Contacts of the helix formed by residues 256 - 266 (chain B) in PDB entry 3DAE
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 SER 256 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 4.1 7.6 - - - +
177A ASP* 3.9 10.4 - - - +
195A ASP* 6.0 0.9 - - - -
254B ASP* 3.0 8.8 + - - +
255B GLU* 1.3 76.0 - - - +
257B ILE* 1.3 67.2 + - - +
258B PRO* 2.8 26.9 - - - +
259B VAL* 3.1 27.7 + - - +
260B LEU* 2.8 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ARG 5.3 1.3 - - - +
177A ASP* 3.0 17.6 + - - +
179A LYS* 3.4 15.0 - - - +
213A GLY 4.2 11.0 - - - +
214A SER 3.2 35.2 - - - +
215A PRO* 3.8 6.5 - - + -
218A ALA* 3.9 20.4 - - + -
222A VAL* 4.3 3.1 - - + -
215B PRO* 4.9 1.3 - - + -
254B ASP 4.7 1.3 + - - +
255B GLU 3.7 3.3 + - - +
256B SER* 1.3 70.5 - - - +
258B PRO* 1.3 61.5 - - + +
260B LEU* 3.4 16.3 + - + +
261B PHE* 2.9 59.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A HIS 5.1 0.2 - - - +
176A ARG* 3.1 46.0 - - + +
177A ASP* 3.4 9.9 - - + +
222A VAL* 4.2 18.8 - - + +
256B SER* 2.8 18.8 - - - +
257B ILE* 1.3 97.2 - - + +
259B VAL* 1.3 62.5 + - + +
261B PHE* 3.3 2.4 + - - +
262B LYS* 3.0 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 3.7 25.4 - - - +
254B ASP* 3.5 29.4 - - - +
256B SER* 3.1 22.8 + - - +
258B PRO* 1.3 73.6 - - + +
260B LEU* 1.3 66.9 + - - +
262B LYS* 3.1 13.1 + - + +
263B ASN* 2.9 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B PRO* 4.3 15.7 - - + -
216B ASN* 4.0 24.2 - - - +
252B PHE* 3.2 39.7 - - + +
253B ASP* 3.5 5.6 - - - +
254B ASP* 3.6 21.7 - - + +
256B SER 2.8 16.4 + - - +
257B ILE* 3.4 22.7 - - + +
259B VAL* 1.3 72.8 - - - +
261B PHE* 1.3 69.1 + - + +
263B ASN* 3.0 8.0 + - - +
264B ILE* 3.0 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A PRO* 3.9 28.0 - - + -
222A VAL* 3.6 30.7 - - + +
223A ILE* 4.1 13.7 - - + +
224A SER 4.2 2.9 - - - +
225A GLY* 6.0 0.2 - - - -
261A PHE* 4.0 7.9 - + - -
215B PRO* 4.2 12.1 - - + -
223B ILE* 3.2 48.0 - - + +
257B ILE* 2.9 57.9 + - + +
258B PRO 4.1 3.1 - - - +
260B LEU* 1.3 79.3 - - + +
262B LYS* 1.3 57.1 - - - +
264B ILE* 3.9 7.8 - - + +
265B SER* 3.0 32.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLY* 5.9 2.7 - - - -
258B PRO 3.0 18.0 + - - +
259B VAL* 3.4 11.9 - - + +
260B LEU 3.1 0.2 - - - -
261B PHE* 1.3 78.7 - - - +
263B ASN* 1.3 65.0 + - - +
265B SER* 3.3 10.9 + - - +
266B ASN* 2.9 36.9 + - - +
268B VAL* 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B PHE* 3.5 29.3 + - + +
253B ASP 5.3 0.2 + - - -
254B ASP* 4.6 5.5 + - - +
259B VAL* 2.9 34.7 + - - +
260B LEU* 3.5 6.7 - - - +
262B LYS* 1.3 80.7 - - - +
264B ILE* 1.3 63.0 + - - +
267B GLY 3.2 2.6 + - - -
268B VAL* 2.9 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B PRO 3.9 21.5 - - - +
216B ASN* 4.4 6.1 - - - +
218B ALA 3.6 21.5 - - - +
220B PRO* 3.7 19.4 - - + +
223B ILE* 4.3 14.4 - - + -
236B TRP* 3.8 18.7 - - + +
252B PHE* 3.6 29.8 - - + -
260B LEU* 3.0 36.5 + - + +
261B PHE* 3.9 8.1 - - + +
263B ASN* 1.3 76.7 - - - +
265B SER* 1.3 65.9 + - - +
266B ASN 2.9 1.7 + - - -
267B GLY* 3.0 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A SER 3.8 16.8 - - - -
225A GLY* 3.7 24.2 + - - +
220B PRO* 4.2 16.3 - - - +
223B ILE* 5.7 2.0 - - - +
261B PHE 3.0 16.1 + - - -
262B LYS* 3.3 11.8 + - - +
263B ASN 3.5 0.2 - - - -
264B ILE* 1.3 76.5 - - - +
266B ASN* 1.3 67.4 + - - +
267B GLY 3.6 0.2 - - - -
289B VAL* 3.1 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLY 5.4 3.0 + - - -
262B LYS* 2.9 34.9 + - - +
264B ILE 3.0 0.6 - - - -
265B SER* 1.3 87.1 + - - +
267B GLY* 1.3 63.4 + - - +
268B VAL* 3.8 19.6 - - + +
289B VAL* 3.5 9.8 - - - +
----------------------------------------------------------
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