Contacts of the helix formed by residues 131 - 135 (chain L) in PDB entry 3STJ
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 131 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130L ALA* 1.3 73.9 - - - +
132L SER* 1.3 56.7 + - - +
133L ASP* 3.1 15.3 + - - +
134L LYS* 3.1 54.6 + - + +
135L LEU* 4.1 4.5 + - - +
199L ILE* 5.6 0.2 - - - +
222L ASN* 2.8 31.7 - - - +
225L ARG* 4.5 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 132 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130L ALA 3.3 2.0 + - - -
131L ASP* 1.3 70.0 - - - +
133L ASP* 1.3 63.3 + - - +
134L LYS 3.2 3.4 - - - -
135L LEU* 3.2 33.5 + - - +
162L LEU* 4.9 3.6 - - - +
176L ILE* 5.9 0.2 - - - +
199L ILE* 3.6 16.6 - - - +
220L PRO* 3.5 19.9 - - - +
221L SER* 3.4 15.3 - - - -
222L ASN* 3.1 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 133 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131L ASP* 3.1 13.5 + - - +
132L SER* 1.3 80.8 + - - +
134L LYS* 1.3 59.0 + - + +
135L LEU 3.3 3.3 + - - +
222L ASN* 3.2 17.3 - - - +
293L LYS* 2.9 37.3 + - + +
304L ARG* 2.6 44.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 134 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131L ASP* 3.1 42.0 + - + +
133L ASP* 1.3 77.1 - - + +
135L LEU* 1.3 64.3 + - - +
136L ARG* 3.9 8.7 + - - +
139L ASP* 4.3 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131L ASP 4.6 2.0 - - - +
132L SER* 3.2 28.7 + - - +
133L ASP 3.3 4.7 - - - +
134L LYS* 1.3 81.4 - - - +
136L ARG* 1.3 64.4 + - - +
139L ASP* 3.6 15.7 - - + +
159L VAL* 4.5 7.9 - - + -
162L LEU* 3.4 28.3 - - + +
176L ILE* 3.7 31.2 - - + -
193L ASN* 5.6 2.5 - - + -
199L ILE* 3.8 44.0 - - + -
293L LYS* 5.2 2.9 + - - -
----------------------------------------------------------
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