Contacts of the helix formed by residues 649 - 660 (chain A) in PDB entry 5C53
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 TYR 649 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A CYS* 4.0 1.0 + - - +
648A PRO* 1.3 74.4 - - - +
650A ARG* 1.3 67.5 + - - +
651A ALA 3.7 0.7 - - - -
652A ILE* 3.7 22.1 - - + +
653A GLU* 4.0 14.0 + - - +
749A PHE 5.1 1.8 - - - +
750A PHE* 3.5 54.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 650 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A PRO* 4.7 1.7 - - + +
649A TYR* 1.3 84.3 - - - +
651A ALA* 1.3 61.8 + - - +
652A ILE 3.0 1.3 - - - -
653A GLU* 3.2 6.4 + - - +
654A SER* 2.9 29.6 + - - -
750A PHE* 6.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 651 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A GLU 3.9 21.1 - - - +
483A PRO* 4.2 20.2 - - + +
648A PRO* 5.4 5.9 - - + +
649A TYR 4.7 0.2 - - - +
650A ARG* 1.3 79.0 - - - +
652A ILE* 1.3 57.2 + - + +
654A SER* 2.9 10.7 + - - -
655A LEU* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 652 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A PRO* 4.3 15.5 - - + +
610A PHE* 3.8 13.4 + - + +
611A PRO* 3.7 44.0 - - + -
647A CYS* 5.9 0.9 - - - -
648A PRO 3.5 22.7 - - - +
649A TYR* 3.7 20.9 - - + +
650A ARG 3.0 0.4 - - - -
651A ALA* 1.3 74.9 - - - +
653A GLU* 1.3 61.4 + - - +
655A LEU* 3.2 4.2 + - - +
656A TYR* 2.9 28.1 + - + +
747A CYS* 6.4 0.7 - - - -
748A TRP* 4.8 13.9 - - + +
749A PHE 5.0 8.5 - - - +
750A PHE 5.8 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 653 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A TYR 4.0 10.8 + - - +
650A ARG* 3.2 10.8 + - - +
652A ILE* 1.3 79.2 - - - +
654A SER* 1.3 59.5 + - - +
656A TYR* 3.1 15.1 + - + +
657A ARG* 2.9 66.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 654 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A ARG 2.9 12.0 + - - -
651A ALA* 2.9 26.5 + - - +
653A GLU* 1.3 77.9 + - - +
655A LEU* 1.3 61.4 + - - +
657A ARG* 3.1 11.4 + - - +
658A LYS* 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 655 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A PRO* 5.7 2.9 - - + -
484A TRP* 4.2 10.3 - - + -
605A LEU* 4.1 31.9 - - + -
609A GLY 4.3 12.6 - - - +
610A PHE* 3.8 17.0 - - + -
651A ALA 2.9 20.9 + - - +
652A ILE 3.4 5.2 - - - +
654A SER* 1.3 75.8 + - - +
656A TYR* 1.3 59.5 + - - +
658A LYS* 3.3 20.2 + - + +
659A HIS* 2.9 28.7 + - + +
364B LYS* 4.3 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 656 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A ASP* 3.2 31.4 - - + -
609A GLY* 4.8 7.2 - - - -
610A PHE* 5.5 0.6 - - - +
652A ILE* 2.9 13.6 + - + +
653A GLU* 3.1 22.0 + - + +
655A LEU* 1.3 78.3 - - - +
657A ARG* 1.3 63.9 + - - +
659A HIS* 3.3 10.9 + + - +
660A CYS* 3.1 44.9 + - + +
741A ASP* 4.3 19.2 + - - +
745A PRO* 5.5 3.5 - - - +
746A GLY 3.6 13.4 + - - -
747A CYS* 4.7 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 657 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A GLU* 2.9 49.3 + - - +
654A SER* 3.1 13.2 + - - +
656A TYR* 1.3 80.5 - - - +
658A LYS* 1.3 60.8 + - - +
660A CYS* 3.4 15.4 - - - -
661A LEU* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 658 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A SER* 2.9 17.5 + - - +
655A LEU* 3.3 21.8 + - + +
657A ARG* 1.3 76.9 - - - +
659A HIS* 1.3 62.7 + - - +
661A LEU* 3.2 22.0 + - + +
662A GLU* 4.6 0.9 + - - +
363B ARG* 6.1 5.8 - - + +
364B LYS* 5.2 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 659 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A LEU* 5.1 3.0 - - + +
608A ASP* 2.9 53.7 + - + +
609A GLY 5.9 1.8 - - - +
655A LEU* 2.9 23.6 + - + +
656A TYR* 3.6 12.8 - + - +
658A LYS* 1.3 79.7 - - - +
660A CYS* 1.3 61.2 + - + +
661A LEU 3.2 0.4 - - - -
662A GLU* 3.4 28.9 + - + +
777A GLY 6.2 0.7 - - - -
778A THR* 4.8 1.6 - - - -
780A GLN* 3.4 34.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 660 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A TYR* 3.1 45.1 + - + +
657A ARG* 3.4 20.6 - - - -
659A HIS* 1.3 77.9 - - + +
661A LEU* 1.3 62.5 - - - +
662A GLU* 3.2 17.1 + - - +
----------------------------------------------------------
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