Contacts of the helix formed by residues 924 - 930 (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 924 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890B TYR* 3.2 50.7 + + + +
920B ARG 4.2 9.4 - - - -
921B ILE* 2.9 11.0 + - - +
922B ARG 4.1 11.0 - - - -
923B GLY* 1.3 82.6 + - - +
925B VAL* 1.3 65.5 + - - +
926B LEU 3.3 2.7 - - - -
927B SER* 3.4 9.6 + - - +
928B LEU* 2.9 30.8 + - + +
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Residues in contact with VAL 925 (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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921B ILE* 3.6 23.7 + - + +
922B ARG* 4.9 0.2 - - - -
924B HIS* 1.3 77.1 - - - +
926B LEU* 1.3 57.2 + - - +
928B LEU* 3.4 1.4 + - - +
929B ALA* 2.8 28.7 + - + +
938B ILE* 4.4 24.2 - - + +
953B MET* 3.6 34.5 - - + +
956B GLU* 2.9 37.1 + - + +
957B LEU* 3.8 21.5 - - + -
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Residues in contact with LEU 926 (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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924B HIS 3.3 0.8 - - - -
925B VAL* 1.3 74.2 - - - +
927B SER* 1.3 69.4 + - - +
929B ALA* 2.9 13.6 + - - +
930B LEU* 3.0 33.9 + - + +
956B GLU* 4.4 5.7 + - + +
957B LEU* 4.3 12.5 - - + +
960B HIS* 3.6 58.6 - - + +
963B LYS* 5.6 4.5 - - + -
964B CYS* 3.8 20.9 - - - -
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Residues in contact with SER 927 (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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890B TYR* 3.4 22.0 + - - -
894B VAL* 5.8 1.2 - - - +
924B HIS* 3.4 16.0 + - - +
926B LEU* 1.3 81.3 - - - +
928B LEU* 1.3 62.6 + - - +
930B LEU* 3.6 8.8 + - - +
931B GLN* 3.4 22.2 + - - +
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Residues in contact with LEU 928 (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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890B TYR* 3.9 15.3 - - + -
893B MET* 3.9 30.1 - - + -
894B VAL* 3.6 30.7 - - + -
920B ARG 5.7 0.2 - - - +
921B ILE* 4.0 13.0 - - + -
924B HIS* 2.9 27.8 + - + +
925B VAL 3.7 0.9 - - - +
927B SER* 1.3 75.1 - - - +
929B ALA* 1.3 60.6 - - - +
930B LEU 3.1 2.0 - - - -
931B GLN* 2.9 9.3 + - - +
934B GLY* 3.2 14.7 - - - +
935B CYS* 2.7 28.6 + - - -
937B VAL* 5.9 0.7 - - + -
938B ILE* 3.7 30.3 - - + -
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Residues in contact with ALA 929 (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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925B VAL* 2.8 22.8 + - + +
926B LEU* 2.9 7.2 + - - +
928B LEU* 1.3 72.6 - - - +
930B LEU* 1.3 59.7 + - + +
931B GLN 3.4 0.3 + - - -
935B CYS* 2.9 22.5 - - - +
938B ILE* 4.2 3.9 - - + +
957B LEU* 4.6 9.0 - - + -
964B CYS* 4.9 4.0 - - - -
969B ASN 3.5 0.7 - - - -
970B GLY* 3.2 21.7 + - - -
973B VAL* 3.6 35.9 - - + -
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Residues in contact with LEU 930 (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* 3.0 44.3 + - + +
927B SER* 3.7 8.3 - - - +
928B LEU 3.1 0.2 - - - -
929B ALA* 1.3 76.1 - - - +
931B GLN* 1.3 56.1 + - - -
963B LYS* 4.2 27.6 - - + +
964B CYS* 4.3 18.4 - - - -
967B ASP* 3.3 40.1 - - + +
969B ASN* 3.7 17.7 + - - -
970B GLY* 4.6 2.5 - - - -
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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