Contacts of the helix formed by residues 739 - 749 (chain A) in PDB entry 1N0U
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 ALA 739 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ARG* 5.8 2.7 - - - +
735A CYS* 4.4 7.0 - - + -
736A PRO* 3.0 15.4 + - + +
737A GLU 2.9 1.2 + - - -
738A GLN* 1.3 79.6 + - - +
740A VAL* 1.3 66.4 + - - +
741A GLY 3.1 3.4 - - - -
742A GLY* 2.9 18.8 + - - +
743A ILE* 3.7 1.0 + - - +
787A ALA 5.9 0.2 - - - -
788A THR* 3.6 27.6 - - - +
791A GLN* 3.8 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 740 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735A CYS* 3.9 11.2 - - - -
736A PRO 3.4 10.3 + - - +
737A GLU* 3.0 24.4 + - + +
739A ALA* 1.3 77.5 - - - +
741A GLY* 1.3 63.4 + - - +
743A ILE* 3.0 20.0 + - - +
744A TYR* 3.3 38.7 + - + +
757A GLU* 4.2 7.9 - - - +
766A PHE* 3.9 26.5 - - + -
768A VAL* 4.0 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 741 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A GLU 4.5 1.6 + - - -
738A GLN 4.7 3.3 + - - -
739A ALA* 3.0 2.2 + - - +
740A VAL* 1.3 79.0 - - - +
742A GLY* 1.3 60.9 + - - +
744A TYR* 3.5 12.4 + - - +
745A SER* 3.2 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 742 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A GLN 5.5 0.2 + - - -
739A ALA* 2.9 11.6 + - - +
741A GLY* 1.3 76.0 - - - +
743A ILE* 1.3 63.2 + - - +
745A SER* 3.2 5.9 + - - -
746A VAL* 3.0 27.1 + - - +
787A ALA* 3.5 29.1 + - - -
788A THR* 4.0 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 743 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A ILE* 3.6 44.2 - - + -
735A CYS* 3.6 27.8 - - - -
739A ALA 3.7 6.8 + - - +
740A VAL* 3.0 11.8 + - - +
742A GLY* 1.3 77.4 - - - +
744A TYR* 1.3 65.6 + - + +
746A VAL* 3.3 2.1 + - - +
747A LEU* 3.0 43.9 + - + +
768A VAL* 3.6 32.3 - - + -
780A PHE* 5.9 0.4 - - + -
784A LEU* 4.3 15.9 - - + -
788A THR* 4.1 5.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 744 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740A VAL* 3.3 39.6 + - + +
741A GLY* 3.9 9.0 - - - +
742A GLY 3.3 0.4 - - - -
743A ILE* 1.3 78.0 - - + +
745A SER* 1.3 60.6 + - - +
747A LEU* 3.4 5.8 + - + +
748A ASN* 2.6 43.5 + - - +
754A VAL* 3.3 44.8 - - + +
757A GLU* 2.4 37.0 + - - +
768A VAL* 4.1 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 745 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A GLY 3.2 9.6 + - - -
742A GLY* 3.2 12.9 + - - -
744A TYR* 1.3 80.4 - - - +
746A VAL* 1.3 65.2 + - - +
748A ASN* 3.4 15.2 + - - +
749A LYS* 3.4 31.4 + - - +
787A ALA* 5.3 3.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
742A GLY 3.0 17.4 + - - +
743A ILE 3.9 2.9 - - - +
745A SER* 1.3 73.1 - - - +
747A LEU* 1.3 66.7 + - - +
749A LYS* 2.9 22.0 + - + +
750A LYS* 3.3 24.5 + - - +
780A PHE* 3.8 29.8 - - + -
783A GLU* 3.7 28.3 - - + +
784A LEU* 4.4 8.5 - - + +
787A ALA* 3.4 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 747 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A VAL* 4.6 8.5 - - + -
733A ILE* 5.4 0.9 - - + -
743A ILE* 3.0 39.5 + - + +
744A TYR* 3.7 4.9 - - + +
746A VAL* 1.3 76.6 - - - +
748A ASN* 1.3 60.0 + - - +
750A LYS* 3.0 13.2 + - - +
752A GLY* 2.8 46.0 + - - -
753A GLN 5.1 0.2 - - - +
754A VAL* 4.1 20.6 - - + +
768A VAL* 5.1 1.3 - - + -
770A ALA* 3.6 31.0 - - + -
771A TYR 4.8 0.9 - - - +
772A LEU* 4.6 8.5 - - + -
780A PHE* 4.1 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 748 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A TYR* 2.6 39.4 + - - +
745A SER* 3.7 10.0 - - - +
746A VAL 3.1 0.4 - - - -
747A LEU* 1.3 78.8 - - - +
749A LYS* 1.3 61.2 + - + +
750A LYS 3.3 0.4 + - - -
751A ARG* 4.3 4.8 + - - +
752A GLY 5.0 5.2 - - - +
754A VAL* 5.9 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 749 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745A SER* 3.4 26.8 + - - +
746A VAL* 2.9 15.0 + - + +
748A ASN* 1.3 80.0 - - + +
750A LYS* 1.3 71.5 + - + +
751A ARG* 3.7 1.2 - - - +
776A GLU* 4.7 1.7 - - - +
783A GLU* 5.0 10.5 + - - +
----------------------------------------------------------
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