Contacts of the helix formed by residues 824 - 833 (chain G) in PDB entry 1X86
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 824 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823G LEU* 1.3 78.6 - - - +
825G PRO* 1.3 71.8 - - - +
826G SER* 2.7 29.4 + - - -
827G GLU* 3.3 19.7 + - - +
828G LEU* 3.1 26.2 + - - +
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Residues in contact with PRO 825 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823G LEU 4.7 0.2 - - - +
824G SER* 1.3 86.3 - - - +
826G SER* 1.3 60.8 + - - +
827G GLU 3.2 0.7 - - - -
828G LEU* 3.7 14.8 - - + +
829G ARG* 3.1 38.4 + - - +
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Residues in contact with SER 826 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824G SER* 2.7 20.3 + - - -
825G PRO* 1.3 80.3 - - - +
827G GLU* 1.3 61.5 + - - +
829G ARG* 4.3 18.3 + - - +
830G LYS* 3.6 19.4 + - - +
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Residues in contact with GLU 827 (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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823G LEU* 3.1 28.6 - - + +
824G SER* 3.3 20.6 + - - +
825G PRO 3.2 0.2 - - - -
826G SER* 1.3 80.9 + - - +
828G LEU* 1.3 57.6 + - - +
829G ARG 3.2 1.6 - - - -
830G LYS* 3.6 6.5 - - + +
831G ILE* 2.8 42.8 + - + +
897G MET* 5.2 10.8 - - + -
901G ARG* 2.8 48.6 + - - -
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Residues in contact with LEU 828 (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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814G TYR* 3.9 32.4 - - + +
817G VAL* 3.9 28.0 - - + -
818G SER* 3.9 28.9 - - - +
823G LEU* 4.1 15.0 - - + +
824G SER 3.1 24.6 + - - +
825G PRO* 3.7 17.3 - - + +
827G GLU* 1.3 76.2 - - - +
829G ARG* 1.3 61.6 + - + +
832G PHE* 3.3 31.1 + - + +
833G SER 3.9 0.9 + - - +
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Residues in contact with ARG 829 (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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825G PRO* 3.1 22.6 + - - +
826G SER* 4.5 17.1 + - - +
827G GLU 3.2 0.6 - - - -
828G LEU* 1.3 77.9 - - + +
830G LYS* 1.3 57.7 + - - +
833G SER* 2.7 40.0 + - - +
890G ASN* 3.8 3.1 + - - -
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Residues in contact with LYS 830 (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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826G SER 3.6 16.9 + - - +
827G GLU* 3.1 8.0 + - - +
829G ARG* 1.3 78.4 - - - +
831G ILE* 1.3 61.0 + - - +
833G SER 4.4 0.4 - - - -
890G ASN* 3.7 22.3 - - - +
893G PHE* 3.5 40.6 + - + +
894G ALA* 3.1 15.9 - - - +
897G MET* 3.6 33.5 - - + +
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Residues in contact with ILE 831 (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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823G LEU* 3.5 39.7 - - + -
827G GLU* 2.8 21.3 + - + +
830G LYS* 1.3 73.2 - - - +
832G PHE* 1.3 85.6 + - + +
833G SER* 3.7 1.0 + - - -
894G ALA* 3.0 23.1 - - - +
897G MET* 3.1 31.0 - - + -
898G ILE* 3.5 31.9 - - + -
901G ARG* 4.7 1.3 - - + -
908G PHE* 4.2 14.4 - - + -
926G LEU* 4.7 0.7 - - + -
930G ILE* 4.2 6.8 - - + +
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Residues in contact with PHE 832 (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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809G LEU* 4.1 26.0 - - + -
813G PHE* 3.9 22.2 - - + -
814G TYR* 3.4 47.1 - + + -
817G VAL* 4.2 16.4 - - + -
823G LEU* 5.0 3.6 - - + -
828G LEU* 3.3 17.8 + - + +
831G ILE* 1.3 96.3 - - + +
833G SER* 1.3 78.3 + - - +
834G ASN 3.2 1.6 + - - -
835G LEU* 3.3 24.7 + - + +
887G PHE* 3.9 9.0 - + - -
908G PHE* 6.4 1.1 - + - -
911G PHE* 5.7 2.0 - + - -
926G LEU* 4.0 25.6 - - + -
930G ILE* 5.0 4.5 - - + -
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Residues in contact with SER 833 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814G TYR* 5.7 2.6 - - - -
828G LEU 4.8 0.5 - - - +
829G ARG* 2.7 33.5 + - - +
830G LYS 5.3 0.2 - - - -
831G ILE 3.7 0.6 - - - -
832G PHE* 1.3 84.6 + - - +
834G ASN* 1.3 65.4 + - - -
835G LEU* 3.4 2.9 + - - +
886G THR 5.0 2.0 - - - -
887G PHE* 3.8 23.2 + - - -
890G ASN* 3.1 35.7 - - - +
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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