Contacts of the strand formed by residues 172 - 178 (chain D) in PDB entry 3BDW
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 172 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D SER* 3.5 3.3 - - - -
171D PRO* 1.3 86.2 - - - +
173D SER* 1.3 65.1 + - - +
211D LEU 3.2 4.5 - - - -
212D GLN* 3.8 25.1 - - - -
225D ILE* 3.6 19.9 - - - +
226D ILE* 3.5 28.1 - - - +
228D HIS* 4.3 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D LEU* 3.8 12.4 - - - +
172D SER* 1.3 78.6 - - - +
174D TRP* 1.3 73.5 + - - +
210D VAL* 3.2 7.6 - - - +
211D LEU* 2.6 47.6 + - - +
225D ILE* 4.6 0.8 - - - +
226D ILE 3.3 9.9 - - - -
228D HIS* 3.3 41.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D ARG 2.9 20.8 + - - -
139D THR 3.6 3.8 - - - -
140D TRP* 3.5 31.9 - + + -
143D SER* 3.1 24.9 - - - -
154D LEU* 4.2 17.2 - - + +
155D LEU* 3.6 8.7 - - - +
173D SER* 1.3 92.4 + - - +
175D ILE* 1.3 63.2 + - - +
208D CYS* 3.7 26.5 - - + -
209D ALA 3.0 24.9 - - - -
210D VAL* 3.2 16.9 - - + +
219D ALA* 4.0 5.6 - - + -
220D GLN 3.5 19.5 - - - -
221D CYS* 4.0 9.4 - - - -
223D SER 3.5 16.2 - - - -
225D ILE* 3.5 37.2 - - + +
226D ILE 3.2 13.7 + - - +
227D TYR* 4.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D TRP* 3.1 15.1 + - - -
154D LEU* 4.1 4.5 - - - -
155D LEU* 3.2 24.2 - - + +
156D SER* 5.1 1.1 - - - -
157D ILE* 3.8 25.4 - - + +
173D SER 3.7 0.2 + - - -
174D TRP* 1.3 80.8 - - - +
176D GLY* 1.3 54.0 + - - +
177D VAL* 2.7 35.4 + - + +
194D PHE* 3.9 10.3 - - + -
209D ALA* 3.2 31.6 + - + +
210D VAL* 4.4 2.0 - - - +
211D LEU* 4.1 15.0 - - + +
216D LEU* 3.6 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D TRP* 4.4 3.1 - - - -
154D LEU* 4.1 20.4 - - - +
155D LEU 2.7 16.5 + - - -
156D SER* 4.8 3.1 - - - +
175D ILE* 1.3 67.4 - - - +
177D VAL* 1.3 65.1 - - - +
188D THR* 3.4 3.3 - - - -
189D MET* 3.3 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D TRP* 3.9 4.6 + - - +
156D SER* 6.5 0.9 - - - -
157D ILE 6.3 0.4 - - - +
175D ILE* 2.7 22.3 + - + +
176D GLY* 1.3 79.3 - - - +
178D PHE* 1.3 69.1 + - - +
186D TRP* 3.6 31.6 - - + -
187D VAL 3.2 11.9 - - - +
188D THR* 4.5 4.3 - - + -
194D PHE* 3.5 46.2 - - + -
198D ILE* 5.5 0.2 - - + -
208D CYS* 3.9 1.2 - - - -
209D ALA* 3.2 34.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D TRP* 4.0 27.6 - + + -
177D VAL* 1.3 79.6 - - - +
179D ARG* 1.3 73.0 + - - +
180D ASN* 3.9 19.3 - - - -
185D PRO 3.9 0.9 - - - +
186D TRP* 3.5 12.7 - - - -
187D VAL* 2.8 60.0 + - + +
188D THR 4.0 9.4 - - - -
189D MET* 3.8 22.9 - - - -
207D ASN 3.4 11.7 - - - +
208D CYS* 4.5 6.5 - - - -
----------------------------------------------------------
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