Contacts of the strand formed by residues 320 - 327 (chain B) in PDB entry 4EFO
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 THR 320 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B PHE* 3.5 4.7 - - - -
315B SER* 2.9 34.4 + - - -
318B GLN* 3.3 34.6 - - + +
319B MET* 1.3 77.2 - - - +
321B ALA* 1.3 61.7 - - - +
322B HIS* 2.9 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A SER* 4.0 13.9 + - - +
313B VAL 3.5 6.5 - - - +
314B PHE* 3.8 15.6 - - + -
320B THR* 1.3 75.9 - - - +
322B HIS* 1.3 69.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B HIS* 3.6 5.4 + - - +
313B VAL* 2.8 46.8 + - + +
315B SER* 3.9 15.1 + - - -
320B THR* 2.9 49.2 + - - -
321B ALA* 1.3 76.8 + - - +
323B LYS* 1.3 63.0 + - - +
324B ILE* 4.1 3.8 - - + -
342B GLN* 3.2 52.8 + - + +
343B THR* 4.0 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B VAL* 3.8 22.4 - - + -
311B ILE 3.7 3.6 - - - -
312B HIS* 4.0 24.2 - - - +
322B HIS* 1.3 75.6 - - - +
324B ILE* 1.3 62.4 + - - +
325B TYR* 3.7 33.9 + - + +
342B GLN* 2.8 22.6 + - - -
375B GLU* 6.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B MET 3.5 0.9 - - - +
310B VAL* 3.4 4.3 - - - -
311B ILE* 2.8 41.7 + - + +
313B VAL* 3.7 29.2 - - + -
322B HIS* 4.7 5.2 - - + +
323B LYS* 1.3 72.7 - - - +
325B TYR* 1.3 63.7 + - - +
326B ILE* 3.8 5.8 + - + +
335B PHE* 4.1 23.1 - - + -
338B LEU* 3.7 50.5 - - + +
339B VAL* 4.2 8.7 - - + -
342B GLN* 3.3 30.7 - - + +
343B THR* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ARG* 4.0 40.4 - - + +
309B MET 3.4 7.0 - - - +
310B VAL* 4.1 18.8 - - + -
323B LYS* 3.7 42.0 + - + +
324B ILE* 1.3 69.4 - - - +
326B ILE* 1.3 62.5 + - - +
338B LEU* 3.5 16.8 - - - +
342B GLN* 5.2 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ARG* 4.8 4.3 - - - +
309B MET* 2.8 39.1 + - + +
311B ILE* 3.6 31.2 - - + -
324B ILE* 4.3 4.7 - - + +
325B TYR* 1.3 76.1 - - - +
327B HIS* 1.3 68.3 + - - +
330B ASN* 3.4 30.7 - - + +
331B THR 4.1 2.2 - - - +
334B ILE* 4.3 0.2 - - + -
335B PHE* 3.9 40.8 - - + +
338B LEU* 4.0 12.8 - - + -
367B ALA* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ASP* 3.2 35.6 + - + -
307B HIS* 3.2 31.9 - + + +
308B ARG* 4.8 1.6 - - - +
326B ILE* 1.3 73.9 - - - +
328B SER* 1.3 58.9 + - - +
329B TYR* 2.9 49.1 + + + +
330B ASN* 2.9 48.2 + - - +
367B ALA* 3.5 8.1 - - - +
----------------------------------------------------------
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