Contacts of the helix formed by residues 831 - 847 (chain G) in PDB entry 6BAA
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 SER 831 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829G ASN 3.8 2.0 + - - -
830G LEU* 1.3 77.0 - - - +
832G GLY* 1.3 61.1 + - - +
833G GLY* 3.2 7.2 - - - -
834G GLN* 3.3 12.8 + - - +
835G ARG* 2.8 27.8 + - - +
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Residues in contact with GLY 832 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777G PRO* 4.4 7.7 - - - +
831G SER* 1.3 74.0 - - - +
833G GLY* 1.3 56.5 + - - +
835G ARG* 3.5 7.2 + - - +
836G GLN* 2.9 28.2 + - - +
859G ALA* 4.1 8.1 - - - +
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Residues in contact with GLY 833 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831G SER* 3.2 4.7 - - - -
832G GLY* 1.3 74.2 - - - +
834G GLN* 1.3 59.9 + - - +
836G GLN* 3.3 3.0 + - - +
837G ARG* 2.9 29.0 + - - +
859G ALA* 3.5 31.2 + - - +
860G LEU* 5.3 3.4 - - - +
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Residues in contact with GLN 834 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811G ASP* 5.5 11.7 - - + -
830G LEU* 4.2 10.1 - - + -
831G SER* 3.3 25.2 + - - +
833G GLY* 1.3 74.7 - - - +
835G ARG* 1.3 58.1 + - - +
837G ARG* 3.4 7.7 + - - +
838G ILE* 2.9 29.1 + - - +
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Residues in contact with ARG 835 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777G PRO* 3.7 24.7 - - + +
779G LEU* 5.7 9.2 - - + -
830G LEU* 4.5 9.7 - - + +
831G SER 2.8 20.7 + - - +
832G GLY* 3.6 7.9 - - - +
834G GLN* 1.3 73.4 - - - +
836G GLN* 1.3 57.4 + - - +
838G ILE* 3.3 7.9 + - - +
839G SER* 2.9 27.9 + - - -
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Residues in contact with GLN 836 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777G PRO* 4.2 9.8 - - + +
832G GLY 2.9 18.2 + - - +
833G GLY* 3.3 6.0 + - - +
835G ARG* 1.3 75.7 - - - +
837G ARG* 1.3 57.4 + - - +
839G SER* 3.2 8.3 + - - -
840G VAL* 2.9 28.4 + - - +
856G PRO* 4.7 14.4 - - + +
859G ALA* 4.3 15.5 - - + -
860G LEU* 6.6 0.2 - - + -
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Residues in contact with ARG 837 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806G CYS* 3.9 27.2 - - + +
833G GLY 2.9 17.0 + - - +
834G GLN* 3.7 7.6 - - - +
836G GLN* 1.3 77.6 - - - +
838G ILE* 1.3 57.2 + - - +
840G VAL* 3.4 7.5 + - - +
841G ALA* 2.9 29.9 + - - +
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Residues in contact with ILE 838 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779G LEU* 6.1 4.7 - - + -
787G ASN* 4.8 15.0 - - + +
788G ILE* 5.3 1.4 - - - -
834G GLN 2.9 18.7 + - - +
835G ARG* 3.5 8.5 - - - +
836G GLN 3.3 0.2 - - - -
837G ARG* 1.3 77.5 - - - +
839G SER* 1.3 55.4 + - - +
841G ALA* 3.3 7.4 + - - +
842G ARG* 2.9 29.7 + - - +
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Residues in contact with SER 839 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772G TYR 5.2 3.0 - - - +
773G ALA* 5.4 13.6 - - - +
774G SER 5.7 4.5 - - - -
777G PRO* 4.8 13.0 - - - -
778G TRP 5.4 7.0 - - - -
835G ARG 2.9 13.3 + - - -
836G GLN* 3.2 11.0 + - - -
838G ILE* 1.3 74.8 - - - +
840G VAL* 1.3 63.4 + - - +
842G ARG* 3.3 8.0 + - - +
843G ALA* 3.0 23.0 + - - +
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Residues in contact with VAL 840 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773G ALA* 5.6 5.1 - - - +
806G CYS* 5.8 2.0 - - + -
836G GLN 2.9 15.7 + - - +
837G ARG* 3.6 8.3 - - - +
839G SER* 1.3 76.8 - - - +
841G ALA* 1.3 55.7 + - - +
843G ALA* 3.3 7.4 + - - +
844G LEU* 2.9 29.9 + - - +
856G PRO* 5.7 9.2 - - + -
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Residues in contact with ALA 841 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788G ILE* 4.9 10.5 - - + -
802G VAL* 4.5 16.3 - - + +
806G CYS* 3.8 21.2 - - + +
837G ARG 2.9 18.9 + - - +
838G ILE* 3.3 7.8 + - - +
840G VAL* 1.3 76.3 - - - +
842G ARG* 1.3 57.1 + - - +
844G LEU* 3.9 5.4 - - - +
845G TYR* 2.8 33.4 + - - +
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Residues in contact with ARG 842 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787G ASN 3.8 18.4 - - - +
788G ILE* 3.7 15.6 - - - +
789G THR 5.5 0.5 - - - +
790G PHE* 4.6 12.1 - - + +
838G ILE 2.9 17.6 + - - +
839G SER* 3.5 8.7 - - - +
840G VAL 3.3 0.2 - - - -
841G ALA* 1.3 76.6 - - - +
843G ALA* 1.3 56.3 + - - +
845G TYR* 3.4 2.3 + - - +
846G GLN* 3.0 29.1 + - - +
1217G PHE* 6.0 7.2 - - + -
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Residues in contact with ALA 843 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771G ALA* 4.5 22.4 - - + +
772G TYR 4.5 15.0 - - - +
773G ALA* 5.3 4.9 - - + -
839G SER 3.0 13.1 + - - +
840G VAL* 3.6 10.1 - - - +
842G ARG* 1.3 77.5 - - - +
844G LEU* 1.3 61.7 + - - +
846G GLN* 3.3 17.5 + - - +
847G GLN* 3.7 4.7 + - - -
848G THR 4.7 1.7 + - - -
851G VAL* 5.7 5.6 - - + -
1217G PHE* 5.7 4.9 - - + -
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Residues in contact with LEU 844 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798G ARG* 3.0 22.4 + - - +
802G VAL* 5.5 7.0 - - + -
805G ALA* 6.5 0.9 - - + -
840G VAL 2.9 17.3 + - - +
841G ALA* 3.9 7.0 - - - +
843G ALA* 1.3 75.7 - - - +
845G TYR* 1.3 60.4 + - - +
847G GLN* 3.3 8.8 + - - -
875G GLU* 6.0 6.1 - - + -
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Residues in contact with TYR 845 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788G ILE* 3.7 21.8 - - + +
789G THR* 3.8 11.0 - - - -
792G SER* 3.2 29.6 - - - -
793G PRO 2.9 11.5 + - - -
794G PHE* 3.3 9.1 - + - +
795G ASN* 2.9 31.4 + - + +
798G ARG* 3.6 34.4 + - + +
799G TYR* 3.5 34.5 - + + -
802G VAL* 4.4 10.0 - - + +
841G ALA 2.8 18.0 + - - +
842G ARG 3.7 4.0 - - - +
844G LEU* 1.3 77.4 - - - +
846G GLN* 1.3 62.3 + - - +
847G GLN* 3.2 6.1 + - - +
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Residues in contact with GLN 846 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771G ALA* 5.4 3.6 - - + -
789G THR 5.8 2.7 - - - +
790G PHE* 6.4 2.0 - - + -
842G ARG 3.0 18.0 + - - +
843G ALA* 3.6 9.6 - - - +
844G LEU 3.3 0.6 - - - -
845G TYR* 1.3 80.2 - - - +
847G GLN* 1.3 66.4 + - - +
848G THR* 3.2 10.7 + - - +
1217G PHE* 6.1 5.2 - - + -
1219G TYR* 4.5 17.4 + - + +
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Residues in contact with GLN 847 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798G ARG* 3.9 22.2 - - - +
843G ALA 3.7 2.6 + - - -
844G LEU 3.3 9.8 + - - -
845G TYR 3.1 5.1 - - - +
846G GLN* 1.3 78.1 - - - +
848G THR* 1.3 66.2 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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