Contacts of the helix formed by residues 905 - 927 (chain q) in PDB entry 6FF7
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 GLN 905 (chain q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853q SER* 2.8 38.3 + - - +
854q ILE* 3.0 11.2 + - - +
856q TYR* 5.1 3.9 - - + +
904q VAL* 1.3 72.9 - - - +
906q PHE* 1.3 65.8 + - - +
907q ARG* 4.3 4.5 - - + +
908q SER* 3.9 7.8 - - - +
909q MET* 3.1 22.2 + - - +
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Residues in contact with PHE 906 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896q SER* 5.4 9.0 - - - +
899q CYS* 4.2 18.6 - - + -
904q VAL 3.4 4.9 + - - -
905q GLN* 1.3 71.2 - - - +
907q ARG* 1.3 60.4 + - - +
909q MET* 3.2 6.3 + - - +
910q ARG* 2.8 34.2 + - + +
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Residues in contact with ARG 907 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651q ASN* 5.9 8.1 - - + +
853q SER* 6.3 0.7 - - - -
905q GLN* 3.2 4.8 - - + +
906q PHE* 1.3 80.8 - - - +
908q SER* 1.3 63.0 + - - +
910q ARG* 3.4 5.2 + - - +
911q ARG* 3.0 23.0 + - - +
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Residues in contact with SER 908 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
850q VAL* 4.0 12.3 - - - +
851q ASN* 4.0 17.5 - - - -
853q SER* 3.9 26.0 - - - -
854q ILE* 4.2 9.4 - - - -
905q GLN* 3.3 9.1 + - - +
906q PHE 3.2 0.4 - - - -
907q ARG* 1.3 75.9 - - - +
909q MET* 1.3 61.9 + - - +
911q ARG* 3.2 8.1 + - - +
912q ALA* 2.9 27.7 + - - +
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Residues in contact with MET 909 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854q ILE* 5.9 1.3 - - - +
889q TRP* 4.8 19.1 - - + -
904q VAL* 6.1 3.4 - - + -
905q GLN 3.1 14.2 + - - +
906q PHE* 3.8 6.1 - - - +
908q SER* 1.3 78.9 - - - +
910q ARG* 1.3 58.2 + - - +
912q ALA* 3.1 9.2 + - - +
913q ARG* 2.9 26.7 + - - +
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Residues in contact with ARG 910 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906q PHE* 2.8 18.1 + - + +
907q ARG* 3.8 5.6 - - - +
909q MET* 1.3 76.7 - - - +
911q ARG* 1.3 63.3 + - - +
913q ARG* 3.0 18.7 + - - +
914q ASP* 3.0 13.2 + - - +
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Residues in contact with ARG 911 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
850q VAL* 5.0 7.9 - - + -
907q ARG 3.0 14.6 + - - +
908q SER* 3.5 10.3 - - - +
910q ARG* 1.3 76.6 - - - +
912q ALA* 1.3 64.0 + - - +
914q ASP* 3.1 8.0 + - - +
915q VAL* 2.9 24.3 + - - +
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Residues in contact with ALA 912 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846q ALA* 3.5 35.0 - - + +
847q MET* 4.5 8.5 - - + +
850q VAL* 4.8 6.0 - - + +
886q TYR* 6.3 3.6 - - + -
908q SER 2.9 14.0 + - - +
909q MET* 3.3 12.6 - - - +
911q ARG* 1.3 77.3 - - - +
913q ARG* 1.3 55.8 + - - +
915q VAL* 3.3 2.6 + - - -
916q ARG* 2.9 27.3 + - - +
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Residues in contact with ARG 913 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909q MET 2.9 12.7 + - - +
910q ARG* 3.0 13.0 + - - +
912q ALA* 1.3 77.8 - - - +
914q ASP* 1.3 64.0 + - - +
916q ARG* 3.2 8.1 + - - +
917q GLU* 3.1 20.8 + - - +
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Residues in contact with ASP 914 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484q PHE* 5.1 12.7 - - + +
910q ARG 3.0 12.3 + - - +
911q ARG* 3.6 9.4 - - - +
913q ARG* 1.3 75.2 - - - +
915q VAL* 1.3 65.4 + - - +
917q GLU* 3.0 9.7 + - - +
918q GLN* 2.9 22.8 + - - +
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Residues in contact with VAL 915 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484q PHE* 4.5 13.2 - - + +
846q ALA* 4.3 16.4 - - + +
849q SER* 5.1 9.0 - - - -
911q ARG 2.9 16.1 + - - +
912q ALA* 3.7 6.3 - - - +
914q ASP* 1.3 75.5 - - - +
916q ARG* 1.3 58.8 + - - +
918q GLN* 3.1 7.2 + - - +
919q LEU* 2.8 31.1 + - - +
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Residues in contact with ARG 916 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842q LEU* 5.0 11.5 - - + +
843q THR* 5.3 5.4 - - - -
846q ALA* 3.8 16.5 - - + +
912q ALA 2.9 18.2 + - - +
913q ARG* 3.6 7.2 - - - +
914q ASP 3.2 0.2 - - - -
915q VAL* 1.3 75.4 - - - +
917q GLU* 1.3 58.0 + - - +
919q LEU* 3.2 6.6 + - - +
920q GLU* 2.8 30.2 + - - +
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Residues in contact with GLU 917 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913q ARG 3.1 10.8 + - - +
914q ASP* 3.0 12.8 + - - +
916q ARG* 1.3 77.3 - - - +
918q GLN* 1.3 62.6 + - - +
920q GLU* 3.2 9.2 + - - +
921q GLY* 3.1 18.2 + - - -
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Residues in contact with GLN 918 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484q PHE* 4.3 25.1 - - + +
914q ASP 2.9 12.7 + - - +
915q VAL* 3.6 6.3 - - - +
917q GLU* 1.3 76.0 - - - +
919q LEU* 1.3 63.2 + - - +
921q GLY* 3.2 3.9 + - - -
922q LEU* 3.1 19.8 + - - +
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Residues in contact with LEU 919 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842q LEU* 5.8 9.6 - - + +
845q ALA* 6.5 0.9 - - + -
846q ALA* 6.2 1.1 - - + -
915q VAL 2.8 17.2 + - - +
916q ARG* 3.6 7.0 - - - +
918q GLN* 1.3 75.3 - - - +
920q GLU* 1.3 60.0 + - - +
922q LEU* 3.0 11.4 + - - +
923q LEU* 2.9 27.3 + - - +
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Residues in contact with GLU 920 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842q LEU* 6.2 5.1 - - + +
916q ARG 2.8 16.9 + - - +
917q GLU* 3.2 8.3 + - - +
919q LEU* 1.3 76.2 - - - +
921q GLY* 1.3 57.8 + - - +
923q LEU* 3.0 10.0 + - - +
924q GLU* 2.8 28.5 + - - +
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Residues in contact with GLY 921 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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917q GLU 3.1 13.0 + - - -
918q GLN* 3.2 4.9 + - - -
919q LEU 3.2 0.4 - - - -
920q GLU* 1.3 76.7 - - - +
922q LEU* 1.3 56.0 + - - +
924q GLU* 3.1 9.4 + - - +
925q ARG* 2.8 29.3 + - - +
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Residues in contact with LEU 922 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818q GLU* 5.5 8.7 - - + +
819q LEU* 6.0 7.0 - - + -
918q GLN 3.1 11.1 + - - +
919q LEU* 3.0 14.8 + - - +
921q GLY* 1.3 76.1 - - - +
923q LEU* 1.3 62.9 + - - +
925q ARG* 3.2 7.1 + - - +
926q VAL* 2.9 27.3 + - - +
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Residues in contact with LEU 923 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919q LEU 2.9 11.9 + - - +
920q GLU* 3.0 12.1 + - - +
922q LEU* 1.3 77.1 - - - +
924q GLU* 1.3 57.5 + - - +
926q VAL* 3.4 2.8 + - - -
927q GLU* 2.8 9.7 + - - -
928q VAL* 2.8 56.2 + - + +
930q LEU* 6.5 0.7 - - + -
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Residues in contact with GLU 924 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920q GLU 2.8 12.6 + - - +
921q GLY* 3.5 12.1 - - - +
923q LEU* 1.3 78.7 - - - +
925q ARG* 1.3 63.0 + - - +
927q GLU* 3.3 11.4 + - - +
928q VAL 5.3 0.7 - - - -
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Residues in contact with ARG 925 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921q GLY 2.8 15.7 + - - +
922q LEU* 3.2 6.7 + - - +
924q GLU* 1.3 78.7 - - - +
926q VAL* 1.3 60.8 + - - +
927q GLU* 3.5 1.4 + - - +
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Residues in contact with VAL 926 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815q LYS* 6.1 4.9 - - + -
818q GLU* 6.0 6.3 - - + -
922q LEU 2.9 17.6 + - - +
923q LEU* 3.9 4.9 - - - +
925q ARG* 1.3 74.6 - - - +
927q GLU* 1.3 72.4 + - - +
928q VAL* 4.5 5.3 - - + +
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Residues in contact with GLU 927 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923q LEU 2.8 6.0 + - - -
924q GLU* 3.3 7.2 + - - +
925q ARG 3.2 5.1 - - - +
926q VAL* 1.3 82.8 - - - +
928q VAL* 1.3 63.0 + - - +
929q GLY* 3.6 3.1 + - - -
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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) + - + + + + + -
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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