Contacts of the strand formed by residues 258 - 264 (chain B) in PDB entry 3A8X
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 LYS 258 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B VAL* 3.9 30.6 - - + +
252B GLY 3.7 4.5 - - - +
253B ARG* 3.5 30.4 - - - +
257B ALA* 1.3 75.2 - - - +
259B VAL* 1.3 63.1 + - - +
260B LEU* 4.1 15.7 - - + -
273B MET 3.5 2.1 - - - +
274B LYS* 3.6 1.0 - - - -
275B VAL* 2.8 42.2 + - + +
550B GLU* 3.9 4.2 + - - -
551B PRO* 4.8 0.6 + - - +
553B GLN* 2.7 34.2 + - - +
554B LEU* 4.2 4.2 - - + +
555B TPO 2.8 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B VAL* 3.7 4.9 - - - +
251B ILE* 2.8 45.2 + - + -
252B GLY* 2.7 33.5 + - - +
253B ARG* 4.9 1.1 - - - +
254B GLY 5.3 2.5 - - - +
257B ALA* 5.1 4.3 - - + +
258B LYS* 1.3 78.5 - - - +
260B LEU* 1.3 65.7 + - - +
272B ALA* 4.1 15.5 - - + -
273B MET 3.3 9.4 - - - +
274B LYS* 4.6 19.1 - - + +
323B ILE* 5.3 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LEU* 4.6 24.5 - - + -
249B ARG 3.2 16.6 - - - +
250B VAL* 4.0 20.2 - - + -
251B ILE* 4.0 5.6 - - - -
258B LYS* 4.1 14.4 - - + -
259B VAL* 1.3 79.5 - - - +
261B LEU* 1.3 67.1 + - - +
262B VAL* 4.1 9.9 - - + -
271B TYR 3.7 0.2 - - - +
272B ALA* 3.3 4.0 - - - -
273B MET* 2.6 43.9 + - + +
275B VAL* 3.6 28.9 - - + -
552B VAL* 4.8 1.3 - - + -
553B GLN 4.3 15.9 - - - +
554B LEU* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LEU 3.9 0.2 - - - -
248B LEU* 2.8 38.0 + - + -
249B ARG* 2.8 20.4 + - + +
251B ILE* 3.9 16.7 - - + +
260B LEU* 1.3 71.2 - - - +
262B VAL* 1.3 77.0 + - - +
270B ILE* 4.1 10.3 - - + -
271B TYR 3.5 11.2 - - - +
325B TYR* 3.8 42.2 - - + +
538B PHE* 3.7 42.0 - - + -
540B LEU* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PHE* 3.6 31.4 - - + -
246B ASP 3.2 9.2 - - - +
247B LEU* 4.0 13.0 - - + -
248B LEU* 4.3 5.4 - - - -
260B LEU* 3.9 4.5 - - + +
261B LEU* 1.3 80.3 - - - +
263B ARG* 1.3 60.3 + - - +
270B ILE* 3.2 8.5 - - - +
271B TYR* 2.8 50.1 + - + +
273B MET* 3.6 47.3 - - + -
322B VAL* 4.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PHE* 3.3 5.7 - - - -
246B ASP* 2.8 55.7 + - + +
248B LEU* 4.1 16.2 - - + +
262B VAL* 1.3 73.6 - - - +
264B LEU* 1.3 75.1 + - - +
265B LYS* 3.2 6.3 + - - +
268B ASP* 3.2 48.3 + - - +
269B ARG 3.5 8.1 - - - +
270B ILE* 3.6 12.6 - - + +
537B GLU* 4.0 8.5 + - - -
538B PHE* 3.4 34.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A PRO* 3.7 15.0 - - + +
240B LEU* 3.8 27.4 - - + -
244B ASP* 3.3 20.2 - - + +
245B PHE* 3.7 25.4 - - + -
262B VAL 4.3 0.2 + - - -
263B ARG* 1.3 68.7 - - - +
265B LYS* 1.3 58.1 + - - +
266B LYS* 3.3 16.8 + - + +
267B THR* 3.3 17.6 + - + +
268B ASP* 2.8 34.8 + - - -
269B ARG 2.9 14.2 + - - +
271B TYR* 4.0 7.8 - - + -
310B HIS* 3.6 32.1 - - + +
----------------------------------------------------------
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