Contacts of the helix formed by residues 3599 - 3607 (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 PHE3599 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3513A LEU* 3.2 48.2 - - + -
3514A ALA* 3.3 8.5 - - - -
3515A LEU* 3.4 27.4 - - + -
3518A ASP 3.3 20.6 - - - -
3520A ALA* 4.1 11.7 - - + -
3549A ILE* 3.5 24.2 - - + -
3595A LEU* 2.8 36.5 + - + -
3598A ALA* 1.3 82.3 - - + +
3600A ILE* 1.3 56.2 + - - +
3601A THR 3.5 0.2 - - - -
3602A TYR 3.9 0.2 - - - -
3603A LEU* 2.8 41.9 + - + +
3657A LEU* 3.9 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3600 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3595A LEU* 2.9 23.4 + - + +
3596A LYS* 3.1 27.4 - - + +
3599A PHE* 1.3 76.0 - - - +
3601A THR* 1.3 63.7 + - - +
3603A LEU* 4.1 1.4 - - - +
3604A GLN* 2.9 43.7 + - - +
3630A PRO* 4.3 0.9 - - - +
3631A PRO* 3.6 25.6 - - + -
3655A PRO* 4.6 3.1 - - + -
3656A HIS 3.4 37.5 - - - +
3657A LEU* 3.4 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR3601 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3596A LYS* 2.6 29.3 + - - +
3597A ALA* 3.5 15.8 + - - +
3599A PHE 3.5 0.2 - - - -
3600A ILE* 1.3 72.8 - - - +
3602A TYR* 1.3 58.3 + - - +
3604A GLN* 3.2 16.2 + - + +
3605A ALA* 2.8 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR3602 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3515A LEU* 4.1 10.3 - - + -
3516A LYS* 3.2 34.3 - - - -
3552A ARG* 2.8 20.4 + - - -
3597A ALA 4.2 1.9 + - - +
3598A ALA 3.1 24.1 + - - +
3599A PHE* 3.4 2.5 + - - +
3600A ILE 3.3 0.4 - - - -
3601A THR* 1.3 79.4 - - - +
3603A LEU* 1.3 68.1 + - + +
3605A ALA* 3.1 6.8 + - + +
3606A LYS* 2.9 64.0 + - + +
2521B LEU* 3.5 24.6 - - + +
2522B SEP 2.7 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3603 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3515A LEU* 5.0 0.9 - - + -
3549A ILE* 4.0 28.5 - - + -
3599A PHE* 2.8 32.8 + - + +
3600A ILE* 4.9 0.2 - - - -
3602A TYR* 1.3 87.3 - - + +
3604A GLN* 1.3 56.8 + - - +
3606A LYS* 3.4 1.4 + - + -
3607A GLN* 2.9 20.6 + - - -
3608A ALA* 3.0 47.0 + - + +
3609A ALA 3.7 0.9 - - - -
3610A GLY* 3.2 20.6 - - - +
3628A ILE* 3.5 20.9 - - + +
3630A PRO* 3.9 20.2 - - + +
3657A LEU* 5.0 0.9 - - + -
2521B LEU* 5.3 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN3604 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3600A ILE* 2.9 42.5 + - - +
3601A THR* 3.2 20.0 + - + +
3603A LEU* 1.3 74.4 - - - +
3605A ALA* 1.3 68.1 + - - +
3607A GLN* 3.1 22.5 + - - +
3630A PRO* 3.9 18.8 - - + +
3631A PRO* 5.3 1.7 - - + +
3632A CYS* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3605 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3601A THR* 2.8 25.1 + - + +
3602A TYR* 3.4 8.1 - - + +
3604A GLN* 1.3 80.4 - - + +
3606A LYS* 1.3 63.4 + - + +
3607A GLN* 3.6 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3606 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3552A ARG* 4.0 12.9 - - + +
3554A ARG* 2.9 45.8 + - - +
3602A TYR* 2.9 65.5 + - + +
3603A LEU* 3.8 2.9 - - - +
3605A ALA* 1.3 80.5 - - + +
3607A GLN* 1.3 69.8 + - - +
3608A ALA* 3.7 19.7 - - + -
2521B LEU* 5.7 0.7 - - + -
2522B SEP 5.2 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN3607 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3554A ARG* 3.4 4.9 - - - +
3555A LEU* 2.8 48.8 + - + +
3603A LEU 2.9 8.2 + - - -
3604A GLN* 3.1 16.9 + - - +
3605A ALA 4.5 3.4 - - - +
3606A LYS* 1.3 81.5 - - - +
3608A ALA* 1.3 57.3 + - - +
3630A PRO* 5.5 0.2 - - - -
----------------------------------------------------------
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