Contacts of the helix formed by residues 241 - 252 (chain A) in PDB entry 1FO4
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 THR 241 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A PRO 5.9 0.2 - - - +
239A ALA* 4.2 0.9 - - - +
240A SER* 1.3 91.9 - - - +
242A LEU* 1.3 65.5 + - - +
243A LYS* 3.6 9.2 + - - +
244A GLU* 3.0 36.0 + - - +
245A LEU 3.1 16.3 + - - -
284A ILE* 3.3 14.1 - - - +
285A PRO* 5.5 1.1 - - - -
286A GLU* 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A THR* 1.3 73.9 - - - +
243A LYS* 1.3 59.6 + - - +
245A LEU* 3.0 22.4 + - + +
246A LEU* 2.9 51.7 + - + +
284A ILE* 3.7 16.6 - - + +
286A GLU* 3.7 37.5 + - + +
287A LEU* 5.3 0.4 - - + -
375A VAL* 4.7 3.6 - - + -
380A ARG* 5.6 3.4 - - - +
403A ILE* 4.6 3.6 - - + -
405A LEU* 4.1 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A THR* 3.2 8.6 + - - +
242A LEU* 1.3 80.2 - - - +
244A GLU* 1.3 57.2 + - + +
246A LEU* 3.3 8.8 + - + +
247A ASP* 2.8 64.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLN* 3.4 39.2 + - - +
239A ALA* 4.4 3.8 - - + -
240A SER* 2.4 48.1 + - - -
241A THR* 3.0 26.1 + - - +
243A LYS* 1.3 78.1 - - + +
245A LEU* 1.3 64.3 + - - +
247A ASP* 3.3 6.8 + - - +
248A LEU* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ALA* 4.2 6.8 - - + +
241A THR 3.1 2.6 + - - -
242A LEU* 3.0 15.8 + - + +
244A GLU* 1.3 79.3 - - - +
246A LEU* 1.3 62.3 + - - +
248A LEU* 3.5 3.9 + - - +
249A LYS* 3.0 27.7 + - + +
257A LEU* 3.7 30.3 - - + -
279A ILE* 4.0 13.9 - - + -
281A PRO* 3.7 14.8 - - + -
284A ILE* 3.6 29.8 - - + -
287A LEU* 3.9 12.1 - - + -
403A ILE* 4.1 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU* 2.9 38.7 + - + +
243A LYS* 3.8 7.4 - - + +
245A LEU* 1.3 74.4 - - + +
247A ASP* 1.3 59.7 + - - +
249A LYS* 3.2 4.5 + - - +
250A ALA* 2.8 30.8 + - - +
375A VAL* 3.9 27.8 - - + -
376A SER* 3.9 30.5 - - - +
377A ARG* 4.0 21.5 + - + +
378A GLY 5.1 1.3 - - - +
401A GLU 5.2 2.6 - - - +
403A ILE* 4.1 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LYS* 2.8 54.9 + - - +
244A GLU* 3.8 6.2 + - - +
246A LEU* 1.3 75.4 - - - +
248A LEU* 1.3 59.6 + - + +
250A ALA* 3.2 2.3 + - - +
251A GLN* 2.9 43.4 + - - +
377A ARG* 3.1 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLN* 4.0 17.7 - - - +
237A ILE* 3.4 45.8 - - + -
239A ALA* 4.6 3.4 - - + -
244A GLU* 2.9 22.9 + - - +
245A LEU* 3.7 1.8 - - - +
247A ASP* 1.3 79.4 - - + +
249A LYS* 1.3 52.0 + - - +
251A GLN* 3.3 14.7 + - - +
252A HIS* 2.6 48.4 + - + +
277A MET* 5.2 1.3 - - + -
279A ILE* 3.6 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 3.0 27.3 + - + +
246A LEU* 3.2 5.8 + - + +
248A LEU* 1.3 73.1 - - - +
250A ALA* 1.3 65.5 + - - +
252A HIS 3.9 7.2 - - - +
253A PRO* 3.2 42.0 + - - +
255A ALA 3.1 27.5 + - - +
257A LEU* 4.2 15.6 - - + +
279A ILE* 4.3 7.0 - - + -
400A PRO 3.4 18.6 + - - -
401A GLU* 3.8 19.9 - - - +
402A GLU 4.3 5.9 + - - -
403A ILE* 4.0 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU 2.8 16.1 + - - +
247A ASP 3.2 1.5 + - - +
249A LYS* 1.3 78.3 - - - +
251A GLN* 1.3 60.6 + - - +
253A PRO* 4.0 8.7 - - - +
376A SER* 5.9 0.4 - - - +
377A ARG* 3.3 48.6 + - + +
401A GLU* 4.2 17.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ASP* 2.9 32.8 + - - +
248A LEU* 3.7 15.9 + - - +
250A ALA* 1.3 79.4 - - - +
252A HIS* 1.3 80.5 + - + +
253A PRO* 3.6 6.0 - - - +
254A GLU* 4.7 0.2 - - - +
377A ARG* 4.6 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 2.6 25.9 + - + +
249A LYS* 3.5 7.6 - - - +
251A GLN* 1.3 96.5 + - + +
253A PRO* 1.3 63.3 - - - +
254A GLU* 2.9 30.8 + - - +
255A ALA* 3.0 18.1 + - + +
277A MET* 3.6 39.1 - - + +
279A ILE* 5.8 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