Contacts of the strand formed by residues 249 - 256 (chain A) in PDB entry 1ORI
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 PHE 249 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PHE* 4.3 5.4 - + - -
180A LEU* 4.9 6.1 - - + -
234A ILE* 3.7 24.2 - - + -
235A LYS* 3.7 43.1 - - + +
246A ASP 3.8 14.4 - - - +
247A LEU 3.9 5.6 - - - -
248A THR* 1.3 74.2 - - - +
250A THR* 1.3 67.1 + - - +
251A SER* 3.7 18.2 - - - -
317A ILE* 4.7 7.2 - - + -
318A GLY* 3.2 2.4 - - - -
319A MET* 2.8 74.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A PHE* 1.3 79.9 + - - +
251A SER* 1.3 69.1 + - - +
252A PRO* 4.5 3.2 - - + +
316A THR* 4.5 20.0 - - + +
317A ILE 3.4 11.9 - - - +
318A GLY* 3.9 6.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ILE* 2.7 43.6 + - - -
235A LYS* 5.3 0.3 - - - +
249A PHE* 3.7 9.0 - - - -
250A THR* 1.3 78.4 + - - +
252A PRO* 1.3 70.8 - - - +
253A PHE 4.0 0.2 + - - -
316A THR* 3.2 5.6 - - - -
317A ILE* 2.8 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A CYS* 4.8 1.0 - - - -
233A LEU 4.7 5.0 - - - +
234A ILE* 4.3 4.2 - - - +
250A THR* 4.5 2.7 - - + +
251A SER* 1.3 91.7 - - - +
253A PHE* 1.3 62.2 + - - +
254A CYS* 6.4 0.9 - - - -
315A GLY 3.4 11.0 - - - +
316A THR* 4.0 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A VAL* 4.0 13.2 - - + -
232A CYS* 3.8 17.0 - - + -
234A ILE* 4.0 10.3 - - + -
251A SER 4.1 2.5 - - - -
252A PRO* 1.3 78.2 - - - +
254A CYS* 1.3 68.0 + - - +
255A LEU* 4.0 30.5 - - + -
266A LEU* 4.1 13.2 - - + -
313A ILE* 4.5 4.9 - - + -
314A PHE* 3.5 19.5 - - - -
315A GLY* 3.0 41.8 + - - +
316A THR* 3.3 33.7 - - - -
317A ILE* 4.1 13.9 - - + -
333A ILE* 4.6 2.2 - - + -
335A LEU* 3.7 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ASN* 4.3 4.2 + - - +
232A CYS* 3.5 24.9 - - - +
252A PRO* 5.8 0.7 - - - -
253A PHE* 1.3 81.5 - - - +
255A LEU* 1.3 61.3 + - - +
256A GLN 4.3 0.2 + - - -
312A GLU* 3.1 20.4 - - - +
313A ILE 3.5 4.9 - - - -
314A PHE* 4.2 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A VAL* 3.6 17.9 - - + +
183A THR* 4.1 7.0 - - - +
184A ALA* 4.0 28.5 - - + +
229A THR* 3.8 14.4 - - + +
230A ASN* 3.6 23.1 - - - +
232A CYS* 3.7 15.0 - - + +
253A PHE* 4.0 25.8 - - + -
254A CYS* 1.3 79.4 - - - +
256A GLN* 1.3 61.2 + - - +
257A VAL 3.8 0.9 + - - -
266A LEU* 4.2 7.0 - - + -
312A GLU* 3.2 8.6 + - - -
313A ILE* 2.8 50.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A THR* 3.3 18.0 - - - -
230A ASN* 3.1 21.8 + - - +
254A CYS 4.3 0.2 - - - -
255A LEU* 1.3 71.9 - - - +
257A VAL* 1.3 68.7 + - - +
258A LYS* 3.0 32.3 + - - +
310A GLY* 3.8 27.6 + - - -
311A GLU 3.5 4.0 - - - -
312A GLU* 3.5 18.0 + - - +
----------------------------------------------------------
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