Contacts of the helix formed by residues 303 - 311 (chain A) in PDB entry 1ASZ
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 GLN 303 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A SER* 2.7 25.9 + - - +
302A PRO* 1.3 77.9 - - - +
304A PHE* 1.3 83.9 + - + +
306A LYS* 2.8 38.7 + - - +
307A GLN* 3.1 27.7 + - - +
342A ASP* 5.0 0.8 + - - -
344A GLU* 4.2 2.2 + - - -
456A TYR* 2.9 39.7 + - + +
485A ARG* 3.0 24.0 + - - +
676R A 4.8 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A SER* 4.0 15.0 - - - -
301A SER 4.7 1.2 + - - -
303A GLN* 1.3 94.7 - - + +
305A ASN* 1.3 64.4 + - - +
307A GLN* 3.3 2.2 + - - +
308A GLN* 2.9 31.6 + - - +
455A PHE* 3.6 22.2 - + - -
456A TYR* 4.3 3.8 - + - -
507A GLY 4.7 3.1 - - - -
508A LEU* 3.8 16.4 - - + -
511A TYR* 3.3 55.2 - + + -
676R A 3.1 41.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A THR* 2.8 38.5 + - + +
273A PRO* 3.3 31.9 - - - +
276A LEU* 4.7 7.7 - - - +
302A PRO* 3.7 11.0 + - - +
303A GLN 3.0 0.8 + - - -
304A PHE* 1.3 79.8 - - - +
306A LYS* 1.3 58.5 + - - +
308A GLN* 3.0 7.9 + - - +
309A LEU* 2.7 32.2 + - + +
548B PHE* 4.0 21.6 - - - -
557B PRO* 5.2 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A VAL* 5.3 6.7 - - + -
272A THR* 5.6 0.9 - - + -
302A PRO* 3.1 30.3 + - + +
303A GLN* 2.8 34.2 + - - +
305A ASN* 1.3 72.9 - - + +
307A GLN* 1.3 68.2 + - - +
309A LEU* 2.8 21.6 + - - +
310A ILE* 3.0 12.8 + - - +
317A VAL* 4.5 13.3 - - + +
319A GLU* 5.3 5.2 - - + +
342A ASP* 3.5 37.7 + - + +
343A MET* 3.4 29.0 + - - +
344A GLU* 3.8 19.6 + - + +
485A ARG* 4.3 3.8 - - - +
525A GLY 4.7 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLN* 3.1 35.4 + - - +
304A PHE* 3.6 7.6 - - - +
306A LYS* 1.3 75.8 - - - +
308A GLN* 1.3 53.5 + - - +
310A ILE* 2.6 39.1 + - - +
311A VAL* 3.0 9.3 + - - +
344A GLU* 3.3 22.4 - - - +
456A TYR* 4.4 1.6 - - - -
485A ARG* 3.4 29.8 - - - +
486A ILE 5.5 0.4 + - - -
492A LEU* 6.2 0.2 - - - +
511A TYR* 2.6 40.5 + - + -
515A PHE* 3.8 13.3 - - + -
522A HIS* 3.5 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PHE* 2.9 24.6 + - - +
305A ASN* 3.0 10.1 + - - +
307A GLN* 1.3 76.2 - - - +
309A LEU* 1.3 50.9 + - - +
311A VAL* 2.9 19.9 + - + +
312A ALA* 2.6 36.1 + - - +
510A ASP 3.9 6.6 + - - +
511A TYR* 2.8 51.9 + - - +
514A GLY* 3.9 13.3 - - - -
515A PHE* 4.8 3.0 - - - -
236B VAL* 3.7 25.5 - - + +
548B PHE* 4.2 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A VAL* 3.4 43.5 - - + -
272A THR* 4.1 9.9 - - + -
305A ASN 2.7 37.5 + - - +
306A LYS* 2.8 14.2 + - - +
308A GLN* 1.3 72.5 - - - +
310A ILE* 1.3 54.5 + - - +
312A ALA* 3.5 8.1 - - + -
313A ASP 3.5 1.2 + - - -
314A PHE* 2.7 65.1 + - + +
317A VAL* 4.4 5.8 - - + -
547B LEU* 3.8 14.8 - - + -
548B PHE* 3.8 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LYS 3.0 12.3 + - - +
307A GLN* 2.6 12.8 + - - +
309A LEU* 1.3 77.2 - - - +
311A VAL* 1.3 51.6 - - - +
312A ALA 3.0 2.5 - - - -
313A ASP* 2.7 27.5 + - - -
314A PHE 3.9 0.3 + - - -
315A GLU* 3.5 39.8 + - - +
316A ARG 4.5 0.2 - - - +
317A VAL* 5.1 5.6 - - + -
344A GLU* 3.6 30.5 - - + +
346A ALA* 4.3 11.7 - - + +
519A CYS* 3.6 11.7 - - - -
520A PRO* 4.3 15.5 - - + +
522A HIS* 3.4 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLN 3.2 15.5 - - - +
308A GLN* 3.4 22.9 - - - +
310A ILE* 1.3 72.7 - - - +
312A ALA* 1.3 57.0 + - - +
313A ASP 3.1 3.4 + - - -
514A GLY 3.3 24.7 - - - +
515A PHE* 3.8 25.6 - - + -
518A GLY 4.9 0.4 - - - +
519A CYS* 3.9 23.3 - - + +
114B ARG* 3.6 4.2 + - - +
236B VAL* 4.0 21.3 - - + -
240B ARG* 2.9 34.6 + - - +
----------------------------------------------------------
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