Contacts of the strand formed by residues 261 - 264 (chain B) in PDB entry 6A5T
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 ILE 261 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ILE* 3.6 21.3 - - + -
248B LYS 3.2 18.2 - - - +
249B LEU* 3.5 14.1 - - + -
259B ARG 4.9 0.9 - - - +
260B THR* 1.3 83.0 - - - +
262B LYS* 1.3 64.7 + - - +
273B PRO* 3.4 6.8 - - - +
274B ILE* 3.0 40.8 + - + +
305B MET 5.8 1.8 - - - +
306B LEU* 5.2 9.0 - - + -
309B CYS* 3.4 21.4 - - + -
375B VAL* 4.8 23.6 - - + -
378B LEU* 4.4 9.0 - - + -
379B LEU* 4.9 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ILE* 3.8 1.0 - - - -
248B LYS* 3.1 34.4 + - + +
250B TYR* 3.4 42.8 - - + +
260B THR* 4.3 12.4 + - - +
261B ILE* 1.3 78.8 - - - +
263B ALA* 1.3 66.6 + - - +
264B THR* 4.4 1.4 + - - +
271B ASP* 4.4 17.3 - - + -
272B ILE 3.1 7.0 - - - +
273B PRO* 3.9 29.1 - - + +
274B ILE* 3.3 4.3 - - - -
312B GLU* 5.5 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B MET* 5.3 2.0 - - + -
246B GLN 3.9 5.6 - - - +
247B ILE* 4.5 8.1 - - + -
262B LYS* 1.3 70.1 - - - +
264B THR* 1.3 66.1 + - - +
265B LEU* 4.5 13.9 - - + -
271B ASP* 3.8 2.9 - - - +
272B ILE* 2.3 51.1 + - + +
274B ILE* 3.0 16.7 - - + +
277B VAL* 4.5 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B THR 4.4 1.0 - - - +
245B MET* 3.5 2.4 - - - +
246B GLN* 2.9 42.6 + - + +
248B LYS* 2.9 34.3 + - - +
262B LYS* 4.4 1.2 + - - +
263B ALA* 1.3 79.4 + - - +
265B LEU* 1.3 78.1 + - - +
268B VAL* 5.3 4.3 - - + -
271B ASP* 3.7 24.8 + - - +
272B ILE* 6.3 0.2 - - - -
----------------------------------------------------------
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