Contacts of the helix formed by residues 323 - 329 (chain B) in PDB entry 1FLO
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 LEU 323 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 4.5 12.8 - - + -
320B LEU* 3.1 23.1 + - + +
322B GLU* 1.3 93.3 - - + +
324B THR* 1.3 63.0 + - - +
325B ASN 3.6 0.4 - - - -
326B VAL* 3.4 8.9 + - + +
327B VAL* 2.8 37.5 + - + +
351B PRO* 3.7 38.8 - - + -
353B HIS* 4.2 20.2 - - + +
354B TYR* 4.0 34.1 - - + -
357B LEU* 6.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B CYS* 5.5 0.8 - - - -
312B THR* 4.5 19.2 + - + +
315B LEU* 4.0 22.7 - - + +
316B SER 5.5 0.2 + - - -
320B LEU 4.1 0.6 + - - -
321B THR* 3.5 29.0 - - - +
322B GLU 3.5 1.6 - - - -
323B LEU* 1.3 76.5 - - - +
325B ASN* 1.3 67.4 + - - +
327B VAL* 3.0 2.6 + - - +
328B GLY* 2.9 23.4 + - - -
330B TRP* 3.8 22.2 - - + -
335C ALA* 4.1 21.0 - - + +
339C ALA* 4.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B THR 5.0 1.2 + - - -
322B GLU 5.2 1.6 + - - +
323B LEU 3.6 0.6 - - - -
324B THR* 1.3 82.0 - - - +
326B VAL* 1.3 59.3 + - + +
329B ASN* 2.9 9.7 + - - -
330B TRP* 2.8 51.5 + - + +
331B SER 4.4 4.7 + - - -
332B ASP* 3.1 33.8 + - + +
334C ARG 2.9 25.3 + - - -
335C ALA* 3.7 2.9 - - - -
336C SER* 3.0 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ARG* 5.7 0.5 - - - -
322B GLU 4.5 12.3 - - - +
323B LEU* 3.9 9.4 - - + +
324B THR 3.1 0.6 - - - -
325B ASN* 1.3 79.3 - - + +
327B VAL* 1.3 67.1 + - + +
329B ASN* 3.9 7.0 + - - +
332B ASP* 5.6 4.3 - - + +
348B THR* 4.1 25.3 - - + +
349B ALA 3.8 26.0 - - - +
350B ILE* 4.0 15.5 - - + +
351B PRO* 4.8 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ASN* 3.1 21.3 - - - +
189B CYS* 3.8 18.4 - - + -
228B ARG* 3.3 15.2 + - - -
311B MET* 4.7 4.3 - - + -
315B LEU* 4.6 5.4 - - + -
323B LEU* 2.8 43.3 + - + +
324B THR* 3.7 3.8 - - - +
326B VAL* 1.3 80.8 - - + +
328B GLY* 1.3 58.9 + - - +
329B ASN 3.6 0.2 + - - -
350B ILE* 4.4 20.4 - - + +
351B PRO* 6.0 0.2 - - + -
354B TYR* 3.7 44.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B CYS* 3.6 29.0 - - - +
191B ARG* 5.4 0.7 + - - -
194B ASP* 5.3 1.9 - - - +
228B ARG* 4.1 5.3 + - - -
308B ARG* 3.1 23.0 + - - -
324B THR 2.9 9.7 + - - -
327B VAL* 1.3 76.5 - - - +
329B ASN* 1.3 68.0 + - - +
330B TRP* 3.7 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ARG* 5.5 8.3 + - - +
194B ASP* 5.4 2.0 + - - +
222B THR* 4.8 5.1 + - - -
224B THR* 4.9 10.7 + - - +
226B VAL* 3.2 41.8 + - - +
227B SER 4.2 1.4 + - - +
228B ARG* 3.7 37.1 - - + +
308B ARG* 4.9 2.1 + - - -
325B ASN 2.9 11.7 + - - -
326B VAL* 3.9 5.8 + - - +
327B VAL 3.3 4.0 - - - +
328B GLY* 1.3 83.0 - - - +
330B TRP* 1.3 61.2 + - - +
-2L T 4.8 3.5 + - - -
----------------------------------------------------------
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