Contacts of the strand formed by residues 206 - 215 (chain S) in PDB entry 5JBA
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 THR 206 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E GLU* 4.5 5.9 + - - -
97E GLN* 4.0 19.6 + - - +
115E TYR* 3.7 24.8 + - + +
132E CYS 3.9 1.8 - - - +
133E GLY 3.4 2.9 - - - -
134E ARG* 5.1 1.6 - - - +
122S CYS* 3.5 31.6 - - - -
202S GLU* 4.4 0.4 - - - -
203S VAL 2.8 36.9 + - - +
204S GLU 4.2 3.8 + - - -
205S GLY* 1.3 82.3 + - - +
207S SER* 1.3 57.9 + - - +
208S PHE* 3.5 21.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 207 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E GLY* 2.8 14.0 + - - -
29S TRP* 3.5 34.7 - - - -
121S ILE* 3.4 12.3 - - - +
122S CYS* 3.2 27.9 + - - +
200S VAL* 4.3 10.7 - - - +
201S THR 3.4 7.4 - - - -
202S GLU* 4.1 20.5 + - - +
206S THR* 1.3 73.0 - - - +
208S PHE* 1.3 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 208 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E GLN* 4.2 13.0 - - + -
98E PHE* 3.9 29.4 - + - -
112E THR* 4.2 11.9 - - + -
121S ILE* 4.0 4.0 - - - -
122S CYS* 3.3 26.9 - - + -
124S ALA* 3.7 22.0 - - + +
129S THR* 6.3 0.4 - - - -
130S PHE* 3.5 40.4 - + + -
200S VAL* 3.3 2.9 - - - -
201S THR 2.9 32.9 + - - +
203S VAL* 4.0 11.2 - - + -
206S THR* 3.5 35.2 - - + -
207S SER* 1.3 74.2 - - - +
209S LEU* 1.3 66.3 + - - +
210S THR* 3.4 3.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45S SER* 4.1 6.7 - - - +
53S VAL* 3.8 27.4 - - + -
121S ILE* 3.6 15.1 - - + +
122S CYS 2.9 15.9 + - - +
123S ILE* 4.1 21.3 - - + +
124S ALA 5.5 0.3 + - - -
129S THR* 3.5 19.2 + - - +
198S PRO* 3.9 23.3 - - + -
199S HIS 3.7 7.4 - - - +
200S VAL* 4.2 3.1 - - + -
208S PHE* 1.3 72.9 - - - +
210S THR* 1.3 59.4 + - - +
211S GLY 3.4 22.4 - - - +
212S VAL* 4.8 4.7 - - + -
231S VAL* 3.7 29.4 - - + +
238S ILE* 4.9 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 210 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129S THR* 3.7 18.6 - - + +
130S PHE* 3.8 6.7 - - + -
131S LEU* 3.7 33.5 - - - +
181S PHE* 3.5 12.1 - - - -
199S HIS* 2.8 30.9 + - - -
201S THR* 2.9 35.3 + - - +
208S PHE* 3.4 4.0 + - + +
209S LEU* 1.3 77.5 - - - +
211S GLY* 1.3 57.5 + - - +
230S LYS* 4.3 0.7 - - - +
231S VAL* 3.4 19.0 + - - +
232S SER 4.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 211 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181S PHE* 3.8 7.2 - - - -
198S PRO* 3.8 0.3 - - - +
199S HIS* 2.9 37.7 + - - +
209S LEU* 3.4 13.0 - - - +
210S THR* 1.3 79.5 - - - +
212S VAL* 1.3 64.8 + - - +
229S THR 3.1 12.1 - - - -
231S VAL* 3.6 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53S VAL* 4.6 10.1 - - + -
54S THR 3.9 15.0 - - - +
55S ALA* 3.9 6.1 - - + +
102S ASP 4.2 3.8 - - - +
103S ILE* 4.2 17.9 - - + -
196S GLY* 3.6 33.2 - - - +
197S GLY 3.6 4.3 - - - +
209S LEU* 4.8 5.6 - - + -
211S GLY* 1.3 78.8 - - - +
213S ILE* 1.3 69.8 + - - +
214S SER* 3.2 1.6 + - - -
228S TYR* 3.4 5.7 - - - +
229S THR* 2.9 39.2 + - - -
231S VAL* 3.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 213 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16S ILE* 4.7 0.4 - - + -
55S ALA* 3.9 2.1 - - - +
138S VAL* 4.0 11.9 - - + -
139S SER 3.6 22.2 - - - +
190S SER* 3.7 24.9 - - - +
194S ASP* 3.5 42.4 - - + +
195S SER* 3.4 7.1 - - - +
196S GLY 2.9 23.2 + - - -
197S GLY 3.0 20.1 + - - +
198S PRO 4.0 11.4 - - - +
211S GLY 4.3 0.2 - - - -
212S VAL* 1.3 72.9 - - - +
214S SER* 1.3 59.2 + - - +
227S ILE 5.4 0.2 - - - +
228S TYR* 3.6 24.2 - - + -
302S 0G6 4.6 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 214 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57S HIS* 3.0 11.9 + - - -
99S TYR 4.2 0.9 + - - -
102S ASP* 2.7 30.5 + - - +
180S MET* 6.1 0.8 - - - +
212S VAL 3.2 2.7 + - - -
213S ILE* 1.3 76.6 - - - +
215S TRP* 1.3 79.3 + - - +
227S ILE 3.2 16.0 + - - -
228S TYR* 4.2 1.1 - - - -
229S THR* 3.6 23.6 - - - -
302S 0G6 2.8 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 215 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98S THR 4.9 4.5 - - - -
99S TYR* 3.8 23.0 - + + +
172S THR* 4.5 6.5 - - + -
174S PHE* 3.7 40.8 - + + -
175S THR 3.8 11.2 - - - -
176S ILE* 3.5 31.0 - - + -
180S MET* 3.5 19.6 - - + +
214S SER* 1.3 100.4 - - - +
216S GLY* 1.3 85.1 + - - +
217S GLU* 4.6 2.7 - - + -
227S ILE* 2.9 62.2 + - + +
302S 0G6 3.4 45.5 + - + +
----------------------------------------------------------
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