Contacts of the strand formed by residues 251 - 255 (chain C) in PDB entry 3FBY
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 ARG 251 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ILE* 5.4 7.9 - - - +
265B LEU* 5.4 5.9 - - - +
229C CYS* 4.0 13.2 - - - -
231C ASP* 3.7 18.4 + - - -
233C SER* 3.4 30.4 + - - -
234C PRO 5.1 3.5 + - - -
236C GLU 6.3 0.2 - - - +
243C CYS* 3.8 18.8 - - - -
244C VAL 3.3 6.1 - - - +
245C LEU* 4.2 6.9 - - + +
246C GLU* 5.0 0.3 - - - +
249C GLY 3.7 19.4 + - - -
250C SER* 1.3 81.0 - - - +
252C SER* 1.3 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C ASP 3.3 2.1 - - - +
243C CYS* 3.6 2.9 - - - -
244C VAL* 2.8 50.8 + - - +
246C GLU* 3.4 28.6 + - - +
251C ARG* 1.3 73.0 + - - +
253C CYS* 1.3 65.4 + - - +
254C VAL* 6.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C GLU* 3.9 10.5 - - - -
237C CYS* 2.1 55.2 - - - -
242C ASP 3.4 3.4 - - - -
243C CYS* 5.6 0.9 - - - -
252C SER* 1.3 75.2 - - - +
254C VAL* 1.3 61.3 + - - +
262C ASN 3.7 9.3 - - - +
263C GLY* 3.4 30.0 + - - +
264C ILE* 4.4 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C ALA* 3.7 1.8 - - - -
242C ASP* 2.6 55.1 + - + +
244C VAL* 4.1 22.4 - - + -
252C SER* 3.8 1.5 + - - +
253C CYS* 1.3 75.4 - - - +
255C CYS* 1.3 74.3 + - - +
263C GLY 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C HIS 3.6 5.6 - - - -
241C ALA* 3.7 3.9 - - - +
254C VAL* 1.3 85.1 - - - +
256C ALA* 1.3 63.9 + - - +
257C VAL 4.0 0.2 + - - -
259C TRP* 3.6 22.7 - - + +
260C ALA* 3.5 2.0 - - - -
261C GLY 3.4 24.5 - - - -
263C GLY* 3.5 13.0 - - - +
266C CYS* 2.1 47.3 - - - -
----------------------------------------------------------
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