Contacts of the helix formed by residues 216 - 222 (chain B) in PDB entry 3DM6
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 ASP 216 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B MET* 1.3 70.8 - - - +
217B CYS* 1.3 60.2 + - - +
218B LYS* 2.8 46.4 + - - +
219B GLU* 2.8 34.3 + - + +
220B TYR 4.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B VAL 3.5 23.3 - - - +
215B MET 2.7 9.3 + - - +
216B ASP* 1.3 77.7 + - - +
218B LYS* 1.3 62.3 + - - +
219B GLU 3.1 0.4 - - - -
220B TYR* 3.1 30.2 + - + +
221B ASN* 3.4 8.7 + - - -
381B ASP* 4.3 8.3 - - - -
382B CYS* 2.0 56.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ASP* 2.8 25.7 + - - +
217B CYS* 1.3 83.8 - - - +
219B GLU* 1.3 60.1 + - + +
221B ASN* 3.2 13.7 + - - -
222B TYR* 3.3 13.7 + - - +
381B ASP* 2.6 33.3 + - - +
382B CYS 3.3 10.4 - - - +
383B GLY 3.4 25.6 + - - +
384B TYR* 4.6 14.7 - - + +
385B ASN* 4.8 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B MET* 4.6 21.1 - - + -
216B ASP* 2.8 29.7 + - + +
218B LYS* 1.3 77.7 - - - +
220B TYR* 1.3 60.2 + - - +
221B ASN 3.4 0.5 + - - -
222B TYR* 3.6 29.6 + - - +
237B PRO* 3.8 7.4 - - - +
239B LYS* 3.4 38.3 + - + +
240B VAL* 3.5 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ILE* 4.2 15.5 - - + +
204B VAL 4.3 1.3 - - - -
205B ARG* 3.7 30.3 - - - -
206B VAL* 3.6 31.4 + - + -
212B ASP* 3.8 7.3 + - - -
213B LEU* 3.7 17.1 - - + +
214B LYS 3.8 3.3 + - - -
215B MET* 3.5 43.6 + - + -
217B CYS* 3.1 33.0 + - + +
219B GLU* 1.3 76.5 - - + +
221B ASN* 1.3 60.8 + - - +
222B TYR 3.6 0.4 - - - -
225B SER* 3.2 4.7 + - - -
237B PRO* 4.5 1.3 - - - +
240B VAL* 3.9 27.8 - - + -
331B THR* 2.5 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B GLU* 6.1 0.9 - - - +
201B VAL 5.1 1.6 - - - +
202B ILE* 3.5 12.7 - - + +
203B ILE* 2.7 48.5 + - - +
217B CYS 3.4 6.1 + - - -
218B LYS 3.2 6.1 + - - +
220B TYR* 1.3 78.3 - - - +
222B TYR* 1.3 56.2 + - - +
223B ASP* 2.9 4.9 - - - +
224B LYS* 2.6 26.9 + - - -
225B SER* 2.9 27.2 + - - +
382B CYS 2.9 27.8 + - - +
383B GLY* 4.6 7.4 - - - -
384B TYR* 3.5 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LYS 3.3 9.8 + - - +
219B GLU* 3.6 29.1 + - - +
220B TYR 3.6 1.8 + - - -
221B ASN* 1.3 78.0 - - - +
223B ASP* 1.3 56.6 + - + +
224B LYS 3.4 1.3 - - - -
237B PRO* 3.2 19.3 - - + +
239B LYS* 6.2 2.0 - - + -
328B SER 5.4 5.9 - - - +
330B GLY* 3.1 19.2 + - - -
384B TYR* 3.3 48.2 + + + -
----------------------------------------------------------
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