Contacts of the strand formed by residues 278 - 283 (chain A) in PDB entry 1RWO
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 278 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A THR* 3.7 23.3 - - + -
232A LEU* 4.9 5.2 - - + -
265A LEU* 3.3 26.9 + - + +
266A ASN* 5.2 2.1 - - - +
267A THR* 5.7 2.4 + - - -
273A LEU* 2.7 42.5 + - + -
274A LYS* 4.7 1.0 - - - +
275A ASP 4.6 1.0 - - - +
276A LYS 2.8 18.0 + - - +
277A PRO* 1.3 73.5 - - - +
279A VAL* 1.3 62.3 + - - +
280A ILE* 3.8 1.6 + - - -
325B LYS 3.3 25.9 + - - -
326B ASP* 2.8 13.2 + - - +
327B PHE* 3.5 38.0 - - + -
328B ILE* 3.0 25.2 + - - +
394B LEU* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A THR* 3.0 9.9 + - - +
231A PHE* 3.3 35.9 - - + +
232A LEU* 2.7 34.0 + - - +
277A PRO* 5.0 0.2 - - + -
278A LYS* 1.3 75.4 - - - +
280A ILE* 1.3 58.8 + - - +
281A ILE* 4.1 8.7 + - + -
328B ILE* 3.3 18.6 - - + +
366B VAL* 4.6 2.7 - - + -
370B PHE* 3.7 29.8 - - + -
398B PHE* 3.9 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LEU* 3.3 20.0 - - + -
234A PHE* 4.0 21.8 - - + -
258A LEU* 4.4 3.6 - - + -
261A ILE* 3.9 21.3 - - + -
262A PHE* 4.0 20.9 - - + -
265A LEU* 5.7 0.4 - - + -
278A LYS 4.5 3.1 - - - +
279A VAL* 1.3 77.9 - - - +
281A ILE* 1.3 60.1 + - - +
282A ILE* 3.7 24.6 + - + -
327B PHE* 3.8 32.1 - - + -
328B ILE 2.7 13.1 + - - +
329B ALA* 3.1 5.1 - - + +
330B PHE* 2.7 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A MET* 4.3 5.2 - - + -
231A PHE* 3.8 31.6 - - + -
232A LEU 2.7 11.9 + - - +
233A VAL* 3.4 22.3 - - + -
234A PHE* 2.8 33.1 + - - +
279A VAL* 4.1 11.2 - - + -
280A ILE* 1.3 77.9 - - - +
282A ILE* 1.3 60.1 + - - +
330B PHE* 3.5 11.7 - - + -
349B PHE* 3.6 26.5 - - + -
350B ILE* 4.3 11.7 - - + -
353B LEU* 3.8 28.5 - - + -
357B MET* 5.9 1.3 - - + -
370B PHE* 4.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A PHE* 3.3 20.0 - - + +
243A ILE* 3.9 32.3 - - + -
258A LEU* 3.5 33.7 - - + -
261A ILE* 4.8 0.7 - - + -
280A ILE* 3.7 18.2 - - + -
281A ILE* 1.3 76.1 - - - +
283A GLN* 1.3 60.4 + - - +
284A ALA* 4.0 16.2 - - + +
329B ALA* 5.0 3.1 - - + -
330B PHE 3.1 8.9 + - - +
331B CYS* 3.5 24.1 - - + +
332B SER* 3.0 28.1 + - - -
349B PHE* 3.8 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG* 3.9 6.7 - - - +
185A ASP* 5.1 0.2 - - - +
234A PHE 2.8 12.9 + - - +
235A MET* 3.4 7.6 - - + +
236A SER 3.1 23.2 + - - +
281A ILE* 4.2 1.2 - - - +
282A ILE* 1.3 69.0 - - - +
284A ALA* 1.3 66.9 + - - +
501A BTH 2.7 28.0 + - - +
332B SER* 3.4 6.6 - - - -
339B SER* 3.7 20.5 - - - -
340B TRP 3.8 9.4 + - - +
347B SER* 3.5 31.6 + - - +
349B PHE* 3.3 30.4 + - + +
350B ILE* 3.8 22.0 - - + -
----------------------------------------------------------
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