Contacts of the strand formed by residues 244 - 251 (chain D) in PDB entry 6DBU
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 244 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D LEU* 4.7 0.9 - - - -
241D LEU* 2.8 54.1 + - - +
242D LEU* 3.3 2.3 - - - +
243D GLY* 1.3 74.0 + - - -
245D PRO* 1.3 64.8 - - - +
246D VAL* 3.2 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D LEU* 3.7 19.9 - - + +
193D THR* 4.0 12.1 - - + +
195D HIS* 3.5 36.6 + - + +
238D VAL* 6.2 0.9 - - + -
239D GLU 3.6 8.5 - - - +
240D LEU* 4.2 17.7 - - + -
243D GLY 4.2 4.3 - - - +
244D SER* 1.3 81.0 - - - +
246D VAL* 1.3 64.1 + - - +
247D LEU* 3.5 7.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D VAL* 3.7 0.2 - - - -
239D GLU* 2.9 65.2 + - + +
241D LEU* 4.6 17.0 - - + -
244D SER* 3.2 10.3 + - - +
245D PRO* 1.3 73.4 - - - +
247D LEU* 1.3 65.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D VAL* 5.4 1.1 - - + -
182D VAL* 4.0 26.0 - - + -
184D LEU* 4.4 12.8 - - + -
195D HIS* 4.4 22.2 - - + -
197D LEU* 3.5 32.0 - - + +
236D LEU* 3.8 22.9 - - + -
237D HIS 3.6 4.0 - - - +
238D VAL* 3.4 24.7 - - + -
239D GLU* 4.7 0.9 - - - -
245D PRO 3.5 6.0 + - - +
246D VAL* 1.3 81.7 - - - +
248D THR* 1.3 90.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D LEU* 3.5 10.5 - - - +
235D ARG* 6.0 0.4 - - - +
236D LEU* 3.4 0.9 - - - -
237D HIS* 2.9 53.9 + - + +
239D GLU* 4.3 9.4 - - - +
247D LEU* 1.3 82.2 - - - +
249D CYS* 1.3 76.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D LEU* 3.5 19.5 - - + +
199D GLU* 3.5 38.2 - - + +
200D LEU* 4.9 8.1 - - + -
234D ILE* 3.6 21.3 - - - -
235D ARG 3.2 16.6 - - - +
236D LEU* 4.0 6.3 - - + +
248D THR* 1.3 87.1 + - - +
250D THR* 1.3 88.7 + - - +
251D ILE* 4.9 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D GLU* 5.3 2.9 - - - -
234D ILE* 3.9 1.2 - - - -
235D ARG* 2.9 73.2 + - + +
249D CYS* 1.3 89.1 - - - +
251D ILE* 1.3 72.6 + - - +
252D LEU* 3.4 10.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D GLU* 4.1 39.5 - - + +
201D THR* 5.4 2.0 - - - +
232D ARG* 4.0 23.6 - - + +
233D LEU 3.9 8.7 - - - +
234D ILE* 3.6 19.7 - - + -
249D CYS* 4.9 1.3 - - - -
250D THR* 1.3 84.8 + - - +
252D LEU* 1.3 75.5 + - - +
----------------------------------------------------------
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