Contacts of the helix formed by residues 5261 - 5266 (chain b) 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 PRO5261 (chain b).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5065b ARG* 5.3 1.3 - - + -
5164b TRP* 3.4 48.0 - - + +
5166b SER* 5.9 2.2 - - - -
5257b SER 3.7 3.5 - - - +
5258b ALA* 3.6 12.3 - - - +
5259b THR 2.8 25.1 - - - +
5260b THR* 1.3 89.9 - - - +
5262b ILE* 1.3 63.8 + - + +
5263b GLU 4.4 3.6 - - - +
5264b LEU* 4.3 18.8 - - + -
5265b PHE* 4.1 8.8 + - + -
5445b ARG* 3.4 14.4 + - - -
5062h TRP* 4.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE5262 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5053b TRP* 4.0 1.6 + - - -
5166b SER* 5.6 7.4 - - - +
5167b ASP 6.2 0.4 - - - -
5168b PRO 4.5 9.0 - - - +
5169b TYR* 4.2 3.4 - - - -
5170b GLY* 3.4 31.6 - - - +
5261b PRO* 1.3 72.0 - - + +
5263b GLU* 1.3 60.5 + - + +
5264b LEU 3.0 5.2 + - - -
5266b GLY* 2.6 50.7 + - - +
5267b PRO* 3.4 21.8 - - + -
5268b THR 4.5 0.7 - - - +
5271b GLN* 3.6 18.4 - - - +
5276b TYR* 6.4 0.2 - - + -
5277b PHE* 5.8 0.2 - - + -
5309b TYR* 4.2 16.2 - - + -
5062h TRP* 3.7 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU5263 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5051b PRO* 4.9 4.2 - - - +
5052b MET* 4.3 5.7 - - - +
5053b TRP* 3.6 17.4 + - - +
5077b ILE* 5.5 2.6 - - - +
5164b TRP* 3.2 23.1 + - + +
5166b SER* 3.1 10.4 + - - -
5170b GLY* 3.5 4.9 - - - -
5171b LEU* 2.7 34.1 + - - +
5173b GLY* 2.6 39.5 + - - -
5261b PRO* 3.6 0.4 - - - +
5262b ILE* 1.3 78.6 - - + +
5264b LEU* 1.3 62.9 + - - +
5305b LYS* 4.3 13.5 + - - +
5309b TYR* 3.2 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5264 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5052b MET* 3.3 24.0 - - + +
5053b TRP* 3.5 11.2 - - - +
5057b MET 5.2 0.3 - - - +
5061b PRO* 3.1 36.0 - - + +
5064b ALA* 3.3 22.9 - - + -
5065b ARG* 3.4 30.3 - - + +
5077b ILE* 5.1 0.2 - - + -
5164b TRP* 3.4 38.6 - - + -
5261b PRO* 4.3 11.6 - - + -
5262b ILE 3.0 2.4 + - - +
5263b GLU* 1.3 83.1 - - - +
5265b PHE* 1.3 79.9 + - + +
5444b PRO* 5.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE5265 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5053b TRP* 3.0 19.1 - - - +
5061b PRO* 3.3 33.2 - - + -
5062b PHE* 4.1 27.4 - + - -
5065b ARG* 4.7 6.7 - - - -
5253b MET* 3.0 37.9 - - + -
5259b THR 4.4 7.0 - - - -
5260b THR* 3.9 20.9 - - + -
5261b PRO* 4.1 4.2 + - + -
5262b ILE 3.4 0.4 + - - -
5264b LEU* 1.3 95.9 - - + +
5266b GLY* 1.3 58.4 + - - +
5443b SER* 3.4 10.6 + - - -
5444b PRO* 3.4 19.0 - - + +
5445b ARG* 3.2 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY5266 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5053b TRP* 3.7 16.3 - - - -
5262b ILE* 2.6 42.6 + - - +
5265b PHE* 1.3 76.7 - - - +
5267b PRO* 1.3 67.1 - - - +
5309b TYR* 6.4 0.2 - - - -
5443b SER* 4.4 0.4 - - - -
5445b ARG* 3.2 17.9 + - - -
----------------------------------------------------------
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