Contacts of the helix formed by residues 232 - 241 (chain A) in PDB entry 5J1T
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 LYS 232 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 4.2 7.4 - - + -
230A ASP* 3.5 14.3 + - - +
231A ILE* 1.3 82.4 - - - +
233A LEU* 1.3 66.9 + - - +
234A LYS* 4.1 31.9 - - + +
235A ASP* 2.8 33.3 + - - +
236A ILE* 3.4 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 4.0 12.9 - - + +
78A ILE* 4.3 17.0 - - + -
232A LYS* 1.3 74.0 - - - +
234A LYS* 1.3 57.5 + - - +
236A ILE* 3.1 13.1 + - + +
237A GLU* 2.9 52.5 + - + +
245A PHE* 6.2 1.1 - - + -
266A PHE* 4.0 12.1 - - + +
268A PRO* 4.0 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LYS* 4.1 31.4 - - + +
233A LEU* 1.3 77.8 - - - +
235A ASP* 1.3 65.1 + - - +
237A GLU* 3.6 17.8 + - - +
238A HIS* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A VAL* 3.8 23.5 - - + +
221A PHE* 3.6 24.0 - - + -
230A ASP 4.2 0.3 - - - +
231A ILE* 4.3 0.7 - - + -
232A LYS* 2.8 41.1 + - - +
234A LYS* 1.3 82.3 - - - +
236A ILE* 1.3 63.4 + - - +
238A HIS* 3.5 6.0 + - - +
239A ALA* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 4.2 17.5 - - + -
101A HIS* 4.9 1.1 - - + +
214A ILE* 4.1 28.0 - - + +
217A VAL* 4.0 30.7 - - + -
231A ILE* 4.1 7.6 - - + -
232A LYS 3.9 11.4 - - - +
233A LEU* 3.1 13.8 + - + +
235A ASP* 1.3 74.3 - - - +
237A GLU* 1.3 66.9 + - - +
239A ALA* 3.2 2.5 + - - +
240A LEU* 2.9 45.1 + - + +
245A PHE* 5.2 1.8 - - + -
268A PRO* 4.0 22.7 - - + -
270A LEU* 4.7 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 2.9 46.0 + - + +
234A LYS* 3.6 19.7 + - - +
236A ILE* 1.3 75.8 - - + +
238A HIS* 1.3 62.8 + - - +
240A LEU 3.3 1.9 + - - -
241A SER* 3.1 23.0 + - - -
245A PHE* 3.9 29.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LYS 2.9 19.1 + - - +
235A ASP* 3.9 5.7 + - - +
237A GLU* 1.3 77.3 - - - +
239A ALA* 1.3 63.5 + - - +
241A SER* 2.7 31.9 + - - -
242A VAL* 5.3 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ARG* 3.1 58.3 + - + +
217A VAL* 3.5 32.5 - - + -
235A ASP 3.1 8.9 + - - +
236A ILE* 3.2 4.2 + - - +
238A HIS* 1.3 80.4 + - - +
240A LEU* 1.3 60.2 + - + +
241A SER 3.6 0.5 + - - -
242A VAL* 3.8 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A HIS* 3.6 29.2 - - + +
210A GLY* 3.8 20.4 - - - +
213A ARG* 3.6 27.4 - - + -
214A ILE* 4.5 4.3 - - + -
236A ILE* 2.9 29.5 + - + +
237A GLU 3.6 0.9 - - - -
238A HIS 3.2 0.2 - - - -
239A ALA* 1.3 75.3 - - + +
241A SER* 1.3 65.0 + - - +
242A VAL 3.1 3.8 - - - -
243A SER* 2.9 28.1 + - - +
244A VAL* 3.4 11.3 + - + -
245A PHE* 3.1 41.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A GLU 3.1 11.1 + - - -
238A HIS* 2.7 30.7 + - - -
240A LEU* 1.3 78.9 - - - +
242A VAL* 1.3 66.9 + - - +
245A PHE* 3.5 12.0 - - - +
246A ASN* 3.3 23.4 - - - +
----------------------------------------------------------
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