Contacts of the helix formed by residues 294 - 308 (chain A) in PDB entry 4NUA
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 GLU 294 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLN* 3.4 22.2 - - - +
293A LYS* 1.3 100.9 + - + +
295A ALA* 1.4 64.1 - - - +
296A GLU* 3.3 29.4 - - - +
297A LYS* 3.0 37.5 + - + +
298A VAL* 3.1 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLN* 6.0 0.9 - - - +
293A LYS 3.2 6.4 + - - +
294A GLU* 1.4 72.6 - - - +
296A GLU* 1.3 60.3 + - - +
298A VAL* 3.3 9.8 + - - +
299A ALA* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ASN* 4.7 0.2 - - - +
294A GLU* 3.3 26.6 - - - +
295A ALA* 1.3 80.2 + - - +
297A LYS* 1.3 74.3 + - + +
299A ALA* 3.7 7.9 - - - +
300A ARG* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLU 4.1 11.8 + - - +
289A ASN* 3.4 35.3 - - - +
292A GLN* 2.8 38.6 + - + +
294A GLU* 3.0 39.8 + - + +
296A GLU* 1.3 90.0 - - + +
298A VAL* 1.3 65.4 + - - +
300A ARG* 3.2 3.6 + - - +
301A VAL* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 5.2 6.7 - - + -
262A ILE* 4.0 34.5 - - + +
263A GLN* 3.6 45.1 - - + +
292A GLN 3.8 7.6 - - - +
293A LYS 4.8 0.2 - - - +
294A GLU 3.1 15.5 + - - +
295A ALA* 3.6 9.6 - - - +
297A LYS* 1.3 76.4 - - - +
299A ALA* 1.4 62.2 + - - +
301A VAL* 3.1 4.7 + - - +
302A LYS* 3.0 20.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ALA 2.9 17.5 + - - +
296A GLU* 3.7 9.0 - - - +
297A LYS 3.3 0.2 - - - -
298A VAL* 1.4 76.7 - - - +
300A ARG* 1.3 57.5 + - - +
302A LYS* 3.3 9.2 + - - +
303A ALA* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ILE* 3.4 52.6 - - + +
289A ASN* 3.8 18.8 - - - +
296A GLU 3.1 14.8 + - - +
297A LYS 3.2 8.7 + - - +
299A ALA* 1.3 72.4 - - - +
301A VAL* 1.4 66.3 + - - +
303A ALA* 3.2 12.3 + - - +
304A LEU* 2.9 36.7 + - - +
307A GLU* 4.7 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ILE* 3.7 24.7 - - + -
285A ILE* 6.0 1.3 - - + -
286A LEU* 4.0 11.2 - - + -
289A ASN* 3.8 29.4 - - + +
290A TYR* 4.0 14.1 - - + +
297A LYS 3.1 14.0 + - - +
298A VAL 3.1 6.0 + - - +
300A ARG* 1.4 76.4 - - - +
302A LYS* 1.4 63.9 + - - +
304A LEU* 3.1 9.5 + - - +
305A TYR* 3.0 54.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 4.0 51.5 + - + +
249A PHE* 3.9 17.4 - - + +
262A ILE* 4.5 0.6 - - - +
298A VAL* 3.0 13.9 + - + +
299A ALA* 3.7 11.0 - - - +
301A VAL* 1.4 76.1 - - - +
303A ALA* 1.3 59.0 + - - +
305A TYR* 3.2 3.4 + - - +
306A GLU* 2.9 52.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ALA 2.9 17.2 + - - +
300A ARG* 3.5 18.4 - - - +
302A LYS* 1.3 75.7 - - - +
304A LEU* 1.4 56.9 + - - +
306A GLU* 3.2 15.0 + - - +
307A GLU* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A CYS* 3.7 27.8 - - - -
282A GLN* 3.5 59.5 - - + +
285A ILE* 4.4 8.7 - - + -
286A LEU* 4.0 18.8 - - + +
300A ARG* 2.9 25.2 + - - +
301A VAL* 3.1 9.8 + - - +
303A ALA* 1.4 74.4 - - - +
305A TYR* 1.3 66.0 + - + +
307A GLU* 3.1 16.6 + - - +
308A LEU* 3.0 25.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 3.4 28.5 - - + -
249A PHE* 4.0 11.4 - + + -
262A ILE* 4.5 5.3 - - + +
268A SER* 5.6 0.3 - - - -
270A LEU* 3.5 30.2 - - + +
271A VAL* 3.3 17.0 + - - +
274A CYS* 3.6 32.1 - - + -
286A LEU* 4.3 3.4 - - + -
290A TYR* 3.3 26.9 + - - -
301A VAL* 3.0 32.2 + - + -
302A LYS 3.5 7.6 - - - +
304A LEU* 1.3 76.9 - - + +
306A GLU* 1.3 60.7 + - - +
308A LEU* 3.3 2.0 + - - -
309A ASP 3.3 3.3 + - - -
310A LEU* 3.0 47.8 + - + +
311A PRO* 4.7 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A PHE* 3.7 18.2 - - + -
302A LYS* 2.9 45.3 + - - +
303A ALA* 3.6 14.0 - - - +
304A LEU 3.1 0.4 - - - -
305A TYR* 1.3 75.4 - - - +
307A GLU* 1.4 64.5 + - - +
309A ASP* 3.0 21.2 + - - +
311A PRO* 4.6 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLN* 3.3 29.7 + - - +
285A ILE* 5.8 0.5 - - - +
300A ARG* 4.7 10.6 + - - -
303A ALA 2.9 14.5 + - - +
304A LEU* 3.1 19.1 + - - +
306A GLU* 1.4 75.3 - - - +
308A LEU* 1.4 58.5 + - + +
309A ASP* 3.5 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A CYS* 3.7 46.4 - - + +
277A ARG* 4.3 28.1 - - + +
278A ALA* 4.6 2.7 - - - +
282A GLN* 3.6 32.1 - - - +
304A LEU* 3.0 26.1 + - + +
305A TYR* 3.8 4.5 - - - +
306A GLU 3.2 0.4 - - - -
307A GLU* 1.4 75.7 - - + +
309A ASP* 1.4 70.1 + - - +
310A LEU* 3.2 16.2 + - + +
313A VAL* 4.3 5.4 - - - +
----------------------------------------------------------
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