Contacts of the helix formed by residues 3643 - 3651 (chain A) in PDB entry 2RT5
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 ALA3643 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3505A TYR* 3.0 30.5 - - + -
3527A VAL* 3.3 26.5 - - + -
3639A LEU* 2.7 14.8 + - + +
3642A LEU* 1.3 76.3 - - - +
3644A PRO* 1.3 53.1 - - - +
3645A ASP 3.1 5.2 - - - -
3646A LEU* 3.9 8.2 - - + +
3647A LEU* 2.7 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO3644 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3504A LYS* 4.9 5.8 - - - +
3505A TYR* 3.6 3.8 - - - +
3640A SER* 3.7 19.0 - - - +
3641A ARG 4.2 4.5 - - - +
3642A LEU 3.7 6.1 - - - +
3643A ALA* 1.3 88.0 - - - +
3645A ASP* 1.3 70.8 + - - +
3647A LEU* 3.7 11.1 - - + +
3648A ALA* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP3645 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3497A ASP 4.8 0.2 - - - +
3500A GLN* 4.2 30.5 - - + +
3501A LEU* 3.7 19.3 + - - +
3504A LYS* 2.7 39.4 + - + +
3505A TYR* 3.0 21.4 + - + +
3644A PRO* 1.3 87.1 - - - +
3646A LEU* 1.3 59.2 + - - +
3648A ALA* 3.9 9.8 + - - +
3649A SER* 4.2 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3501A LEU* 3.4 35.9 - - + -
3505A TYR* 3.5 7.3 - - + -
3525A HIS* 4.5 8.3 - - + -
3526A PHE 3.9 12.1 - - - +
3527A VAL* 3.6 32.1 - - + -
3577A LEU* 3.7 15.9 - - + -
3579A LEU* 5.1 1.8 - - + -
3639A LEU* 5.2 0.4 - - + -
3643A ALA* 3.4 15.5 + - + +
3645A ASP* 1.3 75.6 - - - +
3647A LEU* 1.3 62.8 + - - +
3648A ALA 3.1 2.2 - - - -
3649A SER* 2.8 20.3 + - - -
3650A ILE* 3.1 38.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3636A GLU* 4.2 13.0 - - + +
3639A LEU* 3.8 19.5 - - + +
3640A SER* 3.4 26.5 - - - +
3643A ALA 2.7 21.4 + - - +
3644A PRO* 3.7 10.5 - - + +
3645A ASP 3.4 0.4 - - - -
3646A LEU* 1.3 77.0 - - - +
3648A ALA* 1.3 60.2 + - - +
3650A ILE* 3.0 28.3 + - + +
3651A SER* 3.0 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3648 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3500A GLN* 5.4 5.4 - - - +
3644A PRO 3.2 15.4 + - - +
3645A ASP* 4.1 7.2 - - - +
3646A LEU 3.1 0.8 - - - -
3647A LEU* 1.3 82.9 - - + +
3649A SER* 1.3 57.9 + - - +
3651A SER* 3.0 17.8 + - - -
3652A ASN* 4.9 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER3649 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3496A VAL* 3.2 50.4 - - - +
3497A ASP* 2.9 34.1 + - - +
3501A LEU* 3.8 9.0 - - - +
3579A LEU* 5.9 0.4 - - - -
3645A ASP 4.2 4.0 + - - -
3646A LEU* 2.8 11.1 + - - -
3648A ALA* 1.3 79.5 - - - +
3650A ILE* 1.3 65.0 + - - +
3651A SER 3.2 2.1 + - - -
3652A ASN* 3.6 10.3 + - - +
3653A ILE* 3.6 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3650 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3577A LEU* 3.6 37.0 - - + -
3579A LEU* 3.7 20.4 - - + -
3636A GLU* 5.5 0.5 - - - +
3639A LEU* 3.9 11.4 - - + -
3646A LEU* 3.1 30.2 + - + -
3647A LEU* 3.1 47.8 - - + +
3649A SER* 1.3 73.4 - - - +
3651A SER* 1.3 57.2 + - - +
3652A ASN 3.0 2.2 - - - -
3653A ILE* 3.0 6.5 - - - -
3654A SER* 2.7 35.3 + - - -
3656A HIS* 3.7 13.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER3651 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3636A GLU* 5.8 2.2 - - - -
3647A LEU* 3.0 21.0 + - - -
3648A ALA* 3.0 24.0 + - - -
3650A ILE* 1.3 79.0 - - - +
3652A ASN* 1.3 65.8 + - - +
3654A SER* 2.8 17.4 + - - -
----------------------------------------------------------
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