Contacts of the helix formed by residues 350 - 358 (chain A) in PDB entry 1O69
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 GLY 350 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ASP* 3.1 6.2 + - - -
296A ALA* 5.1 7.6 - - - -
297A CYS* 3.8 10.1 - - - -
348A LEU* 3.8 2.9 - - - +
349A ASN* 1.3 78.4 - - - +
351A ASN* 1.3 63.6 - - - +
352A SER 3.6 1.8 - - - -
353A GLU* 3.6 12.2 + - - +
354A LEU* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ASP* 3.6 0.4 + - - -
101A CYS* 3.0 31.7 + - - +
102A ASP* 4.1 6.9 - - - +
103A GLU 5.0 0.4 - - - +
293A GLU 4.5 1.2 - - - +
294A LEU* 3.4 23.8 - - + +
295A ASN* 2.8 48.1 + - - +
349A ASN* 2.9 15.7 + - - +
350A GLY* 1.3 80.1 - - - +
352A SER* 1.3 56.6 + - - +
354A LEU* 3.2 6.8 + - - +
355A PHE* 2.9 41.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A SER* 4.6 1.6 + - - -
80A PHE* 3.6 39.8 - - - -
100A ASP* 2.8 25.2 + - - -
101A CYS* 3.7 6.8 - - - -
308A ILE* 5.3 0.4 - - - +
332A TRP 5.0 0.3 - - - +
334A ALA* 3.4 11.6 + - - +
336A HIS* 3.3 23.9 + - - -
350A GLY 3.6 0.2 - - - -
351A ASN* 1.3 75.6 - - - +
353A GLU* 1.3 56.2 + - - +
355A PHE* 3.5 5.1 + - - +
356A PHE* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LYS* 2.6 36.7 + - - +
308A ILE* 3.9 31.3 - - + +
334A ALA* 5.3 0.2 - - + -
336A HIS* 2.7 37.5 + - + +
337A THR* 4.0 8.3 - - + +
348A LEU* 4.1 9.0 - - - +
350A GLY* 3.6 12.9 + - - +
351A ASN 3.3 0.4 - - - -
352A SER* 1.3 74.9 + - - +
354A LEU* 1.3 59.8 + - - +
356A PHE* 3.4 3.1 + - - +
357A GLN* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A PHE* 3.8 23.8 - - + -
293A GLU* 3.6 56.8 - - + +
294A LEU* 4.5 9.4 - - + +
350A GLY 3.1 18.6 + - - +
351A ASN* 3.2 6.5 + - - +
353A GLU* 1.3 77.0 - - - +
355A PHE* 1.3 59.3 + - + +
357A GLN* 3.1 21.4 + - - +
358A LYS* 3.0 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 3.8 16.4 - + + -
101A CYS* 3.6 19.7 - - - -
102A ASP 3.5 23.6 - - - -
103A GLU* 4.6 1.1 - - - -
105A TYR* 3.7 21.5 - + - -
270A LEU* 3.9 16.6 - - + -
286A LEU* 3.7 35.7 - - + -
289A PHE* 4.1 8.1 - + - -
294A LEU* 3.6 32.3 - - + -
331A LEU* 3.4 12.2 - - + +
351A ASN* 2.9 22.1 + - + +
352A SER 3.8 4.3 - - - +
353A GLU 3.3 0.2 - - - -
354A LEU* 1.3 77.6 - - + +
356A PHE* 1.3 60.2 + - - +
359A GLY* 2.7 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 5.0 0.8 - - - -
308A ILE* 3.5 49.8 - - + -
310A LEU* 3.4 36.0 - - + +
330A PRO* 3.8 10.1 - - + -
331A LEU* 3.2 37.2 + - - +
332A TRP 3.5 13.0 - - - +
333A LYS* 3.8 20.6 - - + -
334A ALA 5.8 0.2 - - - +
352A SER 3.0 15.0 + - - +
353A GLU 3.5 7.6 - - - +
354A LEU 3.3 0.2 - - - -
355A PHE* 1.3 79.3 - - - +
357A GLN* 1.3 63.9 + - - +
358A LYS 3.3 0.3 + - - -
359A GLY 3.7 6.6 + - - +
218B HIS* 3.8 30.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ILE* 4.5 4.0 - - + -
309A THR 3.4 25.4 - - - +
310A LEU* 3.7 3.5 - - - +
311A HIS* 2.8 50.5 + - - +
312A PRO* 5.5 1.0 - - - +
314A ILE* 4.0 5.2 - - - +
353A GLU 2.9 14.2 + - - +
354A LEU* 3.1 24.5 + - - +
356A PHE* 1.3 78.8 - - - +
358A LYS* 1.3 82.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 3.3 11.5 - - + -
287A ILE* 2.9 48.6 + - + +
288A ASN* 2.8 22.7 + - - +
289A PHE* 4.6 9.0 - - + -
293A GLU* 2.5 29.9 + - - +
311A HIS* 4.2 14.1 - - + -
314A ILE* 3.5 17.4 - - - +
354A LEU* 3.0 24.6 + - + +
355A PHE 3.8 0.2 - - - -
357A GLN* 1.3 109.5 - - - +
359A GLY* 1.3 59.1 + - - +
----------------------------------------------------------
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