Contacts of the helix formed by residues 1018 - 1027 (chain A) in PDB entry 6DBV
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 SER1018 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A LEU* 4.7 5.9 - - - +
588A ASP* 2.4 32.6 + - - -
675A ARG* 3.9 12.3 - - - +
1014A TRP* 3.2 24.8 + - - -
1015A LEU* 3.7 2.0 + - - +
1016A TYR 4.6 0.3 - - - +
1017A THR* 1.3 79.4 + - - +
1019A LYS* 1.3 66.6 + - - +
1020A TYR* 3.0 11.8 + - - +
1021A LEU* 3.9 17.6 + - - +
1022A GLN* 3.4 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1019 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A ASP* 3.6 14.0 + - - +
589A LEU* 3.6 21.7 - - + +
592A ASP* 4.4 16.6 - - - +
663A PHE* 5.2 9.4 - - - -
665A GLU* 3.8 16.4 + - - -
673A SER* 3.2 25.5 + - - -
675A ARG* 4.2 10.6 - - - +
1017A THR 3.5 2.0 + - - -
1018A SER* 1.3 72.1 + - - +
1020A TYR* 1.3 56.3 + - - +
1022A GLN* 2.6 44.2 + - + +
1023A LYS* 2.8 21.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1020 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A HIS* 5.7 2.3 - - - -
484A ALA* 4.2 11.9 - - + +
528A GLU* 6.5 0.4 - - - -
529A LEU* 4.2 30.5 - - + -
588A ASP* 3.9 16.0 + - - +
591A GLU* 6.5 2.2 - - + -
1018A SER* 3.0 13.3 + - - +
1019A LYS* 1.3 78.1 - - - +
1021A LEU* 1.3 62.3 + - + +
1023A LYS* 3.3 9.5 + - + +
1024A PHE* 3.0 71.6 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1021 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ALA* 4.3 5.6 - - + +
487A LEU* 3.8 23.8 - - + +
488A ALA* 3.7 41.7 - - + +
491A VAL* 4.6 3.4 - - + -
492A ASN* 5.9 1.1 - - - -
529A LEU* 3.6 26.7 - - + -
1015A LEU* 3.4 33.4 - - + +
1016A TYR* 6.1 1.3 - - - -
1018A SER* 4.2 15.9 - - - +
1019A LYS 3.3 0.4 - - - -
1020A TYR* 1.3 76.7 - - + +
1022A GLN* 1.3 61.5 + - - +
1024A PHE* 3.3 9.1 + - + +
1025A MET* 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1022 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ASN* 5.5 6.5 - - - +
672A LEU* 2.4 57.6 + - + +
673A SER* 5.0 0.2 + - - -
1016A TYR* 3.6 18.0 + - + +
1017A THR 3.2 12.6 + - - -
1018A SER 3.4 13.2 - - - +
1019A LYS* 2.6 32.5 + - + +
1021A LEU* 1.3 71.0 - - + +
1023A LYS* 1.3 63.1 + - - +
1025A MET* 3.0 15.5 + - - -
1026A GLU* 3.0 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1023 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A GLU* 5.7 3.8 + - - +
592A ASP* 4.5 21.8 + - - +
1019A LYS* 2.8 23.2 + - + +
1020A TYR* 3.3 14.4 - - + +
1022A GLN* 1.3 72.3 - - - +
1024A PHE* 1.3 70.1 + - + +
1026A GLU* 3.1 24.0 + - + +
1027A ALA* 3.4 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1024 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A HIS* 5.4 2.7 - + + -
484A ALA* 3.5 22.2 - - + -
485A VAL* 3.5 51.5 - - + +
488A ALA* 4.8 1.8 - - + -
1020A TYR* 3.0 65.8 + + - +
1021A LEU* 3.3 8.3 + - + +
1022A GLN 3.2 0.2 - - - -
1023A LYS* 1.3 83.0 - - + +
1025A MET* 1.3 60.3 + - - +
1026A GLU 3.4 0.2 - - - -
1027A ALA* 3.9 15.0 - - - +
506C THR* 4.7 0.7 - - - +
510C THR* 4.6 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1025 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ALA* 4.4 16.4 - - + +
489A ILE* 4.5 2.2 - - - +
492A ASN* 3.5 47.6 - - + +
1021A LEU 2.8 11.8 + - - +
1022A GLN* 3.0 14.8 + - - +
1024A PHE* 1.3 77.9 - - - +
1026A GLU* 1.3 73.9 + - - +
1027A ALA* 4.3 2.8 - - - +
502C LYS* 4.6 10.8 - - + -
505C ARG* 5.1 11.6 - - - -
506C THR* 3.5 43.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1026 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022A GLN* 3.0 23.1 + - - +
1023A LYS* 3.1 14.8 + - + +
1025A MET* 1.3 93.6 - - - +
1027A ALA* 1.3 70.3 + - - +
1028A HIS 3.5 0.9 - - - +
1029A LYS* 3.1 30.2 - - - +
505C ARG* 5.7 2.1 - - - -
509C ALA* 4.4 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1027 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023A LYS 3.4 9.7 + - - -
1024A PHE* 3.9 15.3 - - - +
1025A MET 4.3 2.7 - - - +
1026A GLU* 1.3 81.1 - - - +
1028A HIS* 1.3 70.8 + - - +
506C THR* 4.6 1.8 - - - +
509C ALA* 3.1 47.1 - - + +
510C THR* 4.0 10.1 - - + +
----------------------------------------------------------
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