Contacts of the helix formed by residues 324 - 333 (chain D) in PDB entry 1FFX
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 SER 324 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D VAL* 4.7 0.3 - - - +
323D MET* 1.3 76.3 - - - +
325D MET* 1.3 59.7 + - - +
326D LYS* 2.8 15.3 + - - +
327D GLU* 3.0 53.2 + - - +
328D VAL* 3.6 7.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 325 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ARG* 5.5 17.7 - - + -
247D GLN* 3.2 41.5 - - + +
323D MET 2.8 10.7 + - - +
324D SER* 1.3 69.9 - - - +
326D LYS* 1.3 58.8 + - - +
328D VAL* 3.5 12.5 + - - +
329D ASP* 2.4 31.7 - - - +
355D VAL* 3.4 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 326 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C ARG* 5.9 1.2 - - - -
220C GLU* 2.9 47.2 + - + +
221C ARG* 5.9 2.2 - - + -
324D SER* 2.8 11.7 + - - +
325D MET* 1.3 77.6 - - - +
327D GLU* 1.3 65.5 + - + +
328D VAL 2.9 1.6 + - - -
329D ASP* 2.9 7.5 + - - +
330D GLU* 2.9 57.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 327 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D VAL* 2.7 55.7 - - + +
289D PRO* 4.8 5.6 - - + +
323D MET* 3.7 1.6 - - - +
324D SER* 3.0 28.7 + - - +
326D LYS* 1.3 78.6 - - + +
328D VAL* 1.3 52.4 + - - +
330D GLU* 3.3 16.9 + - - +
331D GLN* 2.6 46.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 328 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D VAL* 4.9 8.7 - - + +
292D THR* 5.1 2.2 - - - -
319D PHE* 3.5 53.4 - - + -
323D MET* 4.9 3.8 - - + +
324D SER 3.6 15.5 - - - +
325D MET* 3.6 14.4 - - - +
326D LYS 2.9 0.4 + - - -
327D GLU* 1.3 77.0 - - + +
329D ASP* 1.3 60.6 + - - +
331D GLN* 4.5 3.4 - - - -
332D MET* 2.8 32.1 + - + +
353D THR* 3.6 20.6 - - + -
355D VAL* 4.5 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 329 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D MET* 2.4 30.6 - - - +
326D LYS* 2.9 3.8 + - - +
328D VAL* 1.3 80.9 - - - +
330D GLU* 1.3 63.9 + - + +
331D GLN 3.2 0.7 - - - -
332D MET* 4.0 4.7 - - - +
333D LEU* 3.4 28.6 + - - +
353D THR* 4.6 17.6 - - - +
355D VAL* 5.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 330 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D LYS* 2.9 57.0 + - + +
327D GLU* 3.3 29.0 + - - +
329D ASP* 1.3 80.4 - - + +
331D GLN* 1.3 60.3 + - + +
333D LEU* 5.1 0.8 - - - +
334D ASN* 3.4 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 331 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D VAL 5.4 0.4 - - - +
289D PRO* 3.0 39.4 + - + +
292D THR* 3.1 38.3 + - + +
293D GLN* 5.7 1.4 - - - +
327D GLU* 2.6 23.5 + - + +
328D VAL 4.3 0.2 - - - +
330D GLU* 1.3 78.9 - - + +
332D MET* 1.3 59.9 + - - +
333D LEU 3.2 1.8 - - - -
334D ASN* 2.7 51.4 + - - +
335D VAL* 3.4 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 332 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D THR* 3.7 11.7 - - + -
295D MET* 4.9 2.9 - - - -
296D PHE* 3.6 35.8 - - + -
317D ALA* 4.3 15.7 - - + -
319D PHE* 3.5 31.6 - - + -
328D VAL* 2.8 26.3 + - + +
329D ASP* 4.4 2.2 - - - -
331D GLN* 1.3 73.6 - - - +
333D LEU* 1.3 63.5 + - - +
335D VAL* 4.3 2.6 + - + +
336D GLN* 3.4 16.9 + - - +
351D VAL* 4.4 18.4 - - + +
353D THR* 3.3 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 333 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D ASP 3.4 18.9 + - - +
330D GLU 5.1 0.7 - - - +
331D GLN 3.2 0.2 - - - -
332D MET* 1.3 77.5 - - - +
334D ASN* 1.3 54.7 + - - +
336D GLN* 2.5 20.7 + - + +
337D ASN* 2.4 78.9 + - - +
----------------------------------------------------------
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