Contacts of the strand formed by residues 204 - 216 (chain A) in PDB entry 3RT0
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 ASP 204 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A SER* 4.4 1.0 + - - -
202A MET* 3.6 32.0 - - + +
203A GLU* 1.3 80.8 - - - +
205A ALA* 1.3 62.6 + - - +
242A TYR 3.6 4.7 - - - -
243A ASP* 3.2 28.1 - - - +
251A ALA* 4.7 0.2 - - - -
252A ASP* 4.7 3.5 - - - +
255A ARG* 5.1 2.1 + - - -
431A SER* 2.9 25.4 + - - -
492A ASP* 5.6 0.3 - - - +
493A ASN* 3.5 20.7 + - - +
495A SER* 2.8 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A SER* 4.8 3.8 - - - -
204A ASP* 1.3 76.6 - - - +
206A PHE* 1.3 66.2 + - - +
241A VAL* 3.9 3.5 - - - +
242A TYR* 2.8 33.0 + - - +
251A ALA* 3.5 35.0 - - + +
252A ASP* 3.8 12.6 - - - +
255A ARG* 4.0 17.9 - - + +
495A SER* 4.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A THR* 3.5 35.9 - - + -
194A SER* 3.6 33.7 - - - +
205A ALA* 1.3 78.4 - - - +
207A ALA* 1.3 72.6 + - - +
208A VAL* 4.3 13.0 - - + -
240A GLY 3.3 13.7 - - - +
241A VAL* 4.5 9.9 - - + -
242A TYR* 4.1 4.2 - - - -
255A ARG* 3.3 24.2 - - - +
495A SER* 5.2 4.3 - - - -
497A ILE* 4.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A PHE* 1.3 80.4 - - - +
208A VAL* 1.3 67.5 + - - +
238A PHE* 3.9 14.0 - - + -
239A PHE* 3.6 1.7 - - - -
240A GLY 2.9 33.5 + - - +
242A TYR* 4.3 11.2 - - + -
255A ARG* 3.8 23.3 - - + +
259A HIS* 4.3 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A TRP* 3.5 45.5 - - + +
192A THR* 4.0 9.4 - - - +
206A PHE* 4.3 10.6 - - + -
207A ALA* 1.3 80.6 - - - +
209A SER* 1.3 63.5 + - - +
210A PRO* 3.7 11.0 - - + +
238A PHE 3.4 2.9 - - - +
239A PHE* 3.6 32.1 - - + -
497A ILE* 3.9 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ALA 4.3 0.2 - - - -
208A VAL* 1.3 73.4 - - - +
210A PRO* 1.3 70.1 + - - +
212A PHE* 3.2 39.8 + - - +
238A PHE* 2.9 39.0 + - - -
259A HIS* 4.1 20.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PRO* 4.0 15.5 - - + -
190A TRP* 3.9 23.6 - - + -
208A VAL* 3.7 15.2 - - + +
209A SER* 1.3 84.6 + - - +
211A HIS* 1.3 88.8 + - + +
212A PHE* 3.0 5.6 + - - +
237A HIS* 3.7 9.9 - - + +
239A PHE* 6.1 0.4 - - + -
467A GLY 4.3 3.8 - - - +
468A LYS* 5.7 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A CYS 4.1 5.4 + - - -
187A ILE* 5.2 2.2 - - + -
188A PRO* 3.5 31.1 - - + +
209A SER 3.8 0.4 + - - -
210A PRO* 1.3 85.8 - - + +
212A PHE* 1.3 61.0 + - - +
213A LEU 3.7 1.3 - - - -
235A THR* 3.5 27.1 - - + +
236A GLY 3.9 0.2 - - - -
237A HIS* 2.8 23.4 + + - -
467A GLY* 3.6 12.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A SER* 3.2 39.5 - - - +
210A PRO 3.8 1.3 - - - +
211A HIS* 1.3 79.9 - - - +
213A LEU* 1.3 93.2 + - + +
214A LYS 4.3 0.2 + - - -
236A GLY 3.1 4.7 + - - +
238A PHE* 4.4 4.3 - - + -
259A HIS* 3.3 52.7 - + + -
260A PHE* 3.9 28.7 - + - -
263A ALA* 3.9 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A HIS 4.9 0.2 - - - -
212A PHE* 1.3 112.8 - - + +
214A LYS* 1.3 62.6 + - - +
215A LEU* 4.0 13.0 - - + -
235A THR* 3.5 8.7 - - - +
236A GLY* 2.8 34.8 + - - +
238A PHE* 4.8 6.1 - - + -
259A HIS 4.7 0.2 - - - +
262A LEU* 3.9 18.8 - - + -
263A ALA* 3.5 27.4 - - + +
266A ILE* 3.8 22.9 - - + -
333A LEU* 3.9 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A PHE 4.3 0.2 + - - -
213A LEU* 1.3 75.1 - - - +
215A LEU* 1.3 64.6 + - - +
216A PRO* 3.4 10.0 - - - +
233A HIS* 2.9 58.7 - - + +
234A LEU 3.7 2.5 - - - +
235A THR* 5.8 3.6 - - - +
266A ILE* 4.2 9.6 - - - +
270A LYS* 4.8 7.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LEU* 4.0 16.4 - - + -
214A LYS* 1.3 70.8 - - - +
216A PRO* 1.3 68.9 - - + +
217A ILE* 3.4 1.6 + - - +
220A LEU* 4.2 18.1 - - + +
233A HIS* 3.0 4.5 - - - +
234A LEU* 2.9 42.4 + - - +
236A GLY* 3.8 24.9 - - - +
266A ILE* 3.8 20.2 - - + -
286A TRP* 3.6 30.5 - - + -
333A LEU* 4.3 14.1 - - + -
334A VAL 5.1 0.2 - - - +
335A CYS* 4.2 24.2 - - + +
340A VAL* 6.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LYS 3.4 6.7 - - - +
215A LEU* 1.3 85.3 - - + +
217A ILE* 1.3 61.0 + - - +
218A LYS* 3.0 7.6 - - + +
219A MET* 2.8 61.1 + - + +
220A LEU* 3.8 5.3 + - - +
232A THR 3.9 8.7 - - - +
233A HIS* 4.2 2.2 - - + -
266A ILE* 4.1 8.5 - - + -
270A LYS* 3.4 36.6 - - + -
273A LEU* 5.5 2.5 - - + -
286A TRP* 5.5 0.7 - - + -
----------------------------------------------------------
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