Contacts of the helix formed by residues 1025 - 1039 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895B ALA* 3.6 6.8 - - - +
1000B ARG* 4.0 9.8 - - + +
1024B GLY* 1.3 73.9 - - - -
1026B ALA* 1.3 59.0 + - - +
1027B LYS* 2.8 31.3 + - - +
1028B LYS* 3.0 44.2 + - + +
1029B THR* 2.9 26.9 + - - -
2136B NAP 2.9 28.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1026 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891B GLY 4.0 7.4 - - - +
892B LEU* 4.5 1.1 - - - -
895B ALA* 3.8 10.5 - - + -
897B ALA* 3.8 11.7 - - + -
963B ILE* 4.3 19.1 - - + -
964B GLY 5.3 0.2 - - - +
998B MET* 5.2 5.8 - - - +
1024B GLY 4.2 1.3 - - - -
1025B ASP* 1.3 73.1 - - - +
1027B LYS* 1.3 56.7 + - - +
1029B THR* 3.7 4.3 - - - -
1030B CYS* 2.7 35.7 + - - -
2136B NAP 2.7 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1027 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895B ALA* 3.2 30.2 - - + +
896B LYS* 4.0 18.2 - - + +
897B ALA* 3.8 10.3 - - + +
899B TYR* 6.2 1.6 - - - -
900B PRO* 4.5 5.8 - - + -
1025B ASP* 2.8 14.9 + - - +
1026B ALA* 1.3 71.7 - - - +
1028B LYS* 1.3 60.3 + - + +
1030B CYS* 4.1 1.3 - - - +
1031B ASP* 2.6 71.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1028 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025B ASP* 3.0 40.8 + - + +
1027B LYS* 1.3 77.6 - - + +
1029B THR* 1.3 62.9 + - - +
1031B ASP* 3.7 7.4 - - - +
1032B ALA* 3.2 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1029 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B LEU* 4.2 8.9 - - + +
998B MET* 3.8 22.2 - - + -
1022B LEU* 3.7 34.3 + - + +
1023B LEU 4.3 6.2 + - - -
1024B GLY* 4.0 16.8 + - - -
1025B ASP 2.9 19.9 + - - -
1026B ALA* 3.8 5.2 - - - -
1028B LYS* 1.3 75.3 - - - +
1030B CYS* 1.3 65.6 + - - +
1032B ALA* 3.2 6.1 + - - +
1033B LEU* 3.0 24.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1030 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897B ALA* 4.3 6.3 - - + -
900B PRO* 3.7 25.1 - - + +
901B ILE* 4.4 16.8 - - + +
904B LEU* 5.0 2.1 - - + +
963B ILE* 4.0 37.2 - - - -
998B MET* 4.3 10.5 - - - -
1026B ALA* 2.7 28.8 + - - +
1029B THR* 1.3 74.4 - - - +
1031B ASP* 1.3 61.7 + - - +
1033B LEU* 3.9 7.8 - - - +
1034B GLN* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1031 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900B PRO* 3.2 24.9 - - - +
1027B LYS* 2.6 55.8 + - - +
1028B LYS* 3.7 7.7 + - - +
1030B CYS* 1.3 74.7 - - - +
1032B ALA* 1.3 57.6 + - - +
1034B GLN* 3.6 10.2 + - - +
1035B ALA* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1032 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B LEU* 3.6 31.4 - - + -
1028B LYS 3.2 11.3 + - - +
1029B THR* 3.2 8.0 + - - +
1031B ASP* 1.3 77.7 - - - +
1033B LEU* 1.3 60.4 + - - +
1035B ALA* 3.3 5.8 + - - +
1036B LYS* 2.9 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1033 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B LEU* 4.0 23.8 - - + +
874B ALA* 4.2 11.4 - - + -
875B ILE* 4.0 24.9 - - + +
878B ILE* 4.5 15.5 - - + -
901B ILE* 6.3 0.2 - - + -
904B LEU* 4.0 21.1 - - + -
961B LEU* 5.7 0.2 - - + -
998B MET* 4.1 34.1 - - + -
1022B LEU* 4.3 6.7 - - + -
1029B THR* 3.0 18.7 + - + +
1030B CYS* 3.9 7.4 - - - +
1031B ASP 3.4 0.2 - - - -
1032B ALA* 1.3 76.3 - - - +
1034B GLN* 1.3 59.4 + - - +
1036B LYS* 3.4 3.6 + - - +
1037B VAL* 2.9 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1034 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900B PRO* 4.0 24.1 - - + +
903B ASP* 3.3 34.7 + - + +
904B LEU* 4.2 9.1 - - + +
907B MET* 3.5 24.5 - - + +
1030B CYS 3.0 18.0 + - - +
1031B ASP* 3.6 10.4 + - - +
1033B LEU* 1.3 76.0 - - - +
1035B ALA* 1.3 72.0 + - - +
1037B VAL 3.3 0.3 + - - -
1038B ARG* 2.8 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1035 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1031B ASP 3.0 19.2 + - - +
1032B ALA* 3.5 8.1 - - - +
1034B GLN* 1.3 84.5 + - - +
1036B LYS* 1.3 63.5 + - + +
1038B ARG* 3.3 7.1 - - - +
1039B GLU* 3.1 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1036 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B LEU* 4.6 22.4 - - + +
872B ASP* 2.6 31.3 + - - +
875B ILE* 3.2 37.2 - - + -
1032B ALA* 2.9 21.3 + - + +
1033B LEU 4.0 2.2 - - - +
1035B ALA* 1.3 73.1 - - + +
1037B VAL* 1.3 67.6 + - - +
1039B GLU* 3.2 29.0 + - - +
1040B SER* 3.5 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1037 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875B ILE* 5.4 14.6 - - + -
878B ILE* 5.3 10.1 - - + -
904B LEU* 3.4 23.6 - - + -
907B MET* 3.8 29.8 - - + -
908B LEU* 4.3 17.7 - - + -
911B GLN* 4.8 11.7 + - - +
1033B LEU* 2.9 22.1 + - + +
1034B GLN 3.7 3.6 - - - +
1036B LYS* 1.3 76.6 - - - +
1038B ARG* 1.3 67.9 + - - +
1040B SER* 3.3 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1038 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907B MET* 3.7 25.6 - - + +
1034B GLN* 2.8 16.2 + - + +
1035B ALA* 3.3 13.9 - - - +
1037B VAL* 1.3 76.9 - - - +
1039B GLU* 1.3 56.2 + - + +
1040B SER* 2.5 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1039 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035B ALA* 3.1 29.2 + - - +
1036B LYS* 3.2 14.5 + - - +
1038B ARG* 1.3 74.4 - - + +
1040B SER* 1.3 67.7 + - - +
----------------------------------------------------------
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