Contacts of the helix formed by residues 897 - 910 (chain K) in PDB entry 1SOJ
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 LYS 897 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891K LEU 5.8 0.7 - - - +
894K ASP* 2.9 17.5 + - + +
895K LEU 2.9 1.2 - - - -
896K LYS* 1.3 78.0 - - - +
898K HIS* 1.3 64.3 + - - +
899K PHE 3.3 2.5 - - - -
900K ASP* 3.0 25.9 + - + +
901K PHE* 3.1 34.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 898 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894K ASP 3.7 1.2 + - - -
895K LEU* 2.7 28.0 + - + +
896K LYS 3.4 0.4 - - - -
897K LYS* 1.3 77.2 - - - +
899K PHE* 1.3 95.2 + + + +
901K PHE* 3.4 2.8 + - - +
902K LEU* 3.1 34.0 + - + +
934K LYS* 2.9 37.4 + - - +
938K ILE* 4.5 0.7 - - + -
994K HIS 4.4 0.6 + - - -
995K ILE* 3.2 50.0 + - + +
999K LEU* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 899 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993G THR* 4.6 15.5 - - + -
994G HIS* 3.7 36.3 - + - -
895K LEU 5.3 2.7 - - - -
896K LYS 5.8 2.2 - - - -
897K LYS 3.3 0.8 - - - -
898K HIS* 1.3 95.2 - + + +
900K ASP* 1.3 65.1 + - - +
902K LEU* 3.8 15.2 - - + +
903K ALA* 3.0 28.9 + - - +
994K HIS* 3.4 33.7 - - + -
995K ILE* 4.6 8.1 - - + -
998K PRO* 5.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 900 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073G LYS* 6.0 2.6 - - - +
896K LYS 4.2 4.5 - - - +
897K LYS* 3.0 25.2 + - + +
899K PHE* 1.3 79.8 + - - +
901K PHE* 1.3 67.4 + - + +
903K ALA* 3.3 5.7 + - - +
904K GLU* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 901 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891K LEU 4.9 1.8 - - - -
892K ALA* 3.6 32.1 - - + -
897K LYS* 3.1 41.1 + - + -
898K HIS 3.9 5.2 - - - +
900K ASP* 1.3 78.0 - - + +
902K LEU* 1.3 52.4 + - - +
904K GLU* 3.0 10.9 + - - +
905K PHE* 2.7 38.4 + - - +
927K LEU* 4.2 14.8 - - + +
930K GLN* 3.6 40.4 - - + -
931K VAL* 5.1 6.3 - - + -
934K LYS* 4.0 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 902 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898K HIS* 3.1 31.1 + - + +
899K PHE* 3.8 13.5 - - + +
901K PHE* 1.3 79.7 - - - +
903K ALA* 1.3 62.8 + - - +
905K PHE* 3.3 6.4 + - + +
906K ASN* 2.9 34.2 + - - +
931K VAL* 5.8 1.1 - - + -
998K PRO* 3.9 30.7 - - + +
999K LEU* 3.5 42.4 - - + +
1002K SER* 3.7 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 903 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073G LYS* 6.1 2.5 - - - +
899K PHE 3.0 19.9 + - - +
900K ASP* 3.6 7.0 - - - +
902K LEU* 1.3 76.5 - - - +
904K GLU* 1.3 57.8 + - - +
906K ASN* 3.3 6.5 + - - +
907K ALA* 3.0 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 904 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900K ASP* 2.9 20.4 + - - +
901K PHE* 3.4 11.0 - - - +
903K ALA* 1.3 74.6 - - - +
905K PHE* 1.3 64.7 + - - +
907K ALA* 3.4 14.8 + - + +
908K LYS* 3.4 11.6 + - + +
927K LEU* 3.7 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 905 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901K PHE 2.7 20.1 + - - +
902K LEU* 3.7 6.3 - - + +
904K GLU* 1.3 74.2 - - - +
906K ASN* 1.3 59.6 + - - +
908K LYS* 3.2 3.4 + - + +
909K ALA* 2.8 36.4 + - + +
910K ASN* 3.9 7.2 - - - -
917K ILE* 4.8 2.0 - - + -
927K LEU* 3.8 21.0 - - + +
928K VAL* 4.5 13.7 - - + -
931K VAL* 3.5 37.5 - - + -
1002K SER* 3.4 42.4 - - - -
1003K TYR* 4.0 10.5 - + - -
1006K ALA* 3.6 22.0 - - + -
1008K LEU* 4.2 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 906 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902K LEU* 2.9 32.4 + - - +
903K ALA* 3.8 5.4 - - - +
905K PHE* 1.3 73.4 - - - +
907K ALA* 1.3 66.7 + - - +
910K ASN* 2.9 66.7 + - + +
911K ASP* 3.6 1.2 + - - +
1002K SER* 3.0 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 907 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903K ALA 3.0 17.0 + - - +
904K GLU* 3.6 10.8 - - + +
905K PHE 3.3 0.4 - - - -
906K ASN* 1.3 77.1 - - - +
908K LYS* 1.3 60.2 + - + +
911K ASP* 3.8 11.5 - - - +
914K SER* 3.2 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 908 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904K GLU* 3.4 9.5 + - + +
905K PHE* 3.2 6.1 + - + +
906K ASN 3.0 0.4 - - - -
907K ALA* 1.3 82.4 - - + +
909K ALA* 1.3 63.4 + - + +
914K SER* 3.2 21.1 + - - +
915K ASN 3.3 11.6 + - - +
916K GLY 2.9 14.5 - - - +
917K ILE* 4.6 4.5 - - + -
918K GLU* 4.3 13.3 + - - -
921K ASN* 4.9 4.4 - - - +
924K ASP* 3.2 42.8 + - - +
927K LEU* 4.5 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 909 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905K PHE* 2.8 31.0 + - + +
908K LYS* 1.3 75.5 - - - +
910K ASN* 1.3 61.6 + - - +
911K ASP 3.6 3.7 + - - +
915K ASN 5.4 0.2 - - - -
916K GLY* 3.4 17.9 + - - +
917K ILE* 3.5 22.2 - - + -
1006K ALA* 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 910 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905K PHE* 3.9 9.5 - - - -
906K ASN* 2.9 46.3 + - + +
909K ALA* 1.3 73.1 - - - +
911K ASP* 1.3 56.6 + - - +
912K VAL* 4.2 1.9 - - - +
1002K SER* 2.9 26.1 + - - +
1005K ALA* 2.9 41.7 - - + +
1006K ALA* 3.0 6.1 + - - +
----------------------------------------------------------
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