Contacts of the strand formed by residues 184 - 190 (chain D) in PDB entry 3RZL
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 ILE 184 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D ASP* 4.1 16.2 - - + +
178D LEU* 3.8 21.8 - - + -
183D PRO* 1.3 78.3 - - - +
185D ALA* 1.3 65.8 + - - +
186D SER 4.1 0.2 - - - -
224D LEU 4.0 0.5 - - - +
225D MET* 3.8 5.5 - - - +
226D MET* 3.0 53.4 + - + +
231D ASN* 5.0 5.8 - - - +
252D THR* 3.9 27.6 - - + -
253D PHE 3.5 9.0 - - - +
254D ARG* 3.2 47.1 - - + +
255D LYS 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D VAL* 3.7 22.7 - - + -
153D PHE* 3.7 25.6 - - + -
183D PRO 4.3 0.4 + - - -
184D ILE* 1.3 73.4 - - - +
186D SER* 1.3 61.1 + - - +
223D LEU* 4.1 3.1 - - + -
224D LEU 3.8 3.6 - - - -
225D MET* 3.8 10.1 - - - -
251D LEU 3.4 1.2 - - - +
252D THR* 3.2 1.7 - - - -
253D PHE* 2.6 47.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ILE 4.1 0.2 - - - -
185D ALA* 1.3 72.5 - - - +
187D VAL* 1.3 61.0 + - - +
188D SER* 4.4 2.9 + - - -
195D PHE* 5.9 1.6 - - - -
218D LEU* 5.0 4.7 - - - +
222D SER 3.8 0.7 - - - +
223D LEU* 3.6 2.4 - - - +
224D LEU* 2.8 52.2 + - - +
226D MET* 4.1 17.0 - - - -
248D ARG* 4.9 1.4 + - - -
250D ASN* 2.7 30.7 + - - -
251D LEU 3.1 3.8 - - - -
252D THR* 3.7 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D LEU* 5.5 0.9 - - + -
73D PHE* 4.1 15.5 - - + -
141D ILE* 4.3 4.5 - - + -
145D VAL* 4.1 12.1 - - + -
186D SER* 1.3 77.4 + - - +
188D SER* 1.3 65.0 + - - +
189D PHE* 3.6 29.8 - - + -
222D SER 3.3 12.6 - - - +
223D LEU* 3.8 20.9 - - + -
249D VAL 4.1 0.7 - - - +
250D ASN* 3.0 3.3 - - - +
251D LEU* 2.7 49.4 + - + +
253D PHE* 4.0 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D SER* 4.6 1.9 + - - -
187D VAL* 1.3 72.5 - - - +
189D PHE* 1.3 70.4 + - - +
218D LEU* 3.8 12.3 - - - +
219D ALA 4.0 6.3 - - - -
221D GLY* 2.8 28.0 + - - -
222D SER* 3.3 23.6 + - - -
248D ARG* 3.0 39.8 + - - -
249D VAL 3.6 4.0 - - - -
250D ASN* 3.4 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D PHE* 3.7 29.2 - + - -
78D ALA* 3.7 32.8 - - + -
81D ILE* 3.4 28.9 - - + -
82D PHE* 3.6 24.3 - - + -
85D LEU* 3.6 16.8 - - + -
141D ILE* 3.7 13.2 - - + -
187D VAL* 3.6 32.1 - - + -
188D SER* 1.3 80.5 - - - +
190D GLY* 1.3 61.3 + - - +
191D ALA 5.0 0.2 - - - -
220D HIS* 3.9 3.4 - - - +
221D GLY* 4.0 1.6 - - - +
248D ARG* 3.4 6.2 - - - +
249D VAL* 2.9 39.3 + - + +
251D LEU* 4.4 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D PHE* 3.8 15.7 - - - -
189D PHE* 1.3 72.8 - - - +
191D ALA* 1.3 69.3 + - - +
192D SER 3.3 2.3 + - - -
220D HIS* 3.1 36.7 + - - +
247D PRO 3.8 8.7 - - - -
----------------------------------------------------------
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