Contacts of the helix formed by residues 327 - 333 (chain A) in PDB entry 6APL
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 327 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 3.8 14.1 - - + +
325A PHE 3.4 14.9 + - - +
326A ILE* 1.3 78.8 - - - +
328A SER* 1.3 67.5 + - - +
329A ASN* 2.9 22.8 + - - -
330A TYR* 3.0 28.5 + - - +
333A PHE* 5.1 0.3 - - - -
357A ALA* 4.9 2.4 - - - +
361A ARG* 4.4 7.9 - - + +
371A LEU* 4.2 22.7 - - + -
372A TYR 4.3 15.9 - - - +
373A GLN* 4.4 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A THR* 1.3 75.4 - - - +
329A ASN* 1.3 62.3 + - - +
330A TYR* 3.2 17.8 + - - -
331A TRP* 3.5 8.9 + - - -
361A ARG* 3.6 30.5 - - - +
373A GLN* 5.5 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 4.7 1.7 - - - +
327A THR* 2.9 22.7 + - - -
328A SER* 1.3 77.8 + - - +
330A TYR* 1.3 64.2 + - - +
331A TRP* 3.1 17.5 - - + +
332A LYS* 3.0 31.4 + - + +
333A PHE* 3.3 20.9 - - - -
373A GLN* 5.9 1.5 - - - +
374A ARG 3.4 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ILE* 4.0 29.2 - - + -
327A THR* 3.0 24.8 + - - +
328A SER* 3.1 16.1 - - - -
329A ASN* 1.3 76.1 - - - +
331A TRP* 1.3 88.2 + + + +
332A LYS 2.9 5.9 + - - -
333A PHE* 2.9 31.0 + - - +
334A SER 5.2 0.2 - - - +
344A PRO 6.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A SER 3.5 18.1 + - - -
329A ASN* 3.5 15.2 - - + +
330A TYR* 1.3 105.7 - + + +
332A LYS* 1.3 96.6 + - + +
333A PHE 3.2 5.3 + - - +
342A MSE 5.0 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ASN* 3.0 32.1 + - + +
330A TYR 2.9 1.4 + - - -
331A TRP* 1.3 120.7 - - + +
333A PHE* 1.3 75.9 + - + +
342A MSE 4.3 12.2 - - - +
374A ARG 5.9 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLY 3.5 22.2 - - - +
159A ILE* 3.7 35.2 - - + +
161A ASN 5.6 0.2 - - - -
327A THR* 5.4 0.2 - - - -
329A ASN* 3.3 42.0 - - - -
330A TYR* 2.9 19.4 + - - +
331A TRP* 4.1 5.0 - - - +
332A LYS* 1.3 94.6 - - + +
334A SER* 1.3 68.1 + - - +
342A MSE 4.3 9.2 - - - +
343A LYS 4.7 1.2 - - - +
374A ARG* 3.9 39.9 - - + -
----------------------------------------------------------
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