Contacts of the helix formed by residues 769 - 778 (chain A) in PDB entry 2Y48
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 SER 769 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A HIS* 3.8 24.7 - - - -
764A VAL* 3.7 15.7 - - - +
768A SER* 1.3 88.2 + - - +
770A GLY* 1.3 64.8 + - - +
771A ASN* 3.0 21.6 + - - +
772A ASP* 3.4 10.6 + - - -
773A TYR* 3.7 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 770 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A HIS* 4.7 4.0 + - - -
554A GLN* 3.9 31.6 - - - +
769A SER* 1.3 75.8 + - - +
771A ASN* 1.3 65.6 + - - +
772A ASP 3.2 0.2 - - - -
773A TYR* 3.2 29.9 + - - +
774A ASP 3.7 0.9 + - - -
805A ARG* 3.4 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 771 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769A SER* 3.0 11.6 - - - +
770A GLY* 1.3 82.0 - - - +
772A ASP* 1.3 57.7 + - - +
774A ASP* 2.8 26.9 + - - +
775A LEU* 3.1 26.0 + - - +
805A ARG* 3.2 22.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 772 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A ALA* 4.3 4.5 - - + +
653A ARG* 2.6 55.2 + - - +
654A MET* 3.7 17.4 - - + +
768A SER* 2.8 31.2 + - - +
769A SER* 3.4 7.2 + - - +
770A GLY 3.2 0.4 - - - -
771A ASN* 1.3 79.1 - - - +
773A TYR* 1.3 58.3 + - + +
775A LEU* 3.2 14.0 + - - +
776A MET* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 773 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A GLN* 5.0 1.8 - - - -
654A MET* 3.7 20.2 - - + -
762A SER* 3.0 23.2 + - - -
763A TYR* 3.7 22.1 + - - -
764A VAL* 4.0 21.5 + - + +
768A SER* 5.2 2.0 - - - -
769A SER 3.7 18.6 - - - -
770A GLY* 3.3 15.9 - - - +
772A ASP* 1.3 79.0 - - + +
774A ASP* 1.3 60.5 + - - +
776A MET* 3.5 4.0 + - - +
777A ALA 3.4 10.6 + - - -
802A HIS 3.4 27.1 - - - -
803A THR 3.2 18.5 - - - +
804A ILE 4.4 0.7 - - - -
805A ARG* 3.8 25.4 - - - +
808A PRO* 3.4 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 774 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771A ASN* 2.8 20.2 + - - +
773A TYR* 1.3 76.9 - - - +
775A LEU* 1.3 68.0 + - - +
777A ALA* 2.9 16.7 + - - +
778A GLN* 3.3 18.7 + - - +
803A THR 5.0 2.1 - - - +
805A ARG* 3.1 46.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 775 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A TRP* 3.4 37.8 - - + +
647A LYS* 3.1 15.7 + - - -
650A ALA* 4.1 12.6 - - + -
653A ARG* 3.5 14.6 - - - +
771A ASN* 3.1 19.0 + - - +
772A ASP* 3.3 32.3 - - - +
774A ASP* 1.3 77.8 - - - +
776A MET* 1.3 63.2 + - - +
777A ALA 3.2 0.7 + - - -
778A GLN* 3.3 10.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 776 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A LEU* 5.0 1.1 - - + -
630A LEU* 4.0 17.7 - - + -
647A LYS* 3.0 29.2 + - + +
650A ALA* 4.0 14.4 - - - -
651A VAL* 3.7 26.9 - - + -
654A MET* 3.3 32.1 - - - +
772A ASP 2.9 13.4 + - - +
773A TYR 3.6 4.3 - - - +
774A ASP 3.1 0.2 - - - -
775A LEU* 1.3 74.2 - - - +
777A ALA* 1.3 58.1 + - - +
798A PHE* 3.4 20.4 - - + +
802A HIS* 3.6 42.6 - - + +
803A THR* 3.8 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 777 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A TYR 3.4 1.9 + - - +
774A ASP* 2.9 12.1 + - - +
776A MET* 1.3 77.4 - - - +
778A GLN* 1.3 65.1 + - - +
779A PRO* 3.4 1.6 - - - +
798A PHE* 4.1 5.1 + - - +
803A THR* 3.5 29.2 - - - +
820A ARG* 3.6 26.5 - - - +
821A GLU* 3.8 8.3 - - - +
824A ARG* 3.2 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 778 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A TRP* 3.7 19.4 - - + -
647A LYS* 2.8 26.7 + - - -
774A ASP* 3.3 17.7 + - - +
775A LEU* 3.3 16.0 + - + +
777A ALA* 1.3 77.0 - - - +
779A PRO* 1.3 79.7 - - + +
798A PHE* 3.7 2.5 - - - -
824A ARG* 4.5 9.7 + - - +
----------------------------------------------------------
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