Contacts of the strand formed by residues 330 - 334 (chain O) in PDB entry 4R2G
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 HIS 330 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D PHE* 3.6 42.4 + - - +
295O ASN 3.6 0.2 - - - +
296O CYS* 3.2 3.6 - - - -
297O THR* 3.0 45.2 + - + +
327O ARG* 3.8 11.4 - - - -
328O GLN 3.0 17.9 + - - -
329O ALA* 1.3 75.4 - - - +
331O CYS* 1.3 66.1 + - - +
332O ASN* 4.0 7.2 - - - -
383O PHE* 4.7 0.5 - - - -
415O ILE* 3.9 10.3 - - + -
416O LEU 3.3 13.0 - - - +
418O CYS* 3.8 4.2 - - - +
1R NAG 3.2 49.6 + - + +
2R NAG 5.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 331 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294O ILE* 4.3 9.2 - - + -
295O ASN 3.0 3.6 - - - +
296O CYS* 2.2 43.1 - - - -
330O HIS* 1.3 74.8 - - - +
332O ASN* 1.3 61.0 + - - +
376O PHE* 3.6 2.0 - - - -
385O CYS* 2.6 39.3 - - - -
414O ILE 3.5 1.2 - - - +
415O ILE* 3.5 2.8 - - - -
416O LEU* 2.8 58.1 + - + +
418O CYS* 3.5 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 332 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293O LYS 4.0 1.4 - - - +
294O ILE* 3.6 2.9 - - - -
295O ASN* 2.6 35.6 + - + +
330O HIS* 4.2 0.7 - - - -
331O CYS* 1.3 71.4 - - - +
333O ILE* 1.3 63.0 + - - +
413O THR* 4.4 10.2 + - - +
414O ILE 3.4 1.6 - - - +
415O ILE* 2.9 34.9 - - - +
513O NAG 4.0 15.4 + - - +
1R NAG 1.2 83.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 333 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292O VAL* 4.3 17.3 - - + -
293O LYS 4.2 2.2 - - - +
294O ILE* 3.5 34.3 - - + -
332O ASN* 1.3 77.6 - - - +
334O SER* 1.3 76.0 + - - +
335O ARG 3.3 0.2 + - - -
338O TRP* 4.3 13.2 - - + -
390O LEU* 3.6 36.3 - - + -
413O THR* 3.6 2.0 - - - -
414O ILE* 2.7 51.0 + - + +
416O LEU* 4.1 10.5 - - + -
449O ILE* 4.0 11.4 - - + -
513O NAG 3.7 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 334 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292O VAL* 5.4 0.4 - - - -
293O LYS 4.5 2.9 + - - -
333O ILE* 1.3 87.3 - - - +
335O ARG* 1.3 60.5 + - - +
336O ALA* 4.1 8.7 + - - +
337O GLN* 3.4 33.7 + - - +
338O TRP* 3.3 13.7 + - - +
412O ASP 4.4 5.6 + - - -
413O THR* 4.9 2.2 - - - +
513O NAG 3.1 22.3 - - - +
----------------------------------------------------------
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