Contacts of the helix formed by residues 309 - 320 (chain A) in PDB entry 3E8N
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 309 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A PRO 4.0 0.4 + - - -
308A MET* 1.3 75.7 - - - +
310A ILE* 1.3 68.2 + - - +
311A PHE* 3.4 1.8 - - + +
312A GLU* 2.9 24.6 + - + +
313A LEU* 3.0 20.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
224A VAL* 6.5 1.3 - - + -
226A THR* 5.6 15.5 - - - +
308A MET 3.9 0.4 + - - -
309A ALA* 1.3 74.6 - - - +
311A PHE* 1.3 65.3 + - + +
313A LEU* 3.5 5.3 + - - +
314A LEU* 3.3 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ALA* 3.4 2.3 - - + +
310A ILE* 1.3 77.7 - - + +
312A GLU* 1.3 61.3 + - - +
314A LEU* 3.1 9.3 + - + +
315A ASP* 2.8 64.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A MET* 3.4 34.3 - - + +
309A ALA* 2.9 36.7 + - + +
311A PHE* 1.3 84.8 - - - +
313A LEU* 1.3 59.4 + - - +
315A ASP* 4.0 4.4 - - - +
316A TYR* 3.3 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A THR* 3.0 40.2 - - - +
227A ARG* 3.9 9.9 - - + -
228A SER 4.1 5.6 - - - +
261A TYR* 3.8 17.3 - - + +
263A ILE* 3.5 31.6 - - + +
308A MET* 4.1 20.6 - - + +
309A ALA 3.0 15.4 + - - +
310A ILE* 3.8 4.5 - - - +
312A GLU* 1.3 76.5 - - - +
314A LEU* 1.3 68.4 + - + +
316A TYR* 3.3 3.0 + - - +
317A ILE* 3.1 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A THR 5.1 1.8 - - - +
228A SER* 4.1 20.9 - - - -
235A LEU* 3.9 35.2 - - + -
310A ILE* 3.3 26.6 + - + +
311A PHE* 3.1 11.5 + - + +
313A LEU* 1.3 80.2 - - + +
315A ASP* 1.3 65.8 + - - +
317A ILE* 3.5 7.7 + - + +
318A VAL* 3.1 30.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
311A PHE* 2.8 49.1 + - + +
312A GLU* 4.0 5.3 - - - +
314A LEU* 1.3 73.8 - - - +
316A TYR* 1.3 61.6 + - - +
318A VAL* 3.8 2.0 - - - -
319A ASN* 2.6 59.2 + - - +
320A GLU* 5.4 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ILE* 3.4 26.0 - - + -
264A PRO* 4.6 6.7 - - + -
265A PRO* 2.9 43.4 - - + +
308A MET* 4.4 16.6 - - + -
312A GLU 3.3 12.2 + - - +
313A LEU* 3.3 11.2 - - - +
314A LEU 3.2 0.2 - - - -
315A ASP* 1.3 79.7 + - - +
317A ILE* 1.3 61.8 + - - +
320A GLU* 2.8 72.0 + - + +
321A PRO* 4.3 14.9 + - - +
323A PRO* 6.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A SER* 4.0 17.7 - - - +
230A MET 4.1 10.1 - - - +
232A PRO* 4.0 11.5 - - + +
235A LEU* 3.5 28.7 - - + -
247A TRP* 4.1 21.2 - - + -
251A LEU* 5.5 1.3 - - + -
261A TYR* 3.6 23.1 - - - +
263A ILE* 3.4 23.3 - - + -
313A LEU* 3.1 20.3 + - + +
314A LEU* 3.7 9.2 - - + +
316A TYR* 1.3 80.1 - - - +
318A VAL* 1.3 59.8 + - - +
320A GLU 3.9 0.9 - - - +
322A PRO* 6.0 0.2 - - - +
344A LYS* 3.3 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A PRO* 4.3 9.5 - - + +
235A LEU* 4.1 23.8 - - + -
236A GLN* 3.1 47.8 + - + +
314A LEU* 3.1 18.6 + - + +
315A ASP* 4.1 3.4 - - - +
317A ILE* 1.3 74.8 - - - +
319A ASN* 1.3 66.9 + - - +
344A LYS* 2.7 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ASP* 2.6 52.3 + - - +
318A VAL* 1.3 86.7 - - - +
320A GLU* 1.3 64.8 + - - +
321A PRO* 3.7 1.7 - - - +
344A LYS* 2.9 13.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ASP* 4.9 4.3 - - - +
316A TYR* 2.8 69.8 + - + +
317A ILE 3.9 1.0 - - - +
319A ASN* 1.3 79.1 - - + +
321A PRO* 1.3 77.1 - - + +
322A PRO* 4.6 0.2 - - - +
344A LYS* 2.4 28.2 + - - -
----------------------------------------------------------
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