Contacts of the helix formed by residues 320 - 325 (chain H) in PDB entry 1II4
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 THR 320 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D GLN* 3.7 9.3 + - - +
316H GLY 3.3 6.2 + - - -
317H VAL* 4.1 12.0 + - - -
318H ASN 3.7 1.6 + - - -
319H THR* 1.3 76.8 - - - +
321H ASP* 1.3 67.2 + - + +
322H LYS* 3.0 28.9 - - + +
323H GLU* 2.8 36.1 + - - +
324H ILE* 3.3 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 321 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D PHE* 3.9 24.7 - - + -
27D LYS* 3.6 31.8 - - + +
63D GLN* 5.6 1.4 + - - -
64D LEU 4.6 3.6 - - - +
65D GLN* 3.1 31.6 + - - +
66D ALA 4.8 0.3 + - - -
285H GLN* 4.3 10.6 + - - -
286H PRO 4.6 6.3 - - - +
288H ILE* 5.2 2.6 - - + +
315H ALA* 3.5 13.3 - - - +
320H THR* 1.3 73.9 - - + +
322H LYS* 1.3 66.7 + - - +
323H GLU 2.9 1.7 + - - -
324H ILE* 3.3 20.0 + - + +
325H GLU* 4.1 11.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 322 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LYS* 4.5 9.5 - - - +
320H THR* 3.0 21.1 - - + +
321H ASP* 1.3 78.6 - - - +
323H GLU* 1.3 63.5 + - + +
325H GLU* 5.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 323 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313H LYS* 3.0 26.6 + - - +
319H THR* 3.2 26.2 - - - +
320H THR* 2.8 39.1 + - - +
322H LYS* 1.3 82.0 - - + +
324H ILE* 1.3 62.3 + - - +
325H GLU 3.3 3.1 - - - +
326H VAL* 3.4 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 324 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288H ILE* 3.7 46.5 - - + +
290H TRP* 2.7 45.5 + - + -
313H LYS* 3.6 29.8 - - + +
315H ALA* 3.7 26.5 - - + +
319H THR* 3.8 14.1 - - + +
320H THR 3.6 9.6 - - - +
321H ASP* 3.3 20.4 + - - +
323H GLU* 1.3 79.4 + - - +
325H GLU* 1.3 59.0 + - + +
326H VAL 3.2 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 325 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D HIS* 5.2 0.2 + - - -
26D PHE* 4.4 6.9 - - + -
27D LYS* 2.7 41.8 + - - +
277H VAL* 3.6 4.4 - - + +
278H CYS* 2.8 44.4 + - + +
279H LYS* 3.7 10.7 - - - +
280H VAL* 3.1 34.0 + - - +
288H ILE* 4.1 18.4 - - + -
290H TRP* 3.2 8.1 - - - +
321H ASP* 4.1 5.4 + - - +
322H LYS 5.9 0.9 - - - +
323H GLU* 3.3 1.4 - - - -
324H ILE* 1.3 82.7 - - + +
326H VAL* 1.3 58.3 + - + +
----------------------------------------------------------
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