Contacts of the strand formed by residues 215 - 222 (chain A) in PDB entry 3BRF
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 215 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A TYR 4.1 4.5 - - - -
214A GLU* 1.3 72.0 - - - +
216A VAL* 1.3 62.7 + - - +
248A GLY* 3.5 29.8 - - - -
249A TRP* 3.6 16.8 - - + +
252A LYS* 3.6 28.5 - - - -
546A TYR 3.7 0.7 - - - +
547A ARG* 3.2 6.4 - - - +
548A PHE* 2.8 63.3 + - + +
549A PHE* 5.3 3.1 - - - -
550A GLU 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A GLU* 3.9 14.6 - - + +
215A CYS* 1.3 77.4 - - - +
217A ILE* 1.3 63.1 + - - +
218A SER* 4.0 7.6 - - - +
244A LEU* 3.6 1.6 - - - -
245A ILE* 2.9 58.4 + - + +
246A GLY* 5.2 1.6 - - - -
249A TRP* 3.0 10.2 + - - +
545A GLU* 3.8 31.4 - - + +
546A TYR 3.3 3.6 - - - +
547A ARG* 3.6 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 1.3 75.0 - - - +
218A SER* 1.3 66.2 + - - +
219A ILE* 4.7 7.6 - - + -
242A ILE* 3.7 8.5 - - + -
243A TYR 3.6 2.5 - - - -
244A LEU* 3.3 20.6 - - + -
249A TRP* 4.2 6.1 - - + -
347A PHE* 3.3 44.4 - - + -
358A PHE* 3.8 29.4 - - + -
544A ALA 3.6 1.7 - - - +
545A GLU* 3.4 1.9 - - - -
546A TYR* 2.8 66.8 + - + +
548A PHE* 4.8 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 4.0 6.2 - - - +
217A ILE* 1.3 73.0 - - - +
219A ILE* 1.3 63.0 + - - +
220A PHE* 3.6 24.9 - - - -
241A CYS 3.7 0.7 - - - +
242A ILE* 3.1 6.9 - - - +
243A TYR* 2.8 42.7 + - - -
245A ILE* 4.6 5.9 - - - +
543A LYS* 3.6 8.0 + - - -
544A ALA 3.4 5.2 - - - -
545A GLU* 3.2 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ILE* 4.7 9.2 - - + -
218A SER* 1.3 77.4 - - - +
220A PHE* 1.3 63.0 + - - +
221A HIS* 4.1 6.0 + - - +
240A PRO* 5.7 0.2 - - + -
241A CYS 3.3 10.5 - - - +
242A ILE* 4.0 15.7 - - + -
290A ILE* 5.3 5.2 - - + -
343A LEU* 4.9 10.3 - - + +
345A ALA* 4.6 12.8 - - + +
358A PHE* 3.9 37.2 - - + +
359A VAL 4.0 13.2 - - - +
360A SER* 4.1 20.0 - - - +
542A ASP 4.0 0.3 - - - +
543A LYS* 3.2 4.5 - - - -
544A ALA* 2.8 42.4 + - + +
546A TYR* 4.4 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A SER* 3.6 22.2 - - - -
219A ILE* 1.3 76.4 - - - +
221A HIS* 1.3 61.3 + - - +
240A PRO* 3.2 4.5 - - - +
241A CYS* 2.8 40.1 + - - -
243A TYR* 3.5 36.8 - + + -
245A ILE* 6.0 1.8 - - + -
422A TRP* 3.5 23.4 - + + -
424A ALA* 4.9 19.1 - - + -
460A SER* 6.5 0.4 - - - -
542A ASP 3.5 5.6 - - - +
543A LYS* 3.5 45.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ILE* 4.1 6.9 + - + +
220A PHE* 1.3 77.7 - - - +
222A ALA* 1.3 82.3 + - - +
223A LYS* 4.8 0.4 + - - -
238A PRO 5.5 0.2 - - - -
240A PRO* 4.2 10.8 - - + -
343A LEU* 4.1 18.2 - - + -
360A SER* 3.3 14.8 - - - -
361A GLN* 3.2 52.5 + - + +
362A ARG 4.2 2.4 + - - -
363A ILE* 3.4 18.4 - - + +
422A TRP* 3.6 12.7 - - - -
541A THR* 3.3 3.6 - - - -
542A ASP* 2.7 53.9 + - + +
543A LYS* 4.6 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A HIS* 1.3 92.9 - - - +
223A LYS* 1.3 61.2 + - - +
224A VAL 3.2 10.3 + - - +
237A CYS 4.5 2.9 - - - +
238A PRO* 4.3 13.9 + - + +
240A PRO* 5.6 0.8 - - - +
363A ILE* 3.7 9.7 - - - +
422A TRP* 4.7 0.8 - - - -
539A ILE* 3.4 35.2 - - + -
540A SER 3.4 9.9 - - - +
541A THR* 3.9 8.0 - - + +
----------------------------------------------------------
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