Contacts of the helix formed by residues 822 - 837 (chain A) in PDB entry 5QSY
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 ASP 822 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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777A GLN* 4.7 7.4 + - - +
820A ASN 3.4 3.3 + - - +
821A PRO* 1.3 78.3 - - - +
823A THR* 1.3 62.3 + - - +
824A GLY* 3.0 6.7 + - - -
825A LEU* 2.7 40.0 + - - +
826A GLN* 3.1 22.1 + - - +
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Residues in contact with THR 823 (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 ASP* 1.3 73.0 - - - +
824A GLY* 1.3 66.3 + - - +
826A GLN* 3.4 13.4 + - + +
827A SER* 3.0 24.9 + - - -
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Residues in contact with GLY 824 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777A GLN* 4.2 5.6 - - - -
822A ASP* 3.0 7.9 + - - -
823A THR* 1.3 77.8 - - - +
825A LEU* 1.3 56.3 + - - +
827A SER* 3.2 7.6 + - - -
828A GLU* 2.9 34.6 + - - +
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Residues in contact with LEU 825 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A LEU* 5.6 6.7 - - + +
777A GLN* 3.6 39.3 - - + +
780A LEU* 4.9 4.3 - - + -
795A LEU* 4.1 32.1 - - + -
799A LEU* 4.4 12.8 - - + -
821A PRO* 3.5 29.2 - - + -
822A ASP* 2.7 23.8 + - - +
824A GLY* 1.3 69.7 - - - +
826A GLN* 1.3 61.6 + - - +
828A GLU* 3.0 3.1 + - + +
829A LEU* 2.8 43.9 + - + +
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Residues in contact with GLN 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821A PRO* 3.2 26.9 + - + +
822A ASP 3.1 11.8 + - - +
823A THR* 3.6 12.7 + - + +
825A LEU* 1.3 79.0 - - - +
827A SER* 1.3 56.9 + - - +
829A LEU* 3.4 5.0 + - - +
830A LEU* 3.0 34.7 + - + +
880A ILE 3.7 9.6 + - - +
881A VAL* 3.3 31.8 - - + +
882A ASP* 2.8 34.1 + - + +
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Residues in contact with SER 827 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823A THR* 3.0 15.8 + - - -
824A GLY* 3.4 10.5 - - - -
826A GLN* 1.3 74.0 - - - +
828A GLU* 1.3 63.0 + - - +
830A LEU* 3.0 10.7 + - - +
831A SER* 2.9 32.8 + - - -
834A MET* 5.4 0.2 - - - +
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Residues in contact with GLU 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777A GLN* 2.7 38.6 + - - +
780A LEU* 3.9 26.4 - - + +
781A SER* 4.3 13.7 + - - -
824A GLY* 2.9 18.8 + - - +
825A LEU* 3.0 8.7 + - - +
827A SER* 1.3 76.2 - - - +
829A LEU* 1.3 57.5 + - - +
831A SER* 3.3 10.8 + - - +
832A PHE* 3.2 26.9 + - - +
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Residues in contact with LEU 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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780A LEU* 4.8 4.0 - - + -
792A PHE* 3.4 37.3 - - + -
795A LEU* 3.9 28.5 - - + -
796A CYS* 4.5 2.5 - - - -
799A LEU* 3.6 30.7 - - + -
821A PRO* 5.4 0.2 - - + -
825A LEU* 2.8 31.3 + - + +
826A GLN* 3.6 5.8 - - - +
828A GLU* 1.3 74.8 - - - +
830A LEU* 1.3 60.8 - - - +
832A PHE 4.3 0.4 - - - -
833A VAL* 3.3 22.0 + - - +
872A PHE* 3.6 14.7 - - + -
875A LEU* 4.2 8.1 - - + -
881A VAL* 4.2 14.8 - - + -
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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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826A GLN* 3.0 25.2 + - + +
827A SER* 3.0 11.8 + - - +
829A LEU* 1.3 76.2 - - - +
831A SER* 1.4 64.8 + - - +
833A VAL* 3.1 16.9 + - + +
834A MET* 3.1 25.1 + - + +
872A PHE* 4.0 23.8 - - + -
881A VAL* 4.7 6.7 - - + -
882A ASP* 4.5 19.1 - - + +
885A ALA* 4.0 15.9 - - + +
886A ALA* 3.9 23.8 - - + +
889A ILE* 3.9 23.3 - - + -
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Residues in contact with SER 831 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A SER* 2.9 18.4 + - - -
828A GLU* 3.3 12.0 + - - -
830A LEU* 1.4 74.9 - - - +
832A PHE* 1.3 56.6 + - - +
834A MET* 3.0 21.2 + - - +
835A ASP* 2.8 42.3 + - - +
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Residues in contact with PHE 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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780A LEU* 4.6 9.4 - - + -
788A LYS* 3.7 33.7 - - + -
789A GLU* 3.7 26.9 - - + -
792A PHE* 3.3 51.8 - + + -
828A GLU 3.2 12.3 + - - +
830A LEU 3.4 0.2 - - - -
831A SER* 1.3 77.8 - - - +
833A VAL* 1.3 56.4 + - - +
835A ASP* 5.1 0.2 - - - -
836A HIS* 2.7 72.7 + + + -
837A VAL* 4.6 4.9 - - + -
868A LEU* 4.1 16.4 - - + -
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Residues in contact with VAL 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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792A PHE* 4.0 9.2 - - + -
829A LEU 3.3 19.3 + - - +
830A LEU* 3.1 10.6 + - + +
832A PHE* 1.3 76.7 - - - +
834A MET* 1.3 63.5 + - + +
837A VAL* 3.0 37.2 + - + -
838A PHE* 3.1 39.5 + - + -
869A LEU* 4.2 9.9 - - + -
872A PHE* 3.7 33.0 - - + -
889A ILE* 4.8 5.2 - - + -
890A PHE* 4.7 4.9 - - + -
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Residues in contact with MET 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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827A SER 5.4 0.2 - - - +
830A LEU* 3.1 16.1 + - + +
831A SER* 3.0 34.6 + - - +
833A VAL* 1.3 77.0 - - - +
835A ASP* 1.3 64.8 + - - +
838A PHE* 3.0 15.6 - - - +
889A ILE* 3.5 43.7 - - + -
893A TYR* 3.0 32.8 + - + +
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Residues in contact with ASP 835 (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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831A SER* 2.8 28.8 + - - +
832A PHE* 5.1 0.2 - - - -
834A MET* 1.3 81.7 - - - +
836A HIS* 1.3 86.8 + - + +
839A ILE* 3.2 17.8 - - - +
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Residues in contact with HIS 836 (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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785A THR* 4.2 21.7 - - + +
788A LYS* 3.6 31.6 - - + +
789A GLU* 5.2 8.1 - - + +
832A PHE* 2.7 62.2 + + + +
835A ASP* 1.3 98.2 + - + +
837A VAL* 1.3 61.1 + - - +
839A ILE* 3.7 6.5 - - - +
865A ARG* 3.3 22.5 - - - +
868A LEU* 5.2 1.4 - - - +
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Residues in contact with VAL 837 (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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792A PHE* 5.5 0.2 - - + -
832A PHE* 3.5 6.4 + - + -
833A VAL* 3.0 32.6 + - + +
836A HIS* 1.3 76.4 - - - +
838A PHE* 1.3 75.6 + - + +
839A ILE* 3.2 7.4 + - - +
865A ARG* 3.3 48.6 + - + +
866A ARG* 5.8 0.2 - - - -
868A LEU* 4.3 11.0 - - + -
869A LEU* 3.8 37.7 - - + +
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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