Contacts of the strand formed by residues 306 - 313 (chain D) in PDB entry 2PI8
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 HIS 306 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D VAL* 4.4 1.6 - - - +
97D GLN* 3.4 48.1 + - + +
99D THR* 3.3 41.5 - - + +
260D SER* 4.2 2.1 - - - -
261D ASP 4.6 0.3 + - - -
265D ILE* 5.5 0.4 - - - +
301D ALA 3.5 24.3 + - - -
302D ILE* 3.3 29.3 - - + +
303D LYS 3.6 17.3 - - - +
304D GLY 2.9 11.2 + - - +
305D GLN* 1.3 75.3 - - - +
307D PHE* 1.3 84.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 307 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D MSE 3.7 25.8 - - + -
96D VAL* 3.8 17.3 - - + -
97D GLN 3.1 4.4 + - - -
98D PHE* 3.5 30.4 - + + -
99D THR* 2.8 28.5 + - - +
258D VAL* 4.0 18.4 - - + -
259D ALA 3.4 4.3 - - - +
260D SER* 3.5 31.0 - - - -
265D ILE* 3.7 29.2 - - + -
271D LEU* 3.7 26.7 - - + -
302D ILE* 4.7 0.9 - - - -
306D HIS* 1.3 85.5 + - - +
308D ALA* 1.3 61.0 + - - +
309D ILE 3.9 0.7 - - - -
330D VAL* 3.9 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 308 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D THR* 3.5 22.0 - - + -
101D TYR* 3.1 25.6 - - + -
258D VAL* 3.2 2.0 - - - -
259D ALA* 2.8 51.4 + - + -
302D ILE* 3.6 13.9 - - + +
307D PHE* 1.3 70.9 - - - +
309D ILE* 1.3 61.6 + - - +
2H NAG 5.6 0.9 - - - +
3H NAG 4.4 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 309 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D PHE* 3.6 36.8 - - + -
99D THR 2.8 17.2 + - - +
100D GLY* 3.3 4.2 - - - -
101D TYR* 3.3 17.9 + - - -
255D ARG* 4.2 12.8 - - + -
258D VAL* 3.7 17.7 - - + -
275D VAL* 3.7 35.4 - - + -
291D ARG* 6.0 0.9 - - - -
293D MSE 4.1 16.8 - - - -
308D ALA* 1.3 69.2 - - - +
310D TYR* 1.3 70.1 + - - +
311D GLN* 3.2 28.0 + - - +
324D TYR* 4.8 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 310 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D TYR* 3.5 43.3 - + - +
102D TYR* 4.3 1.6 - - - -
103D THR* 3.0 31.8 + - - -
244D VAL* 3.5 22.5 - - + +
252D LEU* 3.6 34.2 + - + -
253D VAL 3.4 22.9 - - - -
254D GLY* 4.0 1.8 - - - -
255D ARG* 2.6 36.6 + - - -
257D SER* 3.1 23.3 + - - +
308D ALA 3.3 3.0 + - - -
309D ILE* 1.3 69.3 - - - +
311D GLN* 1.3 52.8 + - - +
312D GLY* 3.4 28.0 + - - -
313D ILE* 3.5 14.4 - - + +
4H NAG 5.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 311 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D GLY* 4.7 1.6 - - - -
101D TYR 3.0 11.1 + - - +
102D TYR* 4.4 0.2 - - + -
254D GLY* 3.6 13.2 - - - -
255D ARG* 3.4 17.2 + - - +
309D ILE* 3.5 35.6 + - - +
310D TYR* 1.3 72.4 - - - +
312D GLY* 1.3 58.6 + - - +
317D ALA* 3.3 22.2 - - + +
320D ARG* 2.8 55.1 + - - +
321D ALA* 3.5 28.3 - - + +
324D TYR* 3.8 24.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 312 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D TYR* 3.3 4.1 - - - +
103D THR 2.8 24.6 + - - -
254D GLY* 4.3 5.4 - - - -
310D TYR* 3.4 23.6 + - - -
311D GLN* 1.3 82.3 - - - +
313D ILE* 1.3 65.1 + - - -
317D ALA* 3.6 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 313 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C ASP 5.0 8.7 - - - +
103D THR* 3.3 19.5 - - - +
105D VAL* 4.2 11.2 - - + -
166D TYR* 3.8 28.9 - - + +
244D VAL* 3.8 18.2 - - + +
252D LEU 6.2 0.2 - - - +
310D TYR* 3.5 17.7 - - - +
312D GLY* 1.3 73.4 - - - +
314D GLY* 1.3 62.4 + - - +
317D ALA* 3.7 7.8 + - - +
----------------------------------------------------------
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