Contacts of the strand formed by residues 327 - 331 (chain D) in PDB entry 1I3O
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 327 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C THR* 3.9 17.0 - - + -
265C PHE* 3.5 29.6 - - + -
266C ARG* 3.9 4.3 - - + -
278C LYS* 3.5 25.1 - - + -
280C PHE* 3.4 35.0 - + - -
323D VAL 3.9 17.5 - - - -
324D GLU* 3.4 29.1 + - - +
325D ALA 3.3 8.2 - - - -
326D ASP* 1.3 78.6 - - - +
328D LEU* 1.3 60.3 + - - +
329D TYR* 3.5 35.0 - + + +
393D MET* 2.8 32.9 + - + +
394D LEU* 3.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 328 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C LYS 2.9 7.3 + - - +
279C LEU* 3.2 20.9 - - + +
280C PHE* 2.8 33.1 + - - +
327D PHE* 1.3 76.8 - - - +
329D TYR* 1.3 63.5 + - - +
330D ALA* 4.0 2.9 + - + +
366D PHE* 3.2 42.8 - - + -
367D MET* 3.4 16.4 - - + -
370D LEU* 4.1 4.3 - - + -
389D ILE* 4.2 8.7 - - + -
390D VAL 3.3 9.2 - - - +
392D SER* 3.2 35.9 - - - +
394D LEU* 3.7 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 329 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C LEU* 5.6 4.7 - - + -
259C LYS* 5.0 3.1 + - - -
262C THR* 3.3 36.5 - - + +
280C PHE* 3.4 26.0 - + + +
282C ILE* 4.7 5.8 - - + -
324D GLU* 4.6 6.6 + - - +
327D PHE* 3.5 37.7 - + + +
328D LEU* 1.3 74.1 - - - +
330D ALA* 1.3 60.0 + - - +
331D TYR* 3.4 35.5 + + + -
388D CYS 3.6 0.2 - - - +
390D VAL* 2.9 53.1 + - + +
393D MET* 3.4 29.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 330 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C PHE 2.9 12.8 + - - +
281C ILE* 3.6 15.1 - - + -
282C ILE* 3.1 21.7 + - - -
328D LEU* 4.0 4.3 + - + -
329D TYR* 1.3 68.6 - - - +
331D TYR* 1.3 63.7 + - - +
349D PHE* 3.7 18.7 - - + -
353D LEU* 6.0 0.2 - - + -
366D PHE* 5.5 2.0 - - + -
370D LEU* 4.1 30.5 - - + -
388D CYS 4.0 3.4 - - - -
389D ILE* 4.8 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 331 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C GLY* 5.8 5.1 - - - -
258C LEU* 4.0 30.0 - - + +
282C ILE* 3.9 21.8 - - + +
286C ARG* 3.4 53.6 + - + +
329D TYR* 3.6 32.3 - + + -
330D ALA* 1.3 73.8 - - - +
332D SER* 1.3 60.7 + - - +
333D THR 3.4 4.9 - - - +
349D PHE* 3.6 4.5 - - - -
387D PRO* 3.5 6.1 - - - +
388D CYS* 2.8 34.8 + - + +
390D VAL* 3.7 29.2 - - + -
----------------------------------------------------------
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