Contacts of the strand formed by residues 392 - 397 (chain A) in PDB entry 1FR8
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 THR 392 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A GLY* 3.1 18.1 + - - -
215A ILE 2.9 15.9 + - - -
216A TYR* 3.5 14.5 - - + -
217A VAL* 2.7 28.6 + - - +
242A ASP* 5.3 0.2 - - - +
385A VAL* 4.2 5.6 - - + -
386A GLN 3.5 5.2 - - - +
387A ARG* 3.0 45.3 + - - +
391A TYR* 1.3 73.9 - - - +
393A LYS* 1.3 63.3 + - - +
394A ILE* 4.0 21.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PHE* 4.3 15.9 - - - -
192A GLN* 5.1 7.0 + - - +
217A VAL* 3.6 13.0 - - + +
219A ASN* 3.6 37.2 - - + +
384A GLU 3.8 1.2 - - - +
385A VAL* 3.4 2.8 - - - -
386A GLN* 2.8 60.7 + - + +
388A TYR* 3.9 32.3 + - + +
391A TYR* 3.9 16.1 + - + +
392A THR* 1.3 74.5 - - - +
394A ILE* 1.3 61.7 - - - +
395A THR* 4.0 3.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A TYR* 4.2 18.8 - - + -
217A VAL 3.0 7.8 + - - +
218A ILE* 3.6 23.9 - - + +
219A ASN* 2.9 25.6 + - - +
238A GLU* 3.6 34.1 - - + +
242A ASP* 5.9 0.7 - - - +
382A VAL* 3.9 17.9 - - + -
384A GLU 3.4 9.2 - - - +
385A VAL* 4.1 11.0 - - + -
392A THR* 4.1 14.1 - - + -
393A LYS* 1.3 76.5 - - - +
395A THR* 1.3 62.0 + - - +
396A VAL* 3.6 23.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ASN* 3.1 33.4 + - - +
221A ALA* 3.8 22.9 - - + -
382A VAL* 3.7 0.7 - - - -
383A LEU* 2.9 31.2 + - + -
384A GLU* 2.9 27.1 + - + +
386A GLN* 4.0 17.8 + - - -
393A LYS* 4.0 3.1 + - - -
394A ILE* 1.3 68.8 - - - +
396A VAL* 1.3 68.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ILE* 4.3 5.2 - - + -
219A ASN 3.0 5.9 + - - +
220A GLN* 4.0 1.4 - - - +
221A ALA* 3.0 28.3 + - - +
231A LEU* 3.8 20.4 - - + -
234A VAL* 4.1 18.4 - - + -
380A TYR* 4.3 6.7 - - + -
381A MET 3.3 8.5 - - - +
382A VAL* 4.0 13.5 - - + -
383A LEU* 4.1 1.3 - - - +
394A ILE* 3.6 24.0 - - + +
395A THR* 1.3 83.0 - - - +
397A ASP* 1.3 60.5 + - - +
398A ILE* 3.6 23.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ALA* 4.5 5.6 - - + -
380A TYR* 3.4 6.6 - - - +
381A MET* 2.8 58.3 + - + +
383A LEU* 4.0 20.0 - - + +
396A VAL* 1.3 71.9 - - - +
398A ILE* 1.3 59.9 + - - +
399A GLY* 3.0 20.6 + - - +
----------------------------------------------------------
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