Contacts of the strand formed by residues 355 - 359 (chain A) in PDB entry 1R4L
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 ASP 355 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 3.3 27.7 + - + +
326A GLY* 5.0 3.1 - - - +
330A ASN* 5.0 3.8 - - - +
350A ASP* 4.0 1.9 - - - +
351A LEU* 3.1 47.8 + - + +
352A GLY 2.8 14.9 + - - +
353A LYS 3.3 2.1 - - - +
354A GLY* 1.3 77.1 - - - +
356A PHE* 1.3 66.3 + - - +
357A ARG* 3.3 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A THR* 4.6 14.6 + - + +
326A GLY 5.7 0.4 - - - -
327A PHE* 3.0 34.6 + - + +
349A TRP 3.9 4.3 - - - -
350A ASP* 4.7 11.2 - - - -
352A GLY* 6.4 0.2 - - - -
354A GLY* 3.0 34.0 + - - -
355A ASP* 1.3 77.0 + - - +
357A ARG* 1.3 66.6 + - - +
379A ILE* 4.1 23.3 - - + -
382A ASP* 3.8 16.8 - - + -
383A MET* 3.2 67.1 - - + -
386A ALA* 4.5 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 4.6 3.6 + - - -
45A LEU* 3.7 23.0 - - - +
48A TRP* 3.1 60.0 - - + +
49A ASN* 5.6 0.2 - - - +
327A PHE* 4.1 2.5 - - - -
330A ASN* 3.2 45.0 - - + +
331A SER* 3.5 10.1 - - - +
348A ALA 3.6 0.2 - - - -
349A TRP* 2.6 43.4 + - + +
351A LEU* 3.6 11.5 - - + +
355A ASP* 3.3 31.2 + - - +
356A PHE* 1.3 80.6 - - - +
358A ILE* 1.3 62.2 + - - +
379A ILE* 3.9 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TRP* 4.4 1.8 - - - -
308A PHE* 4.1 14.4 - - + -
327A PHE* 3.7 25.4 - - + -
331A SER* 3.0 11.9 + - - +
332A MET 3.0 23.4 + - - +
333A LEU* 3.6 13.8 - - + +
347A THR 3.4 8.7 - - - +
348A ALA* 3.8 14.1 - - - -
349A TRP 4.4 0.4 - - - +
357A ARG* 1.3 80.8 - - - +
359A LEU* 1.3 67.6 - - - +
360A MET* 4.1 11.0 - - + -
375A GLU* 3.8 37.9 - - + +
376A MET* 3.9 6.5 - - - +
379A ILE* 3.9 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TRP* 4.0 19.3 - - + -
51A ASN* 2.9 38.1 - - + +
52A THR* 3.3 19.3 - - - +
332A MET* 3.5 18.6 - - + +
342A ALA* 4.8 2.7 - - + -
343A VAL* 2.8 27.8 - - + +
344A CYS* 4.5 3.4 - - - -
345A HIS 4.0 6.3 - - - +
346A PRO* 3.3 2.1 - - - +
347A THR* 2.9 40.6 + - - +
349A TRP* 4.2 3.4 - - - +
358A ILE* 1.3 71.0 - - - +
360A MET* 1.3 63.5 + - - +
361A CYS* 5.2 3.1 - - - -
----------------------------------------------------------
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