Contacts of the helix formed by residues 1025 - 1039 (chain A) in PDB entry 1DJL
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 ASP1025 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A ALA* 3.7 7.0 - - - +
1000A ARG* 4.0 11.0 - - + +
1024A GLY* 1.3 73.8 - - - -
1026A ALA* 1.3 64.4 + - - +
1027A LYS* 2.9 31.6 + - - +
1028A LYS* 3.2 35.4 + - + +
1029A THR* 3.0 21.5 + - - -
1136A NAP 3.0 28.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1026 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891A GLY 4.0 7.2 - - - +
892A LEU* 4.4 0.9 - - - -
895A ALA* 3.7 11.9 - - + -
897A ALA* 3.8 10.8 - - + -
963A ILE* 4.1 19.7 - - + -
964A GLY 5.3 0.2 - - - +
998A MET* 4.9 6.3 - - - +
1024A GLY 4.3 1.1 - - - -
1025A ASP* 1.3 73.4 - - - +
1027A LYS* 1.3 59.1 + - - +
1029A THR* 4.0 4.1 - - - -
1030A CYS* 3.0 34.7 + - - +
1136A NAP 2.7 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1027 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A ALA* 3.3 28.5 - - + +
896A LYS* 3.9 15.0 - - + +
897A ALA* 3.8 8.3 - - + -
899A TYR* 6.2 1.8 - - - -
900A PRO* 4.4 9.4 - - + -
1025A ASP* 2.9 12.9 + - - +
1026A ALA* 1.3 72.4 - - - +
1028A LYS* 1.3 63.1 + - + +
1030A CYS* 3.2 1.5 + - - +
1031A ASP* 2.6 68.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1028 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1024A GLY* 6.2 0.2 - - - -
1025A ASP* 3.2 31.2 + - + +
1027A LYS* 1.3 79.8 - - + +
1029A THR* 1.3 57.6 + - - +
1031A ASP* 3.5 9.4 - - - +
1032A ALA* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1029 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A LEU* 4.4 7.6 - - + -
998A MET* 3.6 23.3 - - + -
1022A LEU* 3.5 38.7 + - + +
1023A LEU 4.4 3.5 + - - -
1024A GLY* 3.9 18.5 + - - -
1025A ASP 3.0 17.6 + - - -
1026A ALA* 4.0 0.9 - - - -
1028A LYS* 1.3 73.5 - - - +
1030A CYS* 1.3 61.0 + - - +
1032A ALA* 3.4 6.0 + - - +
1033A LEU* 3.0 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1030 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897A ALA* 4.6 4.0 - - - +
900A PRO* 3.7 25.2 - - + +
901A ILE* 4.2 20.9 - - + +
904A LEU* 5.5 2.0 - - + +
963A ILE* 4.0 21.8 - - - -
998A MET* 3.3 29.2 - - - -
1026A ALA 3.0 18.1 + - - +
1029A THR* 1.3 74.7 - - - +
1031A ASP* 1.3 61.3 + - - +
1033A LEU* 3.8 7.4 - - - +
1034A GLN* 2.8 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1031 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900A PRO* 3.2 25.3 - - - +
1027A LYS* 2.6 60.8 + - - +
1028A LYS* 3.5 8.7 - - - +
1030A CYS* 1.3 74.0 - - - +
1032A ALA* 1.3 55.9 + - - +
1034A GLN* 3.4 7.7 + - - +
1035A ALA* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1032 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A LEU* 3.3 30.7 - - + -
1028A LYS 3.0 16.8 + - - +
1029A THR* 3.7 5.2 - - - +
1031A ASP* 1.3 74.1 - - - +
1033A LEU* 1.3 65.1 + - - +
1035A ALA* 3.3 7.3 + - - +
1036A LYS* 3.0 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1033 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A LEU* 3.5 18.4 - - + -
874A ALA* 4.1 15.0 - - + -
875A ILE* 3.4 29.2 - - + -
878A ILE* 4.2 20.6 - - + -
901A ILE* 6.4 0.2 - - + -
904A LEU* 4.3 18.6 - - + -
961A LEU* 5.5 3.8 - - + -
998A MET* 4.1 26.7 - - + -
1022A LEU* 4.4 7.0 - - + -
1029A THR 3.0 22.3 + - - +
1030A CYS* 3.8 6.5 - - - +
1032A ALA* 1.3 75.8 - - - +
1034A GLN* 1.3 64.8 + - - +
1036A LYS* 3.2 2.1 + - - +
1037A VAL* 2.9 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1034 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900A PRO* 3.8 19.8 - - - +
903A ASP* 2.9 41.0 + - + +
904A LEU* 3.9 14.1 - - + +
907A MET* 3.2 26.4 - - + +
1030A CYS 2.8 18.7 + - - +
1031A ASP* 3.6 8.3 + - - +
1033A LEU* 1.3 77.1 - - - +
1035A ALA* 1.3 62.4 + - - +
1038A ARG* 3.1 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1035 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1031A ASP 3.0 17.3 + - - +
1032A ALA* 3.5 8.1 - - - +
1033A LEU 3.1 0.2 - - - -
1034A GLN* 1.3 81.9 + - - +
1036A LYS* 1.3 66.2 + - + +
1038A ARG* 3.1 17.7 + - - +
1039A GLU* 3.2 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1036 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A LEU* 4.1 25.3 - - + +
872A ASP* 2.5 37.6 + - - +
875A ILE* 3.7 32.9 - - + +
1032A ALA 3.0 19.1 + - - +
1033A LEU 3.2 0.4 + - - -
1035A ALA* 1.3 77.3 - - + +
1037A VAL* 1.3 59.3 + - - +
1039A GLU* 3.5 13.5 + - - +
1040A SER* 3.2 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1037 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A ILE* 4.4 15.9 - - + -
878A ILE* 4.9 11.2 - - + -
879A ARG* 3.8 27.3 + - - +
904A LEU* 3.6 23.1 - - + -
907A MET* 3.8 22.9 - - + +
908A LEU* 4.2 16.4 - - + -
1033A LEU 2.9 19.4 + - - +
1034A GLN 3.9 2.0 - - - +
1036A LYS* 1.3 75.6 - - - +
1038A ARG* 1.3 65.5 + - - +
1039A GLU 3.1 2.3 + - - -
1040A SER* 3.3 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1038 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903A ASP* 4.3 9.7 + - - +
907A MET* 3.5 41.6 - - - +
1034A GLN* 3.1 38.7 + - - +
1035A ALA* 3.1 13.6 + - - +
1037A VAL* 1.3 76.8 - - - +
1039A GLU* 1.3 63.3 + - + +
1040A SER 3.2 8.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1039 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035A ALA 3.2 12.7 + - - +
1036A LYS* 3.7 10.9 - - - +
1037A VAL 3.1 0.4 - - - -
1038A ARG* 1.3 81.3 - - + +
1040A SER* 1.3 65.5 + - - +
----------------------------------------------------------
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