Contacts of the helix formed by residues 235 - 246 (chain A) in PDB entry 4AOR
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 235 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A HIS* 3.6 28.0 - + - -
106A ASN* 2.6 41.7 + - - -
108A ILE* 3.9 31.9 - - + -
182A ASN* 3.1 27.6 - - + +
230A THR* 3.9 15.0 - - + +
231A LYS 3.2 24.5 - - - -
232A VAL* 2.8 13.1 + - - +
234A ASN* 1.3 84.2 - - + +
236A VAL* 1.3 66.5 + - - +
237A SER 3.3 2.7 - - - -
238A TRP* 3.1 9.2 + + + +
239A ILE* 2.8 27.5 + - + +
1250A GOL 3.6 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 4.2 16.4 - - + -
129A PRO* 3.7 42.0 - - + +
232A VAL* 3.9 15.5 - - + +
233A CYS 3.9 9.5 + - - +
234A ASN 3.6 1.8 - - - -
235A TYR* 1.3 78.6 - - - +
237A SER* 1.3 59.0 + - - +
239A ILE* 3.3 6.0 + - + +
240A LYS* 2.9 55.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ASN 5.4 2.8 + - - -
235A TYR 3.3 0.7 - - - -
236A VAL* 1.3 76.7 - - - +
238A TRP* 1.3 60.7 + - - +
240A LYS* 3.5 9.0 + - - +
241A GLN* 3.0 29.1 + - - +
1250A GOL 5.7 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ILE* 3.7 29.7 - - + +
95A VAL 4.1 3.1 - - - -
96A HIS* 3.5 45.8 - + - +
97A PRO* 3.4 19.1 - - + +
108A ILE* 4.0 24.7 - - + -
110A LEU* 3.8 27.1 - - + -
235A TYR* 3.1 13.9 + - + +
237A SER* 1.3 79.5 + - - +
239A ILE* 1.3 78.4 + - + +
241A GLN* 3.4 11.5 + - - +
242A THR* 2.8 50.5 + - - -
1250A GOL 4.2 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 3.7 27.6 - - + -
59A VAL* 4.5 7.4 - - + -
108A ILE* 4.2 17.0 - - + -
110A LEU* 3.8 17.2 - - + +
128A LEU* 3.7 33.0 - - + -
232A VAL* 4.3 11.9 - - + -
235A TYR 2.8 23.7 + - - +
236A VAL* 3.5 6.5 - - - +
238A TRP* 1.3 91.7 - - + +
240A LYS* 1.3 62.8 + - - +
242A THR* 3.2 2.3 + - - -
243A ILE* 3.0 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 4.9 11.7 - - + -
236A VAL* 2.9 41.5 + - + +
237A SER* 3.8 7.4 - - - +
239A ILE* 1.3 76.8 - - - +
241A GLN* 1.3 64.0 + - - +
243A ILE* 3.5 8.3 + - + +
244A ALA* 3.0 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A SER 3.0 18.4 + - - +
238A TRP* 3.7 11.4 + - - +
240A LYS* 1.3 77.1 - - - +
242A THR* 1.3 73.5 + - - +
244A ALA* 3.3 5.9 + - + +
245A SER* 2.9 51.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
57A TRP* 4.4 4.0 - - + -
94A ILE* 3.5 40.1 - - + +
110A LEU* 3.6 23.3 - - + -
238A TRP* 2.8 44.3 + - - -
239A ILE 3.7 0.2 - - - -
241A GLN* 1.3 84.6 + - - +
243A ILE* 1.3 61.0 + - - +
245A SER* 3.8 2.9 - - - -
246A ASN* 2.9 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 3.9 11.7 - - + -
54A ASN* 3.7 23.1 - - - +
57A TRP* 3.9 43.2 + - + +
110A LEU* 4.9 2.7 - - + -
128A LEU* 5.6 1.6 - - + -
239A ILE* 3.0 38.9 + - + +
240A LYS* 3.7 7.9 - - + +
242A THR* 1.3 78.6 - - - +
244A ALA* 1.3 64.0 + - - +
245A SER 3.4 0.3 + - - -
246A ASN* 3.6 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LYS 3.0 18.0 + - - +
241A GLN* 3.8 6.5 - - - +
242A THR 3.3 0.4 - - - -
243A ILE* 1.3 80.4 - - + +
245A SER* 1.3 60.4 + - - +
246A ASN* 3.6 3.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
241A GLN* 2.9 40.3 + - - -
242A THR* 3.8 1.4 - - - -
243A ILE 3.3 0.2 - - - -
244A ALA* 1.3 77.2 - - - +
246A ASN* 1.3 76.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TRP* 3.7 16.6 - - + -
92A LYS* 3.1 31.7 + - + +
94A ILE* 3.7 25.4 - - - +
112A LYS* 2.8 35.3 + - - -
242A THR* 2.9 29.7 + - - +
243A ILE 3.6 11.8 + - - +
244A ALA 3.3 4.4 - - - +
245A SER* 1.3 99.0 + - - +
----------------------------------------------------------
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