Contacts of the helix formed by residues 960 - 966 (chain B) in PDB entry 1M8X
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 HIS 960 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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926B LEU* 3.6 47.0 - - + +
956B GLU 3.5 16.7 + - - -
957B LEU 2.8 9.0 + - - +
958B ASP 3.1 22.5 + - - -
959B GLY* 1.3 83.6 + - - +
961B VAL* 1.3 67.6 + - - +
962B LEU 3.5 2.0 - - - -
963B LYS* 3.3 17.1 + - + +
964B CYS* 3.2 22.7 + - - -
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Residues in contact with VAL 961 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957B LEU* 3.4 5.9 + - - +
959B GLY* 3.6 8.2 - - - +
960B HIS* 1.3 78.4 - - - +
962B LEU* 1.3 64.3 + - + +
964B CYS* 3.3 5.3 + - - +
965B VAL* 2.9 30.5 + - + +
974B VAL* 4.6 2.8 - - + +
988B PHE* 3.6 37.2 - - + +
989B ILE* 4.0 22.9 - - + -
992B ALA* 3.6 33.0 - - + -
993B PHE* 4.1 17.0 - - + -
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Residues in contact with LEU 962 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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960B HIS 3.5 0.4 - - - -
961B VAL* 1.3 81.7 - - + +
963B LYS* 1.3 58.3 + - - +
965B VAL* 3.6 7.3 - - - +
966B LYS* 2.7 51.4 + - + +
992B ALA* 3.2 37.9 - - + +
993B PHE* 5.0 7.0 - - + -
996B GLN* 4.0 32.5 - - + +
1000B LEU* 5.4 4.7 - - + -
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Residues in contact with LYS 963 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926B LEU* 5.6 3.6 - - + -
930B LEU* 4.2 27.1 - - + +
960B HIS* 3.3 21.4 + - + +
962B LEU* 1.3 77.2 - - - +
964B CYS* 1.3 61.9 + - - +
966B LYS* 3.4 4.6 - - - +
967B ASP* 2.9 44.0 + - - +
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Residues in contact with CYS 964 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926B LEU* 3.8 27.4 - - - -
929B ALA* 4.9 5.6 - - - -
930B LEU* 4.3 9.2 - - - -
957B LEU* 4.1 19.3 - - + -
960B HIS 3.2 15.7 + - - -
961B VAL* 3.7 5.2 - - - +
963B LYS* 1.3 77.9 - - - +
965B VAL* 1.3 63.7 + - - +
967B ASP* 3.0 13.4 + - - +
970B GLY* 3.1 10.4 - - - +
971B ASN 2.7 27.4 + - - -
973B VAL* 5.8 0.7 - - + -
974B VAL* 3.6 19.1 - - + -
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Residues in contact with VAL 965 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961B VAL* 2.9 23.5 + - + +
962B LEU* 3.6 6.5 - - - +
964B CYS* 1.3 76.7 - - - +
966B LYS* 1.3 59.8 + - + +
967B ASP 3.1 0.9 + - - -
971B ASN* 2.9 25.3 - - - +
974B VAL* 3.8 25.8 - - + -
993B PHE* 3.7 36.6 - - + -
1000B LEU* 4.4 13.5 - - + -
1005B TYR* 3.4 9.5 - - - +
1006B GLY* 3.8 25.1 - - - -
1009B VAL* 4.1 8.1 - - + -
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Residues in contact with LYS 966 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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962B LEU* 2.7 33.6 + - + +
963B LYS* 3.4 6.5 - - - +
965B VAL* 1.3 73.2 - - + +
967B ASP* 1.3 55.3 + - - +
968B GLN 4.4 0.2 + - - -
996B GLN* 4.6 8.3 + - - -
999B ALA* 4.5 16.3 - - - +
1000B LEU* 3.3 32.4 - - + +
1003B HIS* 3.6 35.9 + - + +
1005B TYR* 4.0 9.9 - - - -
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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