Contacts of the strand formed by residues 183 - 189 (chain D) in PDB entry 5E6J
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 LYS 183 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D GLU 5.8 0.7 - - - +
181D SER 4.3 0.4 - - - -
182D ALA* 1.3 75.1 - - - +
184D ARG* 1.3 64.5 + - - +
185D VAL* 5.8 5.4 - - + -
199D THR* 4.0 18.4 - - - +
200D LEU 3.6 12.3 - - - +
201D THR* 4.1 15.0 - - + -
205D ALA* 3.9 3.1 - - - +
237D GLN* 4.1 3.8 - - - +
238D GLN* 3.7 1.9 + - - -
239D GLU* 2.7 54.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D LYS* 1.3 74.8 - - - +
185D VAL* 1.3 63.5 + - - +
186D LEU* 4.0 28.8 - - + +
199D THR* 3.5 4.0 + - - -
200D LEU* 2.8 40.5 + - + +
204D GLU 4.2 6.2 + - - -
205D ALA* 3.3 25.2 + - - +
206D VAL 3.6 14.6 - - - -
207D MET 3.0 26.2 + - - +
208D TYR* 3.7 24.5 - - - +
214D TYR* 5.6 0.8 - - - -
217D LEU* 4.7 8.3 - - - +
235D LEU* 3.9 12.1 - - + +
237D GLN 3.5 3.6 - - - -
238D GLN* 3.0 24.5 + - - +
243D VAL* 3.2 32.5 - - - +
245D MET* 4.6 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D LYS* 5.7 5.4 - - + -
184D ARG* 1.3 75.4 - - - +
186D LEU* 1.3 64.0 + - - +
197D THR* 3.1 27.8 - - - +
198D THR 3.4 9.4 - - - +
199D THR* 4.5 10.3 - - - +
235D LEU* 3.5 3.8 - - - +
236D VAL* 2.8 39.6 + - + -
237D GLN* 2.9 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ARG* 4.0 29.4 - - + +
185D VAL* 1.3 73.9 - - - +
187D ASN* 1.3 62.0 + - - +
197D THR* 3.3 8.7 + - - -
198D THR* 2.7 45.1 + - + +
200D LEU* 5.2 14.1 - - + -
208D TYR* 4.8 10.1 - - + -
217D LEU* 4.3 20.2 - - + -
233D GLN* 4.3 27.1 - - - +
234D TYR 3.7 7.4 - - - +
235D LEU* 3.9 26.5 - - + +
236D VAL* 3.8 2.2 - - - -
46E ALA 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D LEU* 1.3 78.5 - - - +
188D VAL* 1.3 65.8 + - - +
189D VAL* 4.3 2.0 - - - +
195D GLN* 3.5 30.6 + - - +
196D LYS 3.1 35.6 + - - -
197D THR* 3.2 8.6 + - - -
232D THR 3.6 0.2 - - - +
233D GLN* 3.5 2.5 - - - -
234D TYR* 3.2 65.0 + - + -
236D VAL* 3.6 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D ASN* 1.3 81.3 + - - +
189D VAL* 1.3 64.6 + - - +
190D CYS 4.3 0.3 + - - -
194D GLY 4.4 1.4 - - - +
195D GLN* 3.6 4.9 - - - -
196D LYS* 3.4 33.8 + - + +
198D THR* 5.1 6.5 - - + -
223D ILE* 4.9 10.1 - - + -
231D ALA* 3.9 24.2 - - + -
232D THR 3.5 12.1 - - - +
233D GLN* 3.7 26.7 - - + +
46E ALA* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D ASN* 4.3 7.9 - - - +
188D VAL* 1.3 78.7 - - - +
190D CYS* 1.3 62.3 + - - +
195D GLN* 4.0 27.6 - - + +
230D ASP 4.3 0.5 - - - +
231D ALA* 3.0 26.7 - - - +
232D THR* 3.0 33.3 + - + +
234D TYR* 4.3 14.1 - - + -
316D LYS 6.3 0.9 - - - -
----------------------------------------------------------
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