Contacts of the strand formed by residues 535 - 539 (chain C) in PDB entry 3GZN
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 535 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C GLU* 2.6 25.4 + - - +
528C ILE 4.0 0.2 - - - +
529C TYR* 3.9 2.8 - - - -
530C SER* 3.0 26.1 + - - -
533C SER* 2.7 35.2 + - - +
534C GLN* 1.3 83.2 - - - +
536C SER* 1.3 60.6 + - - +
353D THR* 4.2 3.1 - - - -
355D THR* 3.6 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 536 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C GLU* 3.9 5.4 - - - +
527C TYR* 2.8 38.7 + - - -
528C ILE 3.1 10.3 - - - -
529C TYR* 4.3 7.0 - - - -
535C THR* 1.3 77.7 - - - +
537C ALA* 1.3 64.8 + - - +
352D TYR* 5.0 0.2 - - - -
353D THR* 2.5 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 537 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C ASN* 6.0 0.7 - - - +
429C GLU* 3.9 18.8 - - + +
526C THR 3.5 2.9 - - - +
527C TYR* 4.3 3.3 - - - -
528C ILE 3.0 31.2 + - - +
536C SER* 1.3 77.9 + - - +
538C THR* 1.3 62.3 + - - +
539C PHE* 3.5 30.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 538 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C GLU* 5.1 0.3 - - - +
523C PHE* 3.8 28.9 - - + -
524C ASN* 4.0 21.1 - - + +
526C THR 3.3 9.6 - - - +
527C TYR* 3.7 9.1 - - - +
537C ALA* 1.3 73.6 - - - +
539C PHE* 1.3 65.6 + - - +
540C GLN* 5.3 2.3 - - + +
351D LEU* 3.3 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 539 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C GLU* 3.9 17.0 - - + +
422C SER* 3.4 28.3 - - - -
428C ASN* 3.2 27.8 - - - -
429C GLU* 3.9 10.8 - - + -
430C ILE* 3.7 25.8 - - + -
524C ASN 2.9 16.1 - - - +
526C THR* 2.7 29.8 + - + +
528C ILE* 4.2 12.1 - - + -
537C ALA* 3.5 37.0 - - + -
538C THR* 1.3 74.5 - - - +
540C GLN* 1.3 65.8 + - - +
541C LEU* 3.9 18.4 - - + -
----------------------------------------------------------
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