Contacts of the helix formed by residues 315 - 324 (chain L) in PDB entry 4EC4
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 ASP 315 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283L GLN* 5.1 4.7 - - - +
310L TRP* 4.8 0.7 - - - -
313L SER 5.3 0.4 - - - +
314L GLU* 1.3 73.6 - - - +
316L PRO* 1.4 67.5 - - - +
317L TRP* 3.1 18.8 + - - +
318L GLU* 3.4 39.9 + - + +
319L GLN* 2.9 34.2 + - - +
338L TYR* 4.0 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 316 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279L VAL* 5.2 6.5 - - + -
280L ASN 4.7 2.5 - - - +
283L GLN* 3.5 51.8 - - + +
284L LEU* 3.8 29.6 - - + +
287L ALA* 4.4 6.3 - - + -
289L PHE* 3.8 8.9 - - + -
310L TRP* 4.4 13.9 - - + -
314L GLU 3.8 7.8 - - - +
315L ASP* 1.4 92.3 - - - +
317L TRP* 1.3 59.9 + - - +
319L GLN* 4.1 0.5 - - - +
320L HIS* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 317 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283L GLN* 4.3 23.5 + - + +
286L ARG* 3.2 47.5 - - + +
287L ALA* 3.7 19.3 - - + -
315L ASP* 3.1 12.6 + - - +
316L PRO* 1.3 76.4 - - - +
318L GLU* 1.3 65.4 + - - +
320L HIS* 3.4 9.8 + - - +
321L ALA 3.5 8.8 + - - -
329L TYR* 5.0 2.2 - + - -
330L LEU* 3.9 22.5 - - + +
333L GLN* 3.9 30.1 - - + -
334L LYS* 3.8 38.1 - - + +
338L TYR* 3.4 26.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 318 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315L ASP* 3.3 34.5 + - + +
317L TRP* 1.3 81.3 - - - +
319L GLN* 1.3 79.3 + - - +
320L HIS 3.3 0.3 + - - -
321L ALA 3.5 0.5 + - - -
322L LYS* 3.1 21.3 + - + +
338L TYR* 3.4 9.7 + - - +
342L ILE* 3.5 25.1 - - + +
346L HIS* 4.8 11.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 319 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402E 0O6 3.4 29.6 + - + +
307L LEU* 3.9 18.9 - - + +
310L TRP* 3.7 17.7 - - + -
314L GLU* 3.8 21.9 + - + +
315L ASP 2.9 20.9 + - - +
316L PRO 4.1 1.3 - - - +
318L GLU* 1.3 97.7 + - - +
320L HIS* 1.3 66.9 + - - +
322L LYS* 3.3 24.8 + - - +
323L TRP* 3.3 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 320 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287L ALA* 3.4 22.6 + - + +
289L PHE* 3.9 17.1 - + + -
300L CYS* 3.3 15.8 - - + +
303L CYS* 3.2 8.1 - - - -
307L LEU* 5.3 0.2 - - - -
316L PRO 3.2 18.3 + - - +
317L TRP* 3.9 5.8 - - - +
318L GLU 3.3 0.4 - - - -
319L GLN* 1.3 76.4 - - - +
321L ALA* 1.3 64.4 + - - +
324L TYR* 2.9 48.5 + + + +
327L CYS* 3.5 10.9 - - + -
329L TYR* 5.0 1.5 - + - -
330L LEU* 4.0 19.5 - - + +
401L ZN 2.1 38.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317L TRP 3.5 6.7 + - - +
318L GLU 3.5 1.4 + - - +
320L HIS* 1.3 78.2 - - - +
322L LYS* 1.3 53.2 + - - +
325L PRO* 3.7 11.4 - - - +
330L LEU* 3.4 24.7 - - + +
338L TYR* 4.1 4.3 - - + -
339L ILE* 4.1 17.7 - - - -
342L ILE* 3.3 31.6 - - + -
343L HIS* 2.5 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 322 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246E SER* 2.8 39.5 + - - -
250E PHE* 3.2 42.5 - - + -
402E 0O6 5.3 0.4 + - - -
403E 2PE 4.2 2.1 - - - +
318L GLU* 3.1 19.5 + - + +
319L GLN* 3.6 24.7 + - - +
320L HIS 3.0 0.6 + - - -
321L ALA* 1.3 76.8 - - - +
323L TRP* 1.3 82.5 + - + +
342L ILE* 4.2 10.5 - - + +
343L HIS* 3.1 25.9 - - - -
346L HIS* 3.6 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 323 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246E SER* 4.5 6.5 - - - -
249E ASN* 3.8 13.9 - - + -
250E PHE* 3.5 43.7 - + + -
251E PRO* 4.4 0.4 - - + -
402E 0O6 3.5 89.1 + + + -
403E 2PE 3.4 28.6 - - - +
307L LEU* 3.7 16.2 - - + -
319L GLN* 3.3 19.4 + - - +
320L HIS 3.2 2.4 + - - -
322L LYS* 1.3 112.0 - - + +
324L TYR* 1.3 86.6 + - + +
325L PRO* 3.6 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 324 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402E 0O6 3.2 37.0 + - + +
403E 2PE 5.7 2.2 - - - -
249L ASN 5.7 0.2 - - - -
251L PRO* 3.9 27.4 - - + -
289L PHE* 5.9 0.7 - + - -
303L CYS* 4.0 12.8 - - + -
305L GLY* 3.3 19.7 - - - -
306L GLY 2.7 42.7 + - - -
307L LEU* 4.2 15.7 - - + -
319L GLN 4.9 0.2 - - - -
320L HIS* 2.9 37.7 + + + +
323L TRP* 1.3 101.6 - - + +
325L PRO* 1.3 60.9 - - - +
326L GLY 2.8 11.6 + - - -
327L CYS* 3.1 17.0 + - + +
330L LEU* 4.4 2.3 - - - +
----------------------------------------------------------
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