Contacts of the helix formed by residues 234 - 246 (chain A) in PDB entry 5F8X
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 TYR 234 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A HIS* 3.9 28.7 - + - -
101A HIS* 2.8 49.9 + - + -
103A ILE* 3.7 26.7 - - + -
179A ARG* 3.4 36.6 + - + +
229A THR* 3.5 25.0 - - + +
230A LYS 3.3 17.9 - - - -
231A VAL 2.9 9.5 + - - +
233A GLU* 1.3 79.8 - - - +
235A MET* 1.3 58.8 + - - +
236A ASP 3.3 2.5 - - - -
237A TRP* 3.2 12.2 + - + +
238A ILE* 2.8 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 3.6 33.7 - - + -
124A PRO* 3.4 28.3 - - + +
125A SER* 5.5 0.2 - - - -
126A LYS* 4.3 15.3 - - + +
231A VAL* 3.6 15.0 - - - +
232A ALA* 3.4 19.2 + - - +
233A GLU 3.7 0.6 - - - -
234A TYR* 1.3 74.7 - - - +
236A ASP* 1.3 66.3 + - - +
238A ILE* 3.9 23.9 - - + +
239A LEU* 3.0 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LYS* 5.2 7.8 - - - +
234A TYR* 3.3 0.6 - - - +
235A MET* 1.3 76.5 - - - +
237A TRP* 1.3 57.1 + - - +
239A LEU* 3.9 8.8 - - - +
240A GLU* 2.9 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE* 3.6 32.3 - - + -
90A ILE 4.6 0.2 - - - -
91A HIS* 3.5 46.0 - + + +
92A GLN* 3.1 32.7 + - - -
103A ILE* 3.9 32.8 - - + -
104A ALA* 4.1 5.8 - - - -
105A LEU* 3.7 29.4 - - + -
234A TYR* 3.2 17.0 + - + +
236A ASP* 1.3 75.6 - - - +
238A ILE* 1.3 87.3 + - + +
240A GLU* 4.5 3.4 - - - -
241A LYS* 3.0 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 4.0 24.2 - - + -
53A LEU* 3.9 29.8 - - + -
103A ILE* 4.3 6.5 - - + -
105A LEU* 4.4 4.9 - - + -
123A LEU* 4.5 12.8 - - + -
231A VAL* 4.0 11.0 - - + +
234A TYR 2.8 25.7 + - - +
235A MET* 3.9 24.7 - - + +
236A ASP 3.4 0.2 - - - -
237A TRP* 1.3 92.4 - - + +
239A LEU* 1.3 56.8 + - - +
241A LYS* 4.3 0.2 - - - +
242A THR* 2.7 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A MET* 3.0 23.1 + - + +
236A ASP* 3.9 8.7 - - - +
238A ILE* 1.3 75.6 - - - +
240A GLU* 1.3 66.1 + - - +
242A THR* 3.4 5.3 + - - +
243A GLN* 3.0 65.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ASP 2.9 19.7 + - - +
237A TRP* 3.9 4.9 - - - +
239A LEU* 1.3 78.0 - - - +
241A LYS* 1.3 66.4 + - + +
243A GLN* 3.9 8.4 - - - +
244A SER* 2.9 43.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE* 4.1 27.8 - - + +
92A GLN* 3.8 18.2 + - - +
105A LEU* 3.8 17.5 - - + -
237A TRP* 3.0 54.5 + - + +
240A GLU* 1.3 85.9 - - + +
242A THR* 1.3 58.5 + - - +
244A SER* 4.1 5.0 - - - -
245A SER* 3.1 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 5.1 2.5 - - + -
51A TRP* 3.6 43.5 - - + -
105A LEU* 3.8 23.6 - - + -
238A ILE* 2.7 29.0 + - + +
239A LEU* 3.4 8.8 + - - +
241A LYS* 1.3 73.5 - - - +
243A GLN* 1.3 63.6 + - - +
246A ASP* 3.0 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 3.0 56.7 + - + +
240A GLU* 4.0 8.8 - - - +
242A THR* 1.3 76.8 + - - +
244A SER* 1.3 63.5 + - - +
246A ASP* 3.5 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A GLU* 2.9 31.2 + - - -
241A LYS* 4.1 7.2 - - - -
243A GLN* 1.3 77.4 - - - +
245A SER* 1.3 62.6 + - - +
246A ASP 4.5 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TRP* 3.6 15.9 - - - -
87A GLU* 2.7 30.9 + - - -
89A ILE* 4.6 2.0 - - - -
107A LYS* 3.1 23.8 + - - +
241A LYS 3.1 20.0 + - - -
244A SER* 1.3 79.6 - - - +
246A ASP* 1.3 62.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A HIS* 5.5 6.8 - - - -
50A GLN* 4.9 2.7 - - - +
51A TRP* 3.1 25.7 + - - -
107A LYS* 3.0 30.6 + - - +
242A THR* 3.0 24.0 + - - +
243A GLN* 3.5 15.2 + - - +
244A SER 3.5 2.2 - - - -
245A SER* 1.3 80.4 - - - +
----------------------------------------------------------
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