Contacts of the helix formed by residues 219 - 225 (chain B) in PDB entry 1SOX
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 219 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ALA 3.4 3.6 + - - -
218B ARG* 1.3 70.4 - - - +
220B ARG* 1.3 64.2 + - - +
222B VAL* 3.2 5.3 + - + +
223B LEU* 3.0 41.0 + - + +
238B VAL* 4.2 1.6 - - + -
240B PHE* 3.9 21.3 - - + -
256B ILE* 4.3 0.7 - - + -
261B ALA* 3.5 34.3 - - + +
268B VAL* 2.9 38.8 + - + +
269B LEU* 4.2 0.6 - - - +
270B LEU* 4.1 37.2 - - + -
306B VAL* 4.2 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ARG* 4.4 14.1 - - + +
219B LEU* 1.3 79.9 - - - +
221B ASP* 1.3 64.8 + - - +
223B LEU* 3.4 2.0 + - - +
224B LEU* 2.9 58.4 + - + +
230B GLU* 3.6 35.8 + - - +
261B ALA 3.4 17.2 + - - +
262B LEU* 2.8 38.2 + - + +
263B SER 4.7 3.4 - - - +
264B PRO* 3.8 38.9 - - - +
268B VAL 4.6 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B PHE* 3.9 18.9 - - + +
175B PRO* 4.1 24.8 - - + +
218B ARG* 3.0 39.3 + - + +
220B ARG* 1.3 88.7 + - - +
222B VAL* 1.3 60.1 + - - +
224B LEU* 3.8 9.2 - - - +
225B HIS* 2.8 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL* 4.0 28.7 - - + -
163B LEU* 4.1 4.9 - - + +
165B LEU* 4.0 15.7 - - + -
170B LEU* 4.4 2.2 - - + -
174B PHE* 3.8 31.2 - - + -
217B ALA* 4.1 11.7 - - + -
218B ARG 3.5 13.2 - - - +
219B LEU* 3.2 9.6 + - + +
221B ASP* 1.3 75.0 - - - +
223B LEU* 1.3 63.6 + - - +
225B HIS* 3.3 3.1 + - - +
226B ALA* 3.1 22.0 + - - +
270B LEU* 4.1 22.0 - - + -
306B VAL* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL* 4.2 7.9 - - + -
219B LEU* 3.0 37.9 + - + +
220B ARG 3.9 2.9 - - - +
222B VAL* 1.3 75.7 - - + +
224B LEU* 1.3 64.1 + - - +
226B ALA* 3.1 10.2 + - - -
227B GLY 3.4 0.2 + - - -
228B PHE* 3.1 49.0 + - + -
238B VAL* 3.9 19.1 - - + -
261B ALA* 4.0 5.4 - - + -
262B LEU* 3.5 33.7 - - + -
306B VAL* 4.0 22.0 - - + -
308B VAL* 4.0 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ARG* 2.9 56.6 + - + +
221B ASP* 3.8 10.1 - - - +
223B LEU* 1.3 76.6 - - - +
225B HIS* 1.3 53.6 + - - +
227B GLY* 2.6 27.7 + - - -
228B PHE 3.4 18.8 - - - +
229B PRO* 4.8 0.4 - - + -
230B GLU* 4.2 19.3 - - + +
262B LEU* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 3.9 22.0 - - + -
173B ARG* 3.0 44.2 + - + +
174B PHE* 3.6 22.6 - + + -
221B ASP 2.8 19.1 + - - +
222B VAL 3.4 4.9 - - - +
224B LEU* 1.3 77.1 - - - +
226B ALA* 1.3 59.1 + - - +
227B GLY* 3.2 1.4 + - - -
911B EPE 3.3 31.4 - - - -
----------------------------------------------------------
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