Contacts of the helix formed by residues 823 - 834 (chain A) in PDB entry 5J68
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 ALA 823 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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741A GLN* 3.6 24.7 - - + +
742A VAL 2.9 21.6 + - - +
743A PHE 3.7 13.9 - - - +
744A GLN* 3.7 13.3 - - - +
822A LEU* 1.3 73.9 - - - +
824A ALA* 1.3 61.8 + - - +
825A GLY 4.5 1.1 - - - +
826A PHE* 3.9 7.4 - - + +
827A THR* 2.7 32.1 + - - -
1310A NAG 6.0 3.8 - - - +
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Residues in contact with ALA 824 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744A GLN* 4.9 6.8 + - - +
822A LEU 4.0 0.4 + - - -
823A ALA* 1.3 71.0 - - - +
825A GLY* 1.3 67.0 + - - +
827A THR* 3.3 5.7 + - - -
828A ASN* 2.9 32.1 + - - +
1310A NAG 4.0 22.7 + - - +
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Residues in contact with GLY 825 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823A ALA* 4.5 1.8 - - - +
824A ALA* 1.3 79.1 - - - +
826A PHE* 1.3 62.0 + - - +
828A ASN* 3.5 10.6 + - - +
829A VAL* 3.4 21.0 + - - +
849A TYR* 3.4 15.7 + - - -
1310A NAG 4.5 13.2 + - - -
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Residues in contact with PHE 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741A GLN 3.5 16.6 + - - +
742A VAL* 3.7 33.0 - - + +
822A LEU* 3.7 30.7 - - + -
823A ALA* 3.7 8.6 + - + +
824A ALA 3.2 0.8 - - - -
825A GLY* 1.3 77.2 - - - +
827A THR* 1.3 58.6 + - - +
829A VAL* 3.3 5.2 - - - +
830A LEU* 3.0 48.5 + - + +
845A PHE* 3.6 29.6 - + - -
849A TYR* 3.6 32.6 + + - -
962A LEU* 4.5 11.9 - - + -
965A LEU* 4.0 22.4 - - + -
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Residues in contact with THR 827 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822A LEU* 3.8 20.8 + - + +
823A ALA 2.7 23.8 + - - -
824A ALA* 3.3 3.8 + - - -
826A PHE* 1.3 75.3 - - - +
828A ASN* 1.3 61.7 + - - +
830A LEU* 3.9 14.4 - - + -
831A LYS* 2.8 54.4 + - + +
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Residues in contact with ASN 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824A ALA* 2.9 30.4 + - - +
825A GLY* 3.8 10.4 - - - +
826A PHE 3.3 0.2 - - - -
827A THR* 1.3 77.1 - - - +
829A VAL* 1.3 65.3 + - + +
831A LYS* 3.2 25.3 + - - +
832A ILE* 3.3 18.9 + - - +
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Residues in contact with VAL 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825A GLY 3.4 13.4 + - - +
826A PHE 3.3 12.3 - - - +
828A ASN* 1.3 79.5 - - + +
830A LEU* 1.3 63.8 + - - +
832A ILE* 3.4 17.5 - - + +
833A LEU* 3.2 34.0 + - + +
845A PHE* 4.0 12.8 - - + -
849A TYR* 3.6 32.1 - - + +
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Residues in contact with LEU 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822A LEU* 4.5 6.1 - - + -
826A PHE* 3.0 48.0 + - + +
827A THR* 3.7 12.6 - - + +
828A ASN 3.2 0.2 - - - -
829A VAL* 1.3 81.5 - - + +
831A LYS* 1.3 61.2 + - - +
833A LEU* 4.7 3.0 - - + +
834A THR* 3.4 24.3 + - - -
845A PHE* 4.5 14.8 - - + -
962A LEU 5.9 0.4 - - - +
965A LEU 3.6 24.2 - - - +
966A ILE* 4.4 33.7 - - + +
967A GLN* 6.1 0.9 - - - +
971A THR* 6.2 2.0 - - + -
975A PHE* 6.3 1.6 - - + -
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Residues in contact with LYS 831 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827A THR* 2.8 46.0 + - + +
828A ASN* 3.2 17.2 + - - +
830A LEU* 1.3 79.6 - - - +
832A ILE* 1.3 63.5 + - + +
834A THR* 3.1 23.1 - - - +
835A LYS* 3.4 13.9 + - - +
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Residues in contact with ILE 832 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828A ASN 3.3 12.5 + - - +
829A VAL* 3.4 25.1 - - + +
831A LYS* 1.3 80.5 - - + +
833A LEU* 1.3 79.5 + - + +
834A THR 3.3 0.6 + - - -
835A LYS* 4.0 13.9 + - - +
836A GLU* 3.7 17.8 + - - +
841A GLU* 4.8 0.8 - - - +
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Residues in contact with LEU 833 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829A VAL* 3.2 23.9 + - + +
830A LEU* 4.7 4.0 - - + +
832A ILE* 1.3 93.4 - - + +
834A THR* 1.3 66.5 + - - +
835A LYS 3.2 1.3 - - - -
836A GLU* 3.1 21.4 + - - +
837A SER* 5.0 0.3 - - - -
841A GLU* 3.2 43.7 - - + +
842A LEU* 4.5 19.8 - - + +
845A PHE* 3.9 39.5 - - + -
971A THR* 4.6 5.3 - - - +
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Residues in contact with THR 834 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830A LEU* 3.4 16.7 + - - +
831A LYS* 3.1 22.2 - - - +
833A LEU* 1.3 80.2 - - - +
835A LYS* 1.3 72.5 + - + +
837A SER* 4.7 5.2 + - - -
966A ILE* 5.5 1.8 - - - -
968A ASP* 3.1 18.2 + - - -
971A THR* 2.6 48.5 + - - +
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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