Contacts of the helix formed by residues 338 - 346 (chain A) in PDB entry 3OFN
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 338 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG* 5.4 0.2 - - - +
294A GLU* 5.3 2.5 - - - +
332A GLN* 6.0 4.7 - - + +
335A ASP* 3.2 31.6 + - - +
336A VAL 3.2 0.8 - - - -
337A SER* 1.3 77.4 - - - +
339A TYR* 1.3 63.2 + - - +
340A ILE 3.6 0.7 - - - -
341A PRO* 3.6 16.6 - - + -
342A THR* 2.5 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG* 3.5 79.7 + - + +
294A GLU* 3.3 25.4 + - - +
296A TYR* 3.9 8.7 - + + -
297A PRO 5.0 1.0 + - - -
298A GLY* 4.7 8.7 + - - -
300A VAL* 3.3 33.3 - - + +
301A PHE* 5.1 2.1 + - - +
337A SER 3.8 0.4 + - - -
338A ALA* 1.3 76.8 - - - +
340A ILE* 1.3 73.0 + - + +
342A THR* 3.6 4.1 + - - -
343A ASN* 3.1 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU 4.8 0.9 - - - +
274A SER* 5.1 6.5 - - - +
277A ALA* 4.5 8.3 - - + -
294A GLU* 5.5 0.7 - - - +
296A TYR* 4.0 28.5 - - + +
300A VAL* 3.9 30.7 - - + -
304A HIS* 4.0 27.1 - - + +
329A ILE* 4.4 15.3 - - + -
339A TYR* 1.3 90.8 - - + +
341A PRO* 1.3 78.9 - - + +
343A ASN* 3.0 20.0 + - + +
344A VAL* 3.0 12.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 4.8 0.5 - - - +
170A ILE* 4.2 17.5 - - + -
274A SER* 5.9 0.2 - - - +
329A ILE* 4.0 24.2 - - + -
330A GLU 4.5 4.7 - - - +
331A THR* 4.2 13.0 - - + -
336A VAL* 3.8 17.3 - - - +
338A ALA* 3.4 28.0 - - + +
340A ILE* 1.3 93.2 - - + +
342A THR* 1.3 51.0 + - - +
344A VAL* 3.1 2.1 + - + +
345A ILE* 2.7 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A VAL 3.3 8.8 + - - +
337A SER* 3.2 20.0 + - - +
338A ALA 2.5 24.1 + - - -
339A TYR* 3.8 4.0 - - - -
341A PRO* 1.3 74.7 - - - +
343A ASN* 1.3 64.0 + - - +
345A ILE* 3.8 9.4 - - + +
346A SER* 3.0 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A VAL* 3.8 20.4 + - - +
301A PHE* 3.7 42.3 - - + +
304A HIS* 5.4 2.7 + - - +
339A TYR* 3.1 28.4 + - - +
340A ILE* 3.0 23.1 + - + +
342A THR* 1.3 76.2 - - - +
344A VAL* 1.3 63.3 + - + +
346A SER* 2.8 20.9 + - - -
347A ILE* 3.2 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 3.7 29.2 - - + -
273A LEU* 4.8 2.9 - - + -
304A HIS* 3.5 36.6 - - + +
308A LEU* 4.3 9.9 - - + -
327A PRO* 4.8 3.4 - - + -
329A ILE* 3.9 22.4 - - + -
340A ILE* 3.0 14.0 + - + +
341A PRO 3.8 2.5 - - - +
343A ASN* 1.3 73.6 - - + +
345A ILE* 1.3 65.7 + - - +
346A SER 3.0 1.6 - - - -
347A ILE* 2.9 16.6 + - + +
348A THR* 3.0 25.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 3.7 18.6 - - + -
170A ILE* 3.8 17.9 - - + -
336A VAL* 3.8 33.4 - - + +
341A PRO 2.7 24.1 + - - +
342A THR* 3.8 10.1 - - + +
344A VAL* 1.3 71.6 - - - +
346A SER* 1.3 60.7 + - - +
348A THR* 3.3 22.1 + - - +
351A GLN* 3.4 32.3 + - + +
375A ARG* 4.0 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PHE* 4.0 12.7 - - - -
342A THR* 3.0 17.2 + - - -
343A ASN* 2.8 20.3 + - - -
345A ILE* 1.3 77.1 - - - +
347A ILE* 1.3 61.3 + - - +
348A THR 4.5 2.0 - - - +
----------------------------------------------------------
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