Contacts of the helix formed by residues 308 - 319 (chain Z) in PDB entry 1O1F
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 GLY 308 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219Z VAL* 3.0 18.6 - - - +
221Z LEU* 4.7 5.3 - - - +
307Z PRO* 1.3 71.8 - - - +
309Z ILE* 1.3 63.2 + - - +
310Z ALA* 3.3 3.6 - - - +
311Z ASP* 4.0 22.0 - - - +
312Z ARG* 3.3 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 309 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153Z LEU* 5.7 4.3 - - + -
219Z VAL* 3.9 14.8 - - + -
261Z LEU* 4.3 13.7 - - + -
262Z PHE* 4.6 8.6 - - + -
274Z ILE* 6.2 3.1 - - + -
299Z MET* 4.3 13.0 - - + -
303Z THR 3.9 7.4 - - - +
304Z THR* 3.2 51.6 - - + +
306Z TYR* 3.2 26.5 - - + +
307Z PRO 3.2 1.2 - - - -
308Z GLY* 1.3 78.2 - - - +
310Z ALA* 1.3 72.9 + - + +
312Z ARG* 3.8 2.8 + - - +
313Z MET* 3.0 33.0 + - + +
335Z ARG* 3.5 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 310 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299Z MET* 4.0 22.2 - - + -
308Z GLY* 5.7 1.1 - - - +
309Z ILE* 1.3 82.9 - - + +
311Z ASP* 1.4 52.9 + - - +
313Z MET* 3.1 3.8 + - - +
314Z GLN* 2.8 38.9 + - + +
329Z ILE* 4.1 15.4 - - + +
331Z ALA* 4.1 14.1 - - + -
335Z ARG* 5.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 311 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221Z LEU* 3.8 32.1 - - + +
308Z GLY* 3.8 16.0 + - - +
309Z ILE 3.5 0.2 - - - -
310Z ALA* 1.4 74.0 - - - +
312Z ARG* 1.3 65.6 + - - +
314Z GLN* 3.1 10.2 - - - +
315Z LYS* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 312 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219Z VAL* 3.6 12.8 - - + -
220Z ALA 3.0 20.5 + - - +
221Z LEU* 3.8 15.0 - - - +
222Z ASP 4.9 3.1 - - - +
223Z PHE* 2.9 41.2 - - - +
262Z PHE* 3.3 25.6 - - + +
263Z GLN* 3.4 27.5 + - - +
308Z GLY 3.3 13.8 + - - +
309Z ILE 3.9 3.4 - - - +
311Z ASP* 1.3 78.0 - - - +
313Z MET* 1.3 52.7 + - - +
315Z LYS* 3.3 3.7 + - - +
316Z GLU* 2.7 76.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 313 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153Z LEU* 4.5 9.2 - - + -
262Z PHE* 4.2 10.8 - - + -
274Z ILE* 3.9 17.7 - - + -
275Z HIS* 3.4 34.1 - - - -
278Z THR* 3.0 36.6 - - + +
297Z ASN* 4.4 11.2 - - - +
299Z MET* 4.8 8.5 - - - -
309Z ILE* 3.0 23.0 + - + +
310Z ALA 3.1 4.7 + - - +
312Z ARG* 1.3 71.5 - - - +
314Z GLN* 1.3 58.7 - - - +
316Z GLU* 3.6 1.4 - - - +
317Z ILE* 2.9 39.4 + - + +
329Z ILE* 4.1 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 314 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310Z ALA* 2.8 13.6 + - + +
311Z ASP* 3.1 17.3 - - - +
313Z MET* 1.3 76.5 - - - +
315Z LYS* 1.3 61.8 + - + +
318Z THR* 2.8 35.3 + - - +
327Z ILE* 3.5 32.3 + - - +
328Z LYS* 4.3 2.4 - - - +
329Z ILE* 3.5 30.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 315 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221Z LEU* 6.3 4.3 - - + -
311Z ASP 3.0 12.7 + - - +
312Z ARG* 4.0 3.4 - - - +
314Z GLN* 1.3 83.0 - - + +
316Z GLU* 1.3 66.4 + - - +
318Z THR* 3.1 34.4 + - + +
319Z ALA* 3.5 30.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 316 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262Z PHE* 4.6 2.2 - - + -
275Z HIS* 3.2 56.7 + - + +
312Z ARG* 2.7 59.1 + - - +
313Z MET* 3.2 7.4 + - - +
315Z LYS* 1.3 82.6 - - + +
317Z ILE* 1.3 63.4 + - - +
319Z ALA* 3.9 3.9 + - - +
320Z LEU* 3.8 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 317 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275Z HIS* 3.8 22.9 - - + +
278Z THR* 4.1 16.8 - - + -
279Z TYR* 5.1 5.6 - - + +
294Z TYR* 4.0 24.5 - - + +
297Z ASN* 3.9 13.5 - - - +
313Z MET* 2.9 29.5 + - + +
316Z GLU* 1.3 75.9 - - - +
318Z THR* 1.3 67.0 + - - +
319Z ALA 3.2 1.8 - - - -
320Z LEU* 3.0 6.3 + - + +
321Z ALA* 2.9 25.3 + - - +
327Z ILE* 3.7 26.7 - - + -
329Z ILE* 3.6 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 318 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314Z GLN* 2.8 30.2 + - - +
315Z LYS* 3.1 30.5 + - + +
317Z ILE* 1.3 72.2 - - - +
319Z ALA* 1.3 60.2 + - - +
320Z LEU 3.1 5.7 + - - -
321Z ALA* 3.1 20.6 - - - +
323Z SER* 5.8 1.0 + - - -
325Z MET 6.1 0.4 - - - +
327Z ILE* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 319 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315Z LYS* 3.5 28.7 + - - +
316Z GLU 4.0 4.5 - - - +
317Z ILE 3.2 1.2 - - - -
318Z THR* 1.3 80.8 + - - +
320Z LEU* 1.3 58.9 + - - +
321Z ALA 4.8 0.2 - - - -
----------------------------------------------------------
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