Contacts of the helix formed by residues 1009 - 1024 (chain A) in PDB entry 3F2B
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 ALA1009 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007A THR* 3.4 3.3 + - - +
1008A VAL* 1.3 74.9 - - - +
1010A ASP* 1.3 69.8 + - - +
1011A LYS 3.3 1.8 - - - -
1012A THR 3.1 4.2 + - - -
1013A ALA* 3.0 17.8 + - - +
1041A THR* 4.1 7.0 - - - -
14P A 3.3 30.7 + - - +
15P A 4.5 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1010 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009A ALA* 1.3 75.1 - - - +
1011A LYS* 1.3 68.0 + - + +
1013A ALA* 3.0 3.4 + - - +
1014A TYR* 2.9 49.2 + - + -
1037A ALA* 5.6 0.9 - - - +
1038A ALA* 5.6 2.4 - - - -
1041A THR* 3.9 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1011 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009A ALA 3.3 0.8 - - - -
1010A ASP* 1.3 78.4 - - + +
1012A THR* 1.3 56.6 + - - +
1014A TYR* 3.7 5.8 + - - +
1015A GLY* 3.1 23.7 + - - -
13P C 3.7 48.9 + - + +
14P A 3.8 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1012 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008A VAL* 3.9 11.0 - - + -
1009A ALA 3.1 4.7 + - - -
1011A LYS* 1.3 75.2 - - - +
1013A ALA* 1.3 61.0 + - - +
1015A GLY* 3.2 2.6 + - - -
1016A PHE* 2.8 54.0 + - + -
1045A ARG* 3.3 32.4 + - - +
13P C 3.1 14.0 + - - -
14P A 2.5 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1013 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008A VAL* 3.6 12.7 - - + +
1009A ALA 3.0 11.3 + - - +
1010A ASP* 3.0 8.8 + - - +
1012A THR* 1.3 72.4 - - - +
1014A TYR* 1.3 66.2 + - - +
1016A PHE* 3.2 8.0 + - - +
1017A VAL* 2.9 29.2 + - - +
1037A ALA* 3.5 30.1 - - + +
1040A CYS* 4.2 7.0 - - + -
1041A THR* 3.9 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1014 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010A ASP* 2.9 50.2 + - + +
1011A LYS* 4.1 5.4 - - - +
1013A ALA* 1.3 72.8 - - - +
1015A GLY* 1.3 63.3 + - - +
1017A VAL* 3.3 2.7 + - - +
1018A LYS* 3.0 49.3 + - - +
1033A ILE* 3.7 25.4 - - + -
1034A ASP* 2.7 38.7 + - - +
1037A ALA* 3.7 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1015 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011A LYS 3.1 15.8 + - - -
1012A THR* 3.5 4.5 - - - -
1013A ALA 3.1 0.2 - - - -
1014A TYR* 1.3 77.5 - - - +
1016A PHE* 1.3 65.1 + - - +
1018A LYS* 4.0 5.3 - - - +
1019A ALA* 3.2 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1016 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A MET* 4.4 5.8 - - - -
757A ILE* 4.1 16.0 - - + +
758A LEU* 3.6 33.2 - - + -
760A HIS* 5.7 0.9 - - - -
761A SER* 3.7 37.2 - - - -
1008A VAL* 4.1 13.0 - - + -
1012A THR* 2.8 45.4 + - + -
1013A ALA* 3.2 7.6 + - - +
1015A GLY* 1.3 73.1 - - - +
1017A VAL* 1.3 62.4 + - + +
1019A ALA* 3.6 4.9 + - - +
1020A TYR* 3.1 24.1 + - - +
1040A CYS* 5.5 2.0 - - + -
1045A ARG* 4.1 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1017 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757A ILE* 4.3 19.3 - - + -
1013A ALA 2.9 21.6 + - - +
1014A TYR* 3.8 5.8 - - - +
1016A PHE* 1.3 74.1 - - - +
1018A LYS* 1.3 61.5 + - - +
1020A TYR* 3.3 4.9 + - + +
1021A ALA* 2.8 28.0 + - + +
1028A LEU* 5.1 3.4 - - + -
1033A ILE* 4.2 25.1 - - + +
1036A LEU* 3.8 36.1 - - + +
1037A ALA* 3.7 25.1 - - - +
1040A CYS* 4.5 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1018 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014A TYR* 3.0 36.5 + - - +
1015A GLY* 4.1 4.7 - - - +
1017A VAL* 1.3 77.0 - - - +
1019A ALA* 1.3 54.3 + - - +
1021A ALA* 2.9 9.6 + - - +
1022A SER* 2.7 35.4 + - - -
1033A ILE* 4.7 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1019 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760A HIS* 5.6 3.4 - - + +
1015A GLY 3.2 15.3 + - - +
1016A PHE* 4.0 4.7 - - + +
1018A LYS* 1.3 76.2 - - - +
1020A TYR* 1.3 55.0 + - - +
1022A SER* 3.5 6.8 - - - -
1023A ASP* 2.7 49.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
2A PO4 3.7 10.1 - - - -
753A ILE* 3.9 17.9 - - + +
756A LYS* 3.3 30.9 - - + +
757A ILE* 3.9 35.0 - - + -
760A HIS* 3.9 31.4 - + + -
1016A PHE 3.1 18.7 + - - +
1017A VAL* 3.5 5.4 - - + +
1019A ALA* 1.3 75.1 - - - +
1021A ALA* 1.3 66.8 + - - +
1023A ASP* 4.6 0.2 + - - -
1024A HIS* 3.0 71.3 + + - +
1026A LEU* 4.4 13.8 - - + +
1028A LEU* 6.3 1.8 - - + -
1036A LEU* 5.9 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1021 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017A VAL* 2.8 18.2 + - + +
1018A LYS* 2.9 12.5 + - - +
1020A TYR* 1.3 77.1 - - + +
1022A SER* 1.3 63.1 + - - +
1024A HIS 3.0 7.4 + - - -
1026A LEU* 3.0 47.9 + - + +
1028A LEU* 4.4 21.8 - - + -
1033A ILE* 5.9 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1022 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018A LYS 2.7 18.7 + - - -
1019A ALA* 3.5 8.3 - - - -
1021A ALA* 1.3 73.5 - - - +
1023A ASP* 1.3 66.6 + - - -
1024A HIS 3.0 0.9 + - - -
1025A ASN* 3.1 20.2 + - - +
1026A LEU 4.7 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1023 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760A HIS* 2.6 40.3 + - + +
1019A ALA* 2.7 29.7 + - - +
1020A TYR 4.3 2.2 - - - +
1022A SER* 1.3 76.8 + - - +
1024A HIS* 1.3 58.7 + - + +
1025A ASN* 3.4 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1024 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PO4 3.3 33.8 + - - -
760A HIS* 4.8 1.1 - + - -
1020A TYR* 3.0 65.8 + + - +
1021A ALA 3.0 3.7 + - - +
1022A SER 3.0 1.0 - - - -
1023A ASP* 1.3 83.8 - - + +
1025A ASN* 1.3 70.2 + - - +
1026A LEU* 3.2 24.8 + - + +
----------------------------------------------------------
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