Contacts of the helix formed by residues 241 - 246 (chain D) in PDB entry 1FP1
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 241 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D ASP* 1.3 83.6 + - - +
242D PRO* 1.3 78.1 - - + +
243D GLN* 3.8 26.0 - - + +
244D VAL* 2.8 21.5 + - + -
245D ILE* 3.0 11.1 + - - +
259D GLY 3.5 9.4 - - - +
260D ASP* 5.0 3.4 - - + -
1699D SAH 3.5 63.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D ASP 3.6 0.2 - - - -
241D LEU* 1.3 85.8 - - + +
243D GLN* 1.3 72.9 + - - +
245D ILE* 3.4 2.0 + - + +
246D GLU* 3.1 26.9 + - - +
258D GLY* 4.2 12.3 - - - -
259D GLY* 3.3 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D LEU* 3.8 28.5 - - + +
242D PRO* 1.3 91.2 - - - +
244D VAL* 1.3 66.0 + - + +
246D GLU* 3.3 20.4 - - - +
247D ASN* 3.0 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D GLY* 3.8 29.2 - - - +
220D SER* 5.4 0.4 - - - -
240D ASP* 3.4 28.7 - - - +
241D LEU* 2.8 20.9 + - + +
243D GLN* 1.3 83.8 - - + +
245D ILE* 1.3 59.3 + - - +
247D ASN* 2.9 24.4 + - - +
248D ALA* 3.4 8.0 + - - +
1699D SAH 3.7 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D GLY 4.2 3.4 - - - +
238D ASN* 3.8 38.6 - - - +
240D ASP* 3.6 28.9 - - + +
241D LEU 3.0 16.7 + - - +
242D PRO* 4.0 3.8 - - + +
244D VAL* 1.3 77.4 - - - +
246D GLU* 1.3 62.0 + - - +
248D ALA* 3.0 20.9 + - - +
256D HIS* 3.5 28.7 - - + +
257D VAL 3.6 7.4 - - - +
258D GLY* 3.7 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D PRO 3.1 13.5 + - - +
243D GLN* 3.3 38.7 - - - +
245D ILE* 1.3 76.0 - - - +
247D ASN* 1.3 70.5 + - - +
248D ALA 3.9 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