Contacts of the strand formed by residues 305 - 312 (chain E) in PDB entry 2BQZ
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 CYS 305 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242E VAL* 4.0 32.5 - - - -
303E GLY* 4.8 1.6 - - - -
304E ASN* 1.3 96.8 + - - +
306E GLN* 1.3 60.1 + - - +
320E LEU* 4.2 17.0 - - + -
321E ILE 3.2 7.9 - - - +
323E SER* 3.6 5.5 + - - +
326E ILE* 4.0 6.7 - - - -
332E LEU* 4.1 14.6 - - - -
333E LEU 3.1 9.8 + - - +
334E TYR* 3.4 25.8 - - + +
335E ASP 4.7 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 306 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305E CYS* 1.3 74.8 - - - +
307E THR* 1.3 74.8 + - - +
308E LYS* 3.0 33.5 + - - +
319E ILE 3.6 0.3 - - - +
320E LEU* 3.4 3.7 - - - -
321E ILE* 2.9 37.6 + - + +
323E SER* 4.5 13.7 - - - -
334E TYR* 4.9 1.3 - - - -
24F ASP* 3.9 13.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 307 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245E TYR* 5.8 1.1 - - + -
273E TYR* 2.7 37.1 + - + +
306E GLN* 1.3 80.1 - - - +
308E LYS* 1.3 71.9 - - - +
318E LEU* 4.0 22.2 - - + -
319E ILE 3.2 11.7 - - - +
320E LEU* 3.1 19.2 - - + +
334E TYR* 3.5 8.6 - - - +
335E ASP 5.1 0.2 + - - -
22F LEU* 3.6 27.5 - - + +
24F ASP* 4.2 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 308 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306E GLN* 3.0 32.5 + - - +
307E THR* 1.3 85.9 - - - +
309E LEU* 1.3 65.6 + - - +
318E LEU* 3.5 5.5 - - - -
319E ILE* 2.8 45.9 + - + +
321E ILE* 3.8 27.6 - - + -
22F LEU* 4.8 1.6 - - - -
24F ASP* 3.5 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 309 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E PHE* 3.9 14.4 - - + -
276E GLN 3.5 11.4 - - - +
277E TYR* 3.7 22.0 - - + -
308E LYS* 1.3 76.1 - - - +
310E HIS* 1.3 60.1 + - - +
311E ASP* 4.1 2.6 + - + +
316E PRO* 3.5 29.8 - - + -
317E HIS 3.6 11.0 - - - +
318E LEU* 4.1 6.3 - - + -
22F LEU* 4.0 9.4 - - + +
24F ASP* 5.3 2.0 + - - -
25F ASN* 2.8 44.9 + - - +
26F TYR* 4.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 310 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199E GLN* 5.6 2.2 - - - -
203E ARG* 4.4 20.1 - - + +
206E ILE* 3.6 30.9 - - + +
207E ASP* 2.9 27.6 + - - -
210E ILE* 3.7 17.0 - - + -
308E LYS* 3.6 1.0 + - + -
309E LEU* 1.3 71.9 + - - +
311E ASP* 1.3 72.8 + - - +
312E ILE* 3.8 3.1 - - + -
316E PRO* 4.7 0.7 - - - -
317E HIS* 2.8 39.8 + - - +
319E ILE* 3.8 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 311 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203E ARG* 4.3 22.6 + - - -
207E ASP* 5.1 0.3 - - - +
277E TYR* 3.8 32.4 + - + +
309E LEU* 4.1 4.2 - - + +
310E HIS* 1.3 82.8 + - - +
312E ILE* 1.3 65.1 + - - +
313E ASP 4.3 1.7 + - - -
314E GLY* 4.3 9.5 + - - -
315E VAL 3.3 10.5 - - - +
316E PRO* 4.2 2.2 - - + -
26F TYR 5.2 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 312 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E ASP* 3.9 29.8 - - - +
210E ILE* 3.8 42.2 - - + -
211E GLU* 4.7 15.0 - - + +
310E HIS* 3.8 11.4 - - + -
311E ASP* 1.3 79.2 - - - +
313E ASP* 1.3 87.4 + - - +
315E VAL* 2.9 26.1 + - - +
317E HIS* 3.9 16.8 - - + +
----------------------------------------------------------
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