Contacts of the helix formed by residues 5329 - 5334 (chain b) in PDB entry 2AXT
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 PRO5329 (chain b).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5057b ARG 3.3 4.5 - - - +
5058b GLN* 3.2 20.4 - - - -
5059b GLY* 3.7 9.4 - - - +
5328b GLY* 1.3 88.2 - - - +
5330b MET* 1.3 64.4 + - - +
5331b ASN* 2.9 13.9 + - + +
5332b LYS* 2.9 25.0 + - + +
5437b LEU* 5.1 6.5 - - + -
5444b ARG* 3.6 6.1 - - - -
5445b THR 5.8 0.4 - - - +
5517b CLA 3.2 30.0 - - - -
5530b MGE 3.7 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET5330 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5056b TRP* 4.0 29.6 - - - +
5057b ARG* 2.9 26.0 + - - +
5059b GLY* 4.4 0.8 - - - +
5316b GLY 3.2 26.9 - - - +
5317b ASN* 3.7 19.7 - - - +
5318b ASN 4.6 4.7 - - - +
5329b PRO* 1.3 71.6 - - - +
5331b ASN* 1.3 57.3 + - - +
5332b LYS 3.2 0.4 - - - -
5333b GLY* 3.1 16.9 + - - -
5334b ASP* 3.6 14.7 + - - +
5443b PHE* 5.9 0.2 - - - -
5444b ARG* 3.4 34.3 + - - +
5445b THR* 3.8 11.4 + - - +
5446b SER* 3.6 30.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN5331 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5053b ASN* 3.0 24.5 + - - +
5057b ARG* 3.2 36.3 + - - +
5058b GLN* 3.9 11.5 - - - +
5329b PRO* 2.9 4.5 + - + +
5330b MET* 1.3 74.0 - - - +
5332b LYS* 1.3 52.4 + - - +
5333b GLY 3.0 2.6 + - - -
5335b GLY* 3.2 28.2 - - - +
5336b ILE* 3.8 14.9 - - + +
5337b ALA 4.5 0.2 + - - -
5437b LEU* 3.4 26.1 - - + +
5439b SER* 2.4 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS5332 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5327b THR 4.6 0.7 - - - +
5329b PRO* 2.9 17.3 + - + +
5331b ASN* 1.3 78.4 - - - +
5333b GLY* 1.3 58.2 + - - +
5437b LEU* 3.6 27.5 + - + +
5438b ASN* 3.6 20.4 + - - +
5439b SER* 3.0 6.1 - - - +
5440b ASP* 2.9 34.4 + - - +
5444b ARG* 3.3 31.6 - - - +
5530b MGE 3.7 39.1 + - - +
216m LMT 4.7 18.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY5333 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5330b MET 3.1 7.5 + - - -
5331b ASN 3.0 1.6 - - - -
5332b LYS* 1.3 82.3 - - - +
5334b ASP* 1.3 61.5 + - - -
5335b GLY 3.3 0.9 + - - -
5439b SER* 3.3 3.6 - - - -
5440b ASP* 3.7 2.5 - - - -
5441b GLY 2.6 28.4 + - - -
5442b ILE 2.9 29.8 - - - -
5443b PHE* 4.8 1.1 - - - -
5444b ARG* 3.7 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP5334 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5057b ARG* 2.7 31.6 + - - -
5314b TYR* 2.3 36.1 + - - +
5316b GLY* 4.1 1.6 - - - +
5330b MET 3.6 5.0 + - - +
5333b GLY* 1.3 72.6 - - - +
5335b GLY* 1.3 57.6 + - - +
5432b PHE* 3.3 25.8 - - + +
5434b THR* 3.8 9.0 - - - +
5441b GLY 5.4 0.2 - - - -
5442b ILE 4.4 2.6 + - - +
5443b PHE* 3.8 15.0 - - + +
5202o GLN* 3.3 43.2 - - + +
----------------------------------------------------------
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