Contacts of the strand formed by residues 378 - 382 (chain B) in PDB entry 4O28
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 378 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LYS* 2.7 32.8 + - - +
321B VAL* 3.7 38.8 - - + -
325B LEU* 5.5 1.1 - - + -
349B ARG* 6.2 0.2 - - - -
350B VAL* 3.4 17.5 - - + +
352B GLN* 4.4 4.7 - - + +
364B ILE* 4.5 0.2 - - + -
368B MET* 3.7 27.6 - - + -
375B ILE* 3.2 21.7 - - + +
376B GLU 3.2 0.8 - - - -
377B ASN* 1.3 80.9 - - + +
379B ALA* 1.3 74.1 + - - +
380B PHE* 3.7 36.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B TYR 4.1 8.5 - - - +
189B LYS* 3.7 14.6 - - + +
350B VAL 3.0 8.8 + - - +
351B ILE* 3.3 11.8 - - + -
352B GLN 3.0 21.5 + - - -
378B ILE* 1.3 80.2 - - - +
380B PHE* 1.3 69.0 + - - +
601B 1QS 3.6 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LEU* 3.8 16.4 - - + -
189B LYS* 2.8 18.9 + - + +
190B LEU* 3.4 14.7 - - + -
191B HIS* 2.8 33.9 + - - +
351B ILE* 4.1 6.7 - - - +
352B GLN* 3.2 17.5 - - + +
356B VAL* 4.0 18.2 - - + -
361B LEU* 3.4 27.4 - - + -
364B ILE* 3.8 35.2 - - + -
365B VAL* 3.8 20.0 - - + -
378B ILE* 3.7 37.9 - - + -
379B ALA* 1.3 77.2 - - - +
381B GLY* 1.3 54.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LEU* 4.2 2.9 - - - -
191B HIS 3.2 8.3 - - - -
193B PHE* 3.8 27.4 - - - -
351B ILE* 4.3 0.6 - - - +
352B GLN 2.9 10.1 + - - -
353B GLY* 3.4 19.5 - - - +
356B VAL* 3.6 15.6 - - - +
380B PHE* 1.3 74.6 - - - +
382B SER* 1.3 61.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PHE* 3.4 37.4 - - - -
168B GLN* 4.9 3.9 + - - -
190B LEU* 3.9 12.3 - - - +
191B HIS 2.8 12.9 + - - -
192B ASP* 3.9 4.5 - - - +
193B PHE* 2.9 30.9 + - - +
194B GLY* 3.3 14.4 + - - -
353B GLY 5.2 3.6 - - - -
356B VAL 4.4 14.9 + - - -
381B GLY* 1.3 74.6 - - - -
----------------------------------------------------------
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