Contacts of the helix formed by residues 958 - 969 (chain H) in PDB entry 3AOI
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 THR 958 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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956H GLY 4.3 0.2 + - - -
957H LYS* 1.3 74.2 - - + +
959H PRO* 1.4 61.1 - - - +
960H GLU* 3.2 19.0 + - + +
961H GLU* 2.7 53.8 + - + +
962H GLN* 2.7 15.3 + - - -
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Residues in contact with PRO 959 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936H VAL* 4.1 29.4 - - + -
941H VAL* 5.4 11.4 - - + -
944H LEU* 3.8 26.1 - - + +
957H LYS 3.7 2.4 - - - +
958H THR* 1.4 86.5 - - - +
960H GLU* 1.3 53.1 + - - +
962H GLN* 3.4 6.4 - - + +
963H LEU* 2.7 37.5 + - - +
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Residues in contact with GLU 960 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922H PHE* 4.0 13.9 - - - -
923H GLU* 5.3 1.0 - - - +
926H PHE* 3.5 38.0 - - + -
930H LYS* 3.6 34.4 + - - +
936H VAL* 5.1 1.4 - - - +
958H THR* 2.9 13.6 + - + +
959H PRO* 1.3 80.4 - - - +
961H GLU* 1.3 71.8 + - + +
963H LEU* 3.3 3.2 + - - +
964H LYS* 3.2 19.9 + - - +
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Residues in contact with GLU 961 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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957H LYS* 3.0 37.2 + - + +
958H THR* 2.7 38.3 + - + +
960H GLU* 1.3 83.2 - - + +
962H GLN* 1.3 60.8 + - - +
964H LYS* 3.3 15.6 + - - +
965H GLU* 3.1 21.7 + - - +
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Residues in contact with GLN 962 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944H LEU* 3.5 33.7 - - + +
948H GLU* 2.9 28.8 + - - +
953H VAL* 3.5 28.2 - - + +
954H THR 5.0 0.2 - - - -
956H GLY 4.6 0.8 - - - +
957H LYS* 2.3 42.4 + - + +
958H THR 2.7 24.2 + - - +
959H PRO* 3.4 10.2 - - + +
961H GLU* 1.3 69.0 - - - +
963H LEU* 1.3 66.1 + - - +
965H GLU* 3.1 8.3 + - - +
966H LEU* 2.9 21.3 + - - +
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Residues in contact with LEU 963 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922H PHE* 3.6 16.2 - - + -
925H TYR* 5.7 6.7 - - + -
926H PHE* 3.8 30.7 - - + -
936H VAL* 5.1 4.9 - - + -
940H GLU* 3.3 28.5 - - + +
944H LEU* 4.4 12.7 - - + +
959H PRO 2.7 20.2 + - - +
960H GLU* 3.7 1.6 - - - +
962H GLN* 1.3 72.7 - - - +
964H LYS* 1.3 52.6 + - - +
966H LEU* 3.0 15.8 + - + +
967H PHE* 2.6 37.6 + - + +
972H VAL* 5.1 7.4 - - + -
973H VAL* 4.3 26.7 - - + +
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Residues in contact with LYS 964 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919H ALA* 3.3 41.6 + - - +
922H PHE* 3.3 35.8 - - + +
923H GLU* 3.8 12.8 + - - +
960H GLU* 3.2 6.7 + - - +
961H GLU* 3.4 20.0 - - - +
962H GLN 3.1 0.6 - - - -
963H LEU* 1.3 78.7 - - - +
965H GLU* 1.3 57.9 - - - +
967H PHE* 3.0 2.6 + - - +
968H LEU* 2.8 45.9 + - + +
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Residues in contact with GLU 965 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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952H LEU 4.4 13.5 - - - +
953H VAL* 4.0 6.4 - - + +
954H THR* 2.5 50.8 + - - +
957H LYS* 3.6 18.0 + - - +
961H GLU 3.1 8.6 + - - +
962H GLN 3.1 9.8 + - - +
964H LYS* 1.3 79.1 - - - +
966H LEU* 1.3 60.1 + - - +
968H LEU* 3.5 16.0 + - + +
969H GLN* 3.4 23.9 + - + +
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Residues in contact with LEU 966 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943H VAL* 5.5 0.9 - - + +
944H LEU* 4.1 13.7 - - + -
947H ALA* 3.8 16.4 - - + -
952H LEU* 3.6 34.8 - - + +
953H VAL* 3.9 12.3 - - + +
962H GLN 2.9 11.5 + - - +
963H LEU* 3.0 17.5 + - + +
965H GLU* 1.3 75.0 - - - +
967H PHE* 1.3 59.4 + - - +
969H GLN* 3.5 13.8 + - + +
971H LYS* 2.4 31.4 + - + +
972H VAL* 5.7 0.4 - - - -
973H VAL* 5.6 6.3 - - + -
986H PRO* 3.1 41.3 - - + -
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Residues in contact with PHE 967 (chain H).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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892H LEU* 4.0 22.1 - - + +
896H PHE* 5.0 7.0 - + - -
918H LEU* 3.1 43.1 - - + +
921H ALA* 3.7 21.3 - - + -
922H PHE* 3.3 36.6 - + + -
925H TYR* 3.7 23.3 - + + -
963H LEU* 2.6 20.9 + - + +
964H LYS 3.4 2.0 - - - +
966H LEU* 1.3 70.3 - - - +
968H LEU* 1.3 57.0 + - + +
969H GLN 3.0 1.6 - - - -
970H GLY* 2.5 31.0 + - - -
971H LYS 3.3 9.3 + - - -
972H VAL* 3.4 30.1 - - + -
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Residues in contact with LEU 968 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915H LYS* 2.8 49.6 - - + +
918H LEU* 3.3 14.5 - - - +
919H ALA* 3.5 42.6 - - + +
922H PHE* 5.7 0.2 - - + -
964H LYS* 2.8 37.9 + - + +
965H GLU* 3.5 20.4 - - + +
967H PHE* 1.3 76.0 - - + +
969H GLN* 1.3 60.4 + - - +
970H GLY 2.9 1.3 + - - -
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Residues in contact with GLN 969 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889H HIS* 3.7 13.4 + - - -
915H LYS* 4.4 2.2 - - - +
951H GLY 5.2 1.0 - - - +
952H LEU* 3.3 48.8 - - - +
965H GLU* 3.4 15.1 + - + +
966H LEU* 3.5 15.5 - - + +
967H PHE 3.0 0.8 + - - -
968H LEU* 1.3 77.9 - - - +
970H GLY* 1.3 59.4 + - - +
971H LYS* 3.4 20.4 - - + +
950I GLY* 5.1 2.8 - - - -
952I ASP* 3.5 42.4 - - - +
953I ASP* 4.8 3.2 + - - -
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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