Contacts of the helix formed by residues 742 - 757 (chain A) in PDB entry 5VOT
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 LEU 742 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A VAL* 4.8 22.9 - - + -
436A CYS* 5.3 13.2 - - + +
438A PHE* 4.8 18.6 - - + -
474A ILE* 5.5 7.6 - - + -
740A SER* 3.4 6.4 + - - +
741A SER* 1.3 88.6 - - - +
743A GLY* 1.3 66.3 + - - +
744A ASN 3.0 4.1 + - - -
745A ALA* 3.0 12.1 + - + +
746A VAL* 2.8 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 743 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A SER* 5.0 4.0 - - - -
736A THR* 4.1 27.5 - - - +
740A SER* 4.1 11.3 + - - -
741A SER 3.5 2.0 - - - -
742A LEU* 1.3 76.3 - - - +
744A ASN* 1.3 56.1 + - - +
746A VAL* 3.7 4.3 - - - +
747A ASN* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 744 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740A SER 5.4 0.8 + - - -
741A SER 4.6 5.2 + - - +
742A LEU 3.2 1.2 - - - -
743A GLY* 1.3 75.1 - - - +
745A ALA* 1.3 58.6 + - - +
747A ASN* 3.0 9.6 + - - +
748A LEU* 2.9 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 745 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A CYS* 4.7 13.2 - - - -
741A SER 5.3 1.3 + - - +
742A LEU* 3.0 15.0 + - + +
744A ASN* 1.3 79.6 - - - +
746A VAL* 1.3 62.7 + - - +
748A LEU* 3.1 19.9 + - + +
749A ALA* 2.9 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 746 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A ILE* 3.9 21.3 - - + -
436A CYS* 4.0 20.6 - - - -
438A PHE* 6.2 0.4 - - + -
474A ILE* 4.3 14.6 - - + -
492A SER* 5.4 1.8 - - - -
734A ILE* 4.4 25.1 - - + -
742A LEU* 2.8 43.6 + - + +
743A GLY* 3.7 6.5 - - - +
745A ALA* 1.3 71.5 - - - +
747A ASN* 1.3 63.5 + - - +
749A ALA* 2.9 14.9 + - - +
750A VAL* 2.9 22.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 747 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A PHE 5.1 0.6 + - - -
492A SER* 3.9 12.1 - - - +
493A LYS* 3.1 68.4 + - - +
743A GLY 2.9 18.9 + - - +
744A ASN* 3.3 8.0 + - - +
746A VAL* 1.3 75.1 - - - +
748A LEU* 1.3 65.0 + - + +
750A VAL* 3.1 11.7 + - - +
751A LEU* 2.9 28.9 + - - +
486D GLU* 5.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 748 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A ASN* 2.9 31.4 + - - +
745A ALA* 3.1 24.7 + - + +
747A ASN* 1.3 76.7 - - + +
749A ALA* 1.3 57.5 + - - +
751A LEU* 3.1 17.7 + - + +
752A LYS* 2.9 26.6 + - - +
483D LEU* 3.9 21.3 - - + +
486D GLU* 4.9 12.8 - - + +
487D GLU* 5.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 749 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A ILE* 4.1 17.9 - - + -
435A HIS* 4.0 29.8 - - + -
436A CYS* 5.1 4.5 - - - -
745A ALA 2.9 11.2 + - - +
746A VAL* 2.9 11.5 + - - +
748A LEU* 1.3 71.2 - - - +
750A VAL* 1.3 69.0 + - - +
752A LYS* 2.9 22.3 + - - +
753A LEU* 3.0 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 750 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A LEU* 5.9 5.4 - - + -
432A ILE* 4.4 15.9 - - + -
492A SER* 4.6 4.3 - - - +
493A LYS* 4.1 19.7 - - + +
494A PRO 5.5 0.4 - - - +
495A PHE* 4.4 21.5 - - + -
734A ILE* 4.5 21.1 - - + -
746A VAL* 2.9 19.4 + - + +
747A ASN* 3.3 16.8 - - - +
749A ALA* 1.3 74.8 - - - +
751A LEU* 1.3 62.1 + - + +
753A LEU* 3.4 6.2 + - - +
754A ASN* 2.9 31.0 + - + +
759A LEU* 4.6 5.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 751 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A LYS* 4.7 15.5 - - + -
747A ASN* 2.9 32.5 + - - +
748A LEU* 3.1 15.5 + - + +
750A VAL* 1.3 77.2 - - + +
752A LYS* 1.3 57.8 + - - +
754A ASN* 3.3 17.2 + - + +
755A GLU* 2.9 34.3 + - - +
481D ILE* 5.5 10.1 - - + +
482D THR* 5.0 4.5 - - - +
483D LEU* 3.8 23.6 - - + +
486D GLU* 3.5 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 752 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A HIS* 3.4 39.8 + - + +
748A LEU 2.9 11.3 + - - +
749A ALA* 2.9 15.0 + - - +
751A LEU* 1.3 75.4 - - - +
753A LEU* 1.3 51.6 + - - +
755A GLU* 2.9 8.4 + - - +
756A GLN* 2.6 65.9 + - + +
483D LEU* 4.6 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 753 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A LEU* 4.4 18.2 - - + -
431A GLU* 3.8 31.6 - - + +
432A ILE* 5.0 6.3 - - + -
435A HIS* 4.4 17.3 - - + +
749A ALA 3.0 16.1 + - - +
750A VAL* 4.1 3.6 - - - +
752A LYS* 1.3 76.0 - - + +
754A ASN* 1.3 52.7 + - - +
756A GLN* 3.2 25.7 - - - +
757A GLY* 2.7 30.8 + - - -
758A LEU* 3.5 35.4 + - + -
759A LEU* 3.8 21.9 - - + +
762A LEU* 6.0 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 754 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A PHE* 6.2 2.2 - - - +
750A VAL* 2.9 21.7 + - + +
751A LEU* 3.4 19.0 - - + +
753A LEU* 1.3 76.1 - - - +
755A GLU* 1.3 61.7 + - + +
757A GLY* 3.3 12.6 + - - -
759A LEU* 3.5 21.3 - - + +
658D PHE* 5.5 4.7 - - - -
728D ASP* 5.6 3.3 - - - +
729D SER* 3.6 25.1 + - - +
730D LYS* 5.4 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 755 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751A LEU 2.9 13.1 + - - +
752A LYS* 3.3 6.1 - - - +
754A ASN* 1.3 78.3 - - + +
756A GLN* 1.3 61.5 + - + +
757A GLY 3.3 0.6 + - - -
482D THR* 3.2 16.8 - - + +
483D LEU* 2.5 56.0 + - - +
484D VAL* 4.4 2.4 + - - +
658D PHE* 5.2 17.5 - - + -
661D ARG* 5.1 7.9 - - + +
662D SER* 5.9 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 756 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A HIS* 4.8 5.7 + - - -
752A LYS* 2.6 52.9 + - + +
753A LEU* 3.0 29.8 + - + +
755A GLU* 1.3 78.5 - - + +
757A GLY* 1.3 50.5 + - - +
758A LEU* 2.8 19.2 + - + +
663D LYS* 5.9 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 757 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A LEU 2.7 12.1 + - - -
754A ASN* 3.3 8.4 + - - -
755A GLU 3.3 4.4 + - - -
756A GLN* 1.3 71.1 - - - +
758A LEU* 1.3 57.8 + - - -
759A LEU* 3.0 8.3 + - - -
760A ASP* 3.6 12.1 + - - +
761A LYS* 3.7 9.2 + - - +
658D PHE* 6.6 0.4 - - - -
----------------------------------------------------------
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