Contacts of the helix formed by residues 220 - 224 (chain B) in PDB entry 6Q2J
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 220 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B SER* 1.3 74.1 - - - +
221B GLU* 1.3 62.8 + - - +
223B LEU* 3.5 2.8 + - + +
224B GLY 2.8 6.4 + - - -
225B TRP* 2.6 47.1 + - + +
226B ALA* 4.3 16.8 - - + +
229B VAL* 3.6 47.3 - - + +
230B LEU 4.7 4.0 - - - +
232B PRO 3.3 25.1 - - - +
233B ARG* 4.3 14.3 + - + +
235B VAL* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B SER* 3.7 14.1 + - - +
220B LEU* 1.3 80.2 + - - +
222B ASP* 1.3 68.0 + - - +
224B GLY* 3.3 12.0 + - - +
226B ALA* 4.4 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A SER* 4.7 12.0 - - - +
261A LEU* 4.8 2.7 - - + +
264A LEU* 3.6 42.3 - - + +
265A LYS* 5.4 0.3 + - - -
218B ALA* 4.0 11.2 - - + -
219B SER* 2.8 38.6 + - - +
221B GLU* 1.3 81.2 - - - +
223B LEU* 1.3 62.4 + - - +
224B GLY 3.6 0.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
257A ILE* 3.9 22.4 - - + +
260A SER* 4.3 20.3 + - - -
261A LEU* 3.8 33.7 - - + -
218B ALA* 4.8 5.6 - - + -
219B SER 3.2 12.3 + - - +
220B LEU* 4.0 4.7 - - + +
222B ASP* 1.3 75.7 - - - +
224B GLY* 1.3 58.6 + - - +
225B TRP* 3.1 64.3 + - + +
235B VAL* 4.8 21.5 - - + -
237B VAL* 5.5 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU 2.8 8.2 + - - -
221B GLU* 3.3 11.7 + - - -
222B ASP 3.2 3.8 - - - -
223B LEU* 1.3 80.0 - - - +
225B TRP* 1.3 61.6 + - - -
226B ALA 3.5 3.5 + - - -
227B ASP* 5.2 2.3 + - - +
228B TRP* 4.4 5.2 + - - -
606F TYR* 5.3 5.5 + - - -
----------------------------------------------------------
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