Contacts of the helix formed by residues 309 - 320 (chain A) in PDB entry 1OFD
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 309 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ALA 3.8 22.7 - - - -
306A LEU* 3.0 18.9 + - + +
308A ASP* 1.3 95.9 - - + +
310A PRO* 1.3 66.1 - - - +
311A GLU* 3.2 3.6 - - - +
312A ILE* 3.0 38.7 + - + +
313A SER* 3.5 8.1 + - - -
403A TYR* 3.6 36.3 - + + +
404A GLN* 5.3 0.4 + - - -
407A GLN* 3.8 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LEU 4.0 2.2 - - - +
307A LYS 4.0 8.5 - - - +
308A ASP 3.3 9.6 - - - +
309A TYR* 1.3 89.8 - - - +
311A GLU* 1.3 63.1 + - + +
313A SER* 3.4 9.6 + - - -
314A ASP* 3.0 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A TYR* 3.2 1.7 - - - -
310A PRO* 1.3 82.3 - - + +
312A ILE* 1.3 62.1 + - + +
314A ASP* 3.4 14.3 + - - +
315A PHE* 3.0 21.8 + - - +
407A GLN* 5.4 11.7 + - + +
410A ALA* 3.3 26.8 - - + +
411A GLN* 3.3 36.6 - - + +
413A TYR 5.4 1.6 - - - +
415A TYR* 5.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A MET* 5.2 2.0 - - + -
298A GLU* 4.5 5.2 - - - +
306A LEU* 3.8 18.4 - - + -
309A TYR* 3.0 35.7 + - + +
311A GLU* 1.3 74.8 - - - +
313A SER* 1.3 65.4 + - - +
315A PHE* 3.2 3.7 + - - +
316A HIS* 3.2 41.9 + - + +
403A TYR* 3.7 18.6 - - + +
406A LYS* 3.6 32.1 - - + +
407A GLN* 3.7 26.0 - - + +
410A ALA* 3.9 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TYR* 3.8 25.6 + - - -
306A LEU* 3.9 27.5 + - - +
309A TYR 3.5 4.4 + - - -
310A PRO* 3.4 11.8 + - - +
312A ILE* 1.3 79.2 - - - +
314A ASP* 1.3 56.9 + - - +
316A HIS 3.4 0.9 + - - -
317A ASP* 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A PRO* 3.0 27.1 + - - +
311A GLU* 3.5 16.2 - - - +
312A ILE 3.2 0.2 - - - -
313A SER* 1.3 75.3 - - - +
315A PHE* 1.3 58.6 + - - +
317A ASP* 3.3 10.7 - - - +
318A TYR* 2.9 29.6 + - - +
415A TYR* 3.7 5.6 - - + +
416A GLY* 3.7 34.5 + - - +
419A ILE* 3.7 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLU* 3.9 26.7 - - + -
293A MET* 3.8 37.9 - - + -
294A ILE* 3.6 27.8 - - + -
311A GLU 3.0 13.6 + - - +
312A ILE* 3.2 9.8 + - - +
314A ASP* 1.3 73.9 - - - +
316A HIS* 1.3 79.4 + + - +
318A TYR* 3.2 2.6 + - - +
319A TYR* 2.9 55.6 + + + -
409A ALA* 4.4 3.6 - - + -
410A ALA* 3.9 18.4 - - + -
415A TYR* 3.6 34.9 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A MET* 3.5 38.1 + - + +
297A PRO* 3.5 25.1 - - + +
298A GLU* 4.0 16.2 + - + +
300A TYR* 3.4 39.0 - + + -
312A ILE* 3.2 35.9 + - + +
313A SER 4.0 0.4 - - - +
315A PHE* 1.3 92.6 - + - +
317A ASP* 1.3 57.8 + - - +
319A TYR* 4.3 4.4 - - - +
320A SER* 2.6 40.9 + - - +
406A LYS* 5.5 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TYR* 3.5 19.1 + - + +
301A LYS* 5.6 1.1 - - - -
313A SER 2.8 18.6 + - - +
314A ASP* 3.3 12.4 - - - +
316A HIS* 1.3 77.2 - - - +
318A TYR* 1.3 60.7 + - - +
320A SER* 3.6 9.9 - - - -
419A ILE* 3.6 18.2 - - + +
423A ARG* 2.8 51.5 + - - -
521A PHE* 5.7 0.2 - - - -
540A LYS* 4.2 7.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
314A ASP 2.9 14.4 + - - +
315A PHE 3.5 6.5 - - - +
316A HIS 3.2 0.2 - - - -
317A ASP* 1.3 76.3 - - - +
319A TYR* 1.3 82.3 + + - +
321A GLY* 3.1 13.0 + - - -
322A LEU* 3.4 41.3 - - + +
415A TYR* 3.5 32.3 - + + -
418A TRP* 3.5 26.9 - + - -
419A ILE* 3.5 15.0 - - + +
423A ARG* 4.5 2.2 + - - +
531A PRO* 3.7 5.7 - - + +
532A LYS 3.0 34.0 + - - -
535A SER* 3.3 10.2 - - - -
536A ALA* 4.1 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ARG* 3.0 32.9 + - - -
294A ILE* 3.8 42.0 - - + +
297A PRO* 6.5 0.9 - - + -
315A PHE* 2.9 63.2 + + + +
316A HIS* 3.4 5.8 + - - +
318A TYR* 1.3 89.7 - + - +
320A SER* 1.3 60.7 + - - +
321A GLY 3.0 2.2 - - - -
322A LEU* 2.8 19.7 + - + +
323A GLN* 2.8 35.4 + - + +
415A TYR* 3.0 24.5 + + - -
528A LEU* 4.6 6.3 - - + -
531A PRO* 3.4 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TYR* 3.5 20.6 + - - -
301A LYS* 5.6 0.2 + - - -
316A HIS* 2.6 25.3 + - - +
317A ASP* 3.6 9.6 - - - -
319A TYR* 1.3 77.5 - - - +
321A GLY* 1.3 58.4 + - - +
322A LEU 3.6 0.2 + - - -
323A GLN 4.3 11.5 + - - +
324A GLU* 5.2 0.7 + - - -
521A PHE* 3.3 27.4 - - - -
540A LYS* 6.3 0.4 - - - -
722A LEU* 5.5 8.4 - - - +
724A ALA* 5.1 8.5 - - - +
----------------------------------------------------------
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