Contacts of the helix formed by residues 954 - 961 (chain M) in PDB entry 6D6Q
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 954 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943M ALA* 5.4 0.3 - - - +
952M GLU 4.2 0.4 + - - -
953M ILE* 1.3 85.8 - - - +
955M GLU* 1.3 79.8 + - - +
956M GLU* 3.4 17.6 + - - +
957M THR* 3.4 31.4 + - + +
958M TYR* 3.3 23.9 - - - +
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Residues in contact with GLU 955 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940M LYS* 3.7 30.9 - - - +
943M ALA* 3.8 28.9 - - + -
944M LYS* 5.3 12.3 - - - +
953M ILE 4.4 0.2 + - - -
954M ASP* 1.3 85.3 + - - +
956M GLU* 1.3 74.9 + - + +
958M TYR* 3.4 2.0 + - - +
959M LEU* 2.9 37.1 + - + +
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Residues in contact with GLU 956 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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954M ASP* 3.4 11.7 + - - +
955M GLU* 1.3 86.5 - - + +
957M THR* 1.3 59.3 + - + +
959M LEU* 3.8 10.4 - - - +
960M SER* 2.9 41.1 + - - +
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Residues in contact with THR 957 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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953M ILE* 5.2 3.5 - - - +
954M ASP* 3.4 36.5 + - + +
956M GLU* 1.3 75.0 - - + +
958M TYR* 1.3 62.0 + - - +
960M SER* 2.9 5.6 + - - -
961M SER* 2.6 44.6 + - - -
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Residues in contact with TYR 958 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567M TYR* 5.5 7.5 - + - -
884M ASP* 2.3 34.6 + - - -
886M LEU* 5.4 0.9 - - - +
887M LEU* 4.5 10.2 + - + +
939M ALA* 4.2 28.9 - - + -
942M ILE* 3.8 26.3 - - + +
943M ALA* 4.7 11.0 - - + -
953M ILE* 4.6 19.5 - - + -
954M ASP 3.3 17.3 - - - +
955M GLU* 3.4 4.2 + - - +
957M THR* 1.3 82.4 + - - +
959M LEU* 1.3 66.2 + - + +
961M SER* 3.5 18.5 + - - -
962M PHE* 4.1 18.1 - + - -
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Residues in contact with LEU 959 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935M MET* 4.7 3.5 - - - +
936M GLN* 4.1 36.1 - - + +
939M ALA* 4.6 13.7 - - + -
940M LYS* 3.5 45.5 - - + +
955M GLU* 2.9 24.7 + - + +
956M GLU* 3.8 9.6 - - - +
958M TYR* 1.3 83.1 - - + +
960M SER* 1.3 68.8 + - - +
961M SER 3.6 0.3 + - - -
962M PHE* 3.9 19.0 + - - +
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Residues in contact with SER 960 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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956M GLU* 2.9 26.0 + - - +
957M THR* 3.3 4.9 - - - -
959M LEU* 1.3 83.4 - - - +
961M SER* 1.3 56.7 + - - +
962M PHE 2.9 13.7 + - - +
963M LYS* 3.3 21.0 + - - +
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Residues in contact with SER 961 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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912M PHE 5.0 0.2 - - - +
914M PHE 4.4 5.5 - - - +
915M GLN* 4.6 10.0 + - - +
957M THR* 2.6 30.7 + - - -
958M TYR* 3.6 14.2 - - - -
959M LEU 3.3 1.2 - - - -
960M SER* 1.3 71.7 - - - +
962M PHE* 1.3 74.3 - - - +
963M LYS* 3.7 20.4 + - - +
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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