Contacts of the strand formed by residues 361 - 366 (chain J) in PDB entry 1I43
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 ALA 361 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214J LEU* 3.4 16.2 - - + +
239J PHE* 3.7 36.3 - - + -
262J PHE* 4.7 3.7 - - + -
339J TYR* 3.4 21.3 - - - -
358J PHE 4.5 0.7 - - - +
359J GLY* 3.3 1.9 - - - -
360J GLY* 1.3 79.0 - - - +
362J VAL* 1.3 59.3 + - - +
389J PHE* 5.0 8.5 - - + -
423J ARG* 5.1 9.0 - - + -
424J PHE 3.7 5.4 - - - +
425J SER* 4.7 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 362 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321J ALA* 3.7 20.2 - - + +
325J ALA* 4.5 6.3 - - + -
328J LEU* 4.5 10.5 - - + -
337J VAL* 4.5 13.0 - - + -
338J TYR 4.0 8.7 - - - +
339J TYR* 3.5 19.5 - - + -
361J ALA* 1.3 81.0 - - - +
363J SER* 1.3 69.2 - - - +
364J PHE* 4.3 11.3 - - + -
422J VAL 4.0 0.3 - - - +
423J ARG* 4.9 0.9 - - - +
424J PHE* 2.7 42.2 + - + +
426J PHE* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 363 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212J PRO* 2.9 30.9 + - - +
214J LEU* 4.4 3.0 - - - +
337J VAL* 3.7 0.2 - - - -
338J TYR* 2.6 48.4 + - - +
362J VAL* 1.3 74.5 - - - +
364J PHE* 1.3 60.0 + - - +
421J LEU* 4.2 12.7 - - - +
422J VAL 3.3 7.2 - - - -
423J ARG* 2.9 28.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 364 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328J LEU* 3.7 35.4 - - + -
334J VAL* 4.2 11.4 - - + -
336J HIS 3.1 16.4 - - - +
337J VAL* 3.5 15.5 - - + +
338J TYR* 4.1 3.3 - - - -
362J VAL* 4.3 4.7 - - + -
363J SER* 1.3 82.0 - - - +
365J GLU* 1.3 64.1 + - - +
366J VAL* 4.0 18.2 - - + -
376J PHE* 3.7 30.7 - + - -
421J LEU* 4.2 2.2 - - - +
422J VAL* 2.9 57.8 + - + +
424J PHE* 4.0 24.5 - + + -
438J ILE* 5.5 1.1 - - + -
442J LEU* 5.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 365 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213J PHE* 4.6 4.2 - - - -
334J VAL* 3.7 5.7 - - - +
335J ARG* 3.0 36.0 + - + +
336J HIS* 2.8 31.0 + - + +
338J TYR* 2.9 39.7 + - + -
364J PHE* 1.3 74.0 - - - +
366J VAL* 1.3 62.9 + - - +
416J GLY 5.0 0.7 - - - +
418J MET* 4.2 19.1 - - - +
420J ASN* 3.6 24.3 - - + +
421J LEU* 4.5 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 366 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333J LYS 3.8 10.1 - - - +
334J VAL* 4.7 0.9 - - + +
335J ARG* 4.0 5.2 + - - +
364J PHE* 4.0 16.2 - - + -
365J GLU* 1.3 77.5 - - - +
367J ASP* 1.3 71.4 + - - +
368J GLY 2.9 8.8 + - - +
372J THR* 4.5 4.7 - - + -
373J THR* 3.8 19.1 - - + +
376J PHE* 4.0 27.1 - - + -
420J ASN* 3.1 26.4 + - - +
422J VAL* 4.4 9.2 - - + -
442J LEU* 5.0 4.9 - - + -
445J ILE* 3.8 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