Contacts of the strand formed by residues 318 - 323 (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 ARG 318 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B VAL* 3.6 27.2 - - + +
276B VAL 3.6 3.4 - - - +
277B LYS* 3.7 29.7 - - + +
278B LYS* 3.6 3.5 - - - +
314B GLN* 3.3 7.4 - - - +
315B THR* 3.0 39.8 + - - +
317B SER* 1.3 104.0 + - - +
319B LEU* 1.3 63.7 + - - +
320B PHE* 3.5 19.7 - - + -
554B LEU* 3.8 22.1 - - - +
555B TPO 2.6 55.5 + - - -
557B ASP* 3.2 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LYS 3.7 0.7 - - - +
275B VAL* 3.4 5.0 - - - +
276B VAL* 2.8 45.5 + - + +
278B LYS* 3.7 28.7 - - + -
281B VAL* 4.7 7.0 - - + -
290B VAL* 4.2 21.8 - - + -
313B PHE 3.8 1.8 - - - -
314B GLN* 4.1 3.1 - - + -
318B ARG* 1.3 74.0 - - - +
320B PHE* 1.3 65.7 + - - +
321B PHE* 4.3 9.4 - - + -
570B PHE* 3.8 31.2 - - + -
573B PHE* 3.7 43.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 4.0 6.5 - - + -
273B MET* 3.7 28.0 - - + -
274B LYS 3.4 3.6 - - - +
275B VAL* 3.7 28.0 - - + -
311B SER 3.9 0.2 - - - +
312B CYS* 3.2 25.6 - - - +
313B PHE* 2.9 53.2 + + + +
315B THR* 3.6 29.2 - - + -
318B ARG* 3.5 37.7 - - + -
319B LEU* 1.3 74.8 - - - +
321B PHE* 1.3 64.1 + - - +
322B VAL 4.0 0.4 - - - -
554B LEU* 4.0 18.8 - - + -
573B PHE* 3.6 4.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B MET* 3.4 1.9 - - - -
274B LYS* 2.8 60.6 + - + -
276B VAL* 4.3 20.4 - - + -
290B VAL* 4.5 17.3 - - + -
293B GLU* 4.7 10.3 - - + -
294B LYS* 3.8 31.9 - - + -
297B PHE* 4.2 22.9 - + + -
309B LEU* 4.1 3.4 - - + -
311B SER 3.6 4.3 - - - -
312B CYS* 4.0 11.9 - - - -
319B LEU* 4.3 9.0 - - + -
320B PHE* 1.3 73.9 - - - +
322B VAL* 1.3 64.1 + - - +
323B ILE* 3.6 16.0 + - + +
573B PHE* 3.7 25.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PHE* 3.9 14.8 - - + -
262B VAL* 4.8 0.9 - - + -
271B TYR* 3.4 39.3 - - + -
272B ALA 3.5 3.6 - - - +
273B MET* 4.2 11.2 - - + +
309B LEU* 3.3 4.3 - - - +
310B HIS* 2.6 43.7 + - + +
311B SER* 2.8 25.3 + - - +
313B PHE* 3.5 37.7 - - + -
321B PHE* 1.3 71.5 - - - +
323B ILE* 1.3 53.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B VAL* 5.3 5.2 - - + -
271B TYR* 3.4 11.4 - - - +
272B ALA* 2.9 47.1 + - + +
274B LYS* 4.6 20.4 - - + +
297B PHE* 3.8 32.1 - - + -
307B VAL* 4.0 15.3 - - + -
308B GLY 3.3 11.9 - - - +
309B LEU* 4.1 3.4 - - + -
310B HIS* 4.2 1.6 - - - +
321B PHE* 3.7 16.8 - - + +
322B VAL* 1.3 80.7 - - - +
324B GLU* 1.3 69.4 + - - +
325B TYR 3.3 0.3 + - - -
386B THR* 5.8 2.9 - - - +
----------------------------------------------------------
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