLY* 3.5 4.0 + - - -
494A VAL* 3.4 44.2 - - + +
496A PRO* 3.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ARG* 5.8 6.7 - - - +
269A SER* 6.6 0.7 - - - -
272A ILE* 3.1 26.6 - - + +
302A PRO* 6.0 3.4 - - + -
313A ARG* 5.9 2.5 - - - +
315A ASP* 2.9 16.7 + - + +
316A VAL* 3.7 5.6 - - - +
318A TYR* 1.3 85.8 - - + +
320A ALA* 1.3 58.4 + - - +
322A VAL* 3.2 12.6 - - - +
323A VAL* 3.9 3.2 - - - +
407A GLN* 3.5 16.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
302A PRO* 5.0 10.5 - - + -
316A VAL* 2.7 25.6 + - + +
319A ALA* 1.3 71.8 - - + +
321A MET* 1.3 56.5 + - - +
322A VAL 3.5 0.2 - - - -
323A VAL* 3.0 22.3 + - + +
324A LYS* 2.8 32.2 + - - +
336A ASN* 5.5 0.7 - - - +
369A PHE* 3.3 24.7 - - + -
372A ASN* 3.5 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ARG* 4.2 7.9 - - + -
317A THR 2.8 5.1 + - - -
318A TYR 3.3 12.3 + - - +
320A ALA* 1.3 73.5 - - - +
322A VAL* 1.3 52.0 + - - +
324A LYS* 2.9 13.2 + - - +
325A VAL* 2.7 54.5 + - + +
372A ASN* 3.0 37.2 - - - +
375A ARG* 3.1 40.4 - - + +
376A PRO* 4.4 9.9 - - + -
403A ALA* 3.8 19.3 - - + -
404A GLU 5.4 1.1 - - - +
405A VAL* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 3.4 29.2 - - + -
272A ILE* 3.5 22.2 - - + -
276A GLU* 4.5 2.1 - - - +
318A TYR 4.1 0.7 - - - +
319A ALA 3.2 11.0 - - - +
321A MET* 1.3 77.4 - - - +
323A VAL* 1.3 57.1 + - - +
325A VAL* 2.6 31.6 - - + +
326A ILE* 3.1 11.6 - - - +
388A THR 3.1 26.9 - - - +
389A ALA* 5.6 0.2 - - - -
405A VAL* 4.7 6.1 - - + -
407A GLN* 3.2 30.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A VAL* 5.6 2.7 - - + -
272A ILE* 4.4 17.9 - - + +
275A GLN* 3.2 36.3 - - + +
276A GLU* 5.4 2.2 - - + -
300A ALA* 6.0 2.0 - - + -
301A ASP 6.5 0.7 - - - -
319A ALA 3.9 13.5 - - - +
320A ALA* 3.0 29.6 + - + +
322A VAL* 1.3 77.5 - - - +
324A LYS* 1.3 78.2 + - - +
325A VAL 3.3 0.4 - - - -
326A ILE* 4.0 6.0 - - + +
327A ALA* 3.0 26.0 + - - +
334A LEU* 5.1 5.8 - - + +
336A ASN* 4.7 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TRP 2.5 18.9 - - - +
48A ARG 4.3 9.6 - - - +
49A SER* 3.7 8.4 - - - +
50A THR* 3.6 21.2 - - + +
320A ALA 2.8 27.3 + - - +
321A MET* 3.0 6.5 - - - +
323A VAL* 1.3 83.6 - - - +
325A VAL* 1.3 58.2 + - + +
326A ILE 2.7 8.7 + - - -
327A ALA* 3.3 10.0 + - - +
336A ASN* 2.9 33.4 + - - +
369A PHE* 3.4 31.5 - - - -
372A ASN* 3.8 19.7 - - - +
373A ASN* 3.4 24.2 - - - +
376A PRO* 4.6 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ARG* 3.3 14.1 - - - +
46A PHE* 2.9 46.5 - - + +
47A TRP 2.9 12.8 - - - -
48A ARG* 3.6 25.8 - - + -
321A MET* 2.7 43.6 + - + +
322A VAL* 2.6 28.1 - - + +
324A LYS* 1.3 69.1 - - + +
326A ILE* 1.3 51.7 + - - +
387A LEU 5.2 1.6 - - - +
390A MET 4.9 9.9 - - - +
391A GLY 5.4 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