Contacts of the helix formed by residues 5066 - 5070 (chain d) in PDB entry 3A0B
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 SER5066 (chain d).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5051d GLY 4.0 1.1 + - - -
5052d THR 3.6 9.9 - - - -
5053d THR 2.6 22.7 + - - -
5054d PHE* 3.1 19.9 + - - -
5055d VAL 3.1 18.5 + - - -
5065d SER* 1.3 82.0 - - - +
5067d TYR* 1.3 57.7 + - - +
5068d LEU* 2.8 15.0 + - - +
5069d GLU* 2.9 34.9 + - - +
5071d CYS* 3.2 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR5067 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5048d TRP* 5.1 1.0 - - - -
5052d THR* 2.9 25.2 + - + +
5053d THR* 3.0 39.0 - - + +
5066d SER* 1.3 71.1 + - - +
5068d LEU* 1.3 57.2 + - - +
5070d GLY 2.6 21.3 + - - -
5071d CYS 4.0 11.0 - - - -
5073d PHE* 3.6 23.7 + - - -
5076d VAL* 3.2 32.1 - - + -
6050d BCR 5.7 1.1 - - + -
6059d MGE 2.9 86.4 + - - +
5037f ILE* 3.4 16.6 - - + -
5040f MET* 3.7 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5068 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5053d THR 3.6 3.6 + - - +
5054d PHE* 4.3 14.8 - - + +
5066d SER* 2.8 14.7 + - - +
5067d TYR* 1.3 79.4 - - - +
5069d GLU* 1.3 59.3 + - + +
5070d GLY* 3.2 0.7 + - - -
6059d MGE 5.5 0.2 - - - -
5038e VAL* 5.7 2.9 - - + -
5043e ALA* 3.3 33.9 - - + -
5044e TYR* 3.2 47.6 - - + +
5049e THR* 4.4 5.8 - - + -
5050e PRO 5.4 0.7 - - - +
5040f MET* 3.2 27.7 - - + +
5043f ILE* 4.2 14.1 - - + +
5036j LEU* 3.2 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU5069 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5306a VAL* 4.2 14.4 - - - +
5307a ILE 5.3 0.2 - - - +
5056d THR* 2.4 43.9 + - - -
5064d ALA* 3.8 17.2 - - + +
5065d SER 2.6 24.0 + - - -
5066d SER* 2.9 24.1 + - - +
5068d LEU* 1.3 77.1 - - - +
5070d GLY* 1.3 55.9 + - - +
5071d CYS 3.3 2.0 + - - +
5049e THR* 4.0 12.4 - - + +
5050e PRO 6.0 0.4 - - - -
5055e TYR* 2.8 41.1 + - - +
5036j LEU* 3.9 19.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY5070 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5306a VAL* 4.3 5.1 - - - +
5067d TYR 2.6 19.5 + - - -
5068d LEU 3.0 1.4 + - - -
5069d GLU* 1.3 73.8 - - - +
5071d CYS* 1.3 69.9 + - - +
5072d ASN* 5.1 0.3 - - - +
6059d MGE 3.3 13.4 - - - -
5036j LEU* 4.0 4.0 - - - -
5037j GLY* 3.1 39.7 - - - +
----------------------------------------------------------
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