Contacts of the helix formed by residues 903 - 916 (chain B) in PDB entry 6MZL
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 SER 903 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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897B TYR* 3.9 30.5 - - - -
898B THR* 3.3 26.0 - - - +
901B ASP* 3.4 7.8 + - - -
902B ARG* 1.3 72.9 - - - +
904B TYR* 1.3 61.8 + - - +
905B GLU* 3.8 4.6 + - - +
906B GLU* 3.3 29.9 + - - +
907B LEU* 3.6 3.1 + - - +
936B PHE* 5.8 1.0 - - - -
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Residues in contact with TYR 904 (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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902B ARG 3.0 8.6 + - - +
903B SER* 1.3 73.2 - - - +
905B GLU* 1.3 72.4 + - + +
907B LEU* 3.2 11.2 + - + +
908B GLN* 3.0 48.8 + - + +
936B PHE* 4.6 19.3 - + + -
943B PRO 5.3 3.1 - - - -
944B LEU 5.7 3.4 - - - -
947B GLU* 5.2 10.9 + - - -
948B ALA* 5.3 6.8 + - - +
949B LEU* 4.6 31.5 + - + +
952B GLN* 5.4 3.5 + - - -
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Residues in contact with GLU 905 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903B SER* 3.3 4.6 + - - +
904B TYR* 1.3 94.0 - - + +
906B GLU* 1.3 62.3 + - + +
908B GLN* 3.2 8.2 + - - +
909B TRP* 2.9 24.9 + - - +
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Residues in contact with GLU 906 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B PRO* 4.4 22.5 - - + +
875B LYS* 3.3 28.3 - - - +
894B VAL* 4.8 10.5 - - + +
897B TYR* 5.4 1.3 - - + -
898B THR* 4.6 9.9 - - - +
903B SER* 3.3 19.3 + - - +
905B GLU* 1.3 78.1 - - + +
907B LEU* 1.3 60.5 + - - +
909B TRP* 3.1 36.7 - - + +
910B LEU* 2.8 28.4 + - - +
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Residues in contact with LEU 907 (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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898B THR* 3.7 25.1 - - + +
903B SER 3.6 5.2 + - - +
904B TYR* 3.2 14.5 + - + +
906B GLU* 1.3 76.2 - - - +
908B GLN* 1.3 60.5 + - - +
910B LEU* 3.1 16.6 + - + +
911B LEU* 2.9 49.0 + - + +
930B LEU* 5.3 6.1 - - + -
935B PRO* 4.8 10.1 - - + -
936B PHE* 3.6 33.9 - - + -
949B LEU* 3.7 25.1 - - + -
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Residues in contact with GLN 908 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904B TYR* 3.0 36.9 + - + +
905B GLU* 3.3 11.4 - - - +
907B LEU* 1.3 76.2 - - - +
909B TRP* 1.3 54.4 + - - +
911B LEU* 3.3 6.5 + - - +
912B ASN* 2.6 69.9 + - - +
949B LEU* 4.7 6.7 - - - +
952B GLN* 2.9 39.5 + - - +
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Residues in contact with TRP 909 (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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875B LYS* 3.2 46.3 - - + +
878B ALA* 3.7 22.2 - - + -
879B GLU* 6.2 0.4 - - - -
891B LEU* 4.6 8.5 - - + -
894B VAL* 4.8 12.8 - - + -
905B GLU 2.9 13.6 + - - +
906B GLU* 3.1 32.3 - - + +
908B GLN* 1.3 76.0 - - - +
910B LEU* 1.3 72.8 + - + +
912B ASN* 3.2 11.6 + - + +
913B MET* 2.9 68.8 + - + +
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Residues in contact with LEU 910 (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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891B LEU* 4.4 16.2 - - + -
894B VAL* 5.3 5.4 - - + +
895B VAL* 4.1 26.5 - - + -
898B THR* 5.8 4.0 - - - +
906B GLU 2.8 21.0 + - - +
907B LEU* 3.1 18.4 + - + +
909B TRP* 1.3 84.4 - - + +
911B LEU* 1.3 59.0 + - + +
913B MET* 3.1 6.1 + - + +
914B ILE* 2.8 32.3 + - + +
926B ILE* 3.7 38.6 - - + -
930B LEU* 4.4 16.6 - - + -
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Residues in contact with LEU 911 (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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907B LEU* 2.9 42.3 + - + +
908B GLN* 3.8 10.1 - - - +
910B LEU* 1.3 77.4 - - + +
912B ASN* 1.3 60.3 + - - +
914B ILE* 3.3 23.6 - - + +
915B GLN* 2.9 26.7 + - - +
930B LEU* 5.0 6.5 - - + -
949B LEU* 4.5 14.4 - - + -
952B GLN* 5.1 7.9 - - + +
953B LEU* 3.7 37.0 - - + +
956B LEU* 4.1 23.1 - - + +
974B LEU* 6.2 1.3 - - + -
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Residues in contact with ASN 912 (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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908B GLN* 2.6 56.4 + - - +
909B TRP* 3.5 11.7 - - + +
911B LEU* 1.3 77.3 - - - +
913B MET* 1.3 50.5 + - - +
915B GLN* 3.3 9.4 - - - +
916B ASN* 2.7 36.1 + - - +
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Residues in contact with MET 913 (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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878B ALA 3.9 18.2 - - - +
879B GLU* 6.0 0.7 - - - -
887B ARG* 4.8 11.2 - - - +
891B LEU* 4.2 24.7 - - + -
909B TRP* 2.9 59.8 + - + +
910B LEU* 3.1 6.0 + - + +
912B ASN* 1.3 75.7 - - - +
914B ILE* 1.3 60.5 + - - +
916B ASN 3.1 18.9 + - - +
917B ASP* 2.9 42.9 - - + +
922B VAL* 6.5 0.4 - - + -
926B ILE* 4.8 8.1 - - + -
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Residues in contact with ILE 914 (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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910B LEU* 2.8 24.9 + - + +
911B LEU* 3.2 31.6 + - + +
913B MET* 1.3 74.4 - - - +
915B GLN* 1.3 58.4 + - - +
923B ARG* 2.9 39.0 + - + +
926B ILE* 3.7 30.0 - - + +
927B LEU* 3.7 43.7 - - + -
930B LEU* 4.9 1.6 - - + -
956B LEU* 5.3 8.3 - - + -
967B LEU* 6.2 2.7 - - + -
974B LEU* 5.8 0.9 - - + -
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Residues in contact with GLN 915 (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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911B LEU 2.9 13.4 + - - +
912B ASN* 3.3 13.0 - - - +
914B ILE* 1.3 77.0 - - - +
916B ASN* 1.3 61.4 + - + +
923B ARG* 2.4 27.9 + - - -
956B LEU* 3.8 20.4 - - + +
960B GLY* 3.2 33.7 - - - +
963B HIS* 4.1 16.8 + - - -
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Residues in contact with ASN 916 (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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912B ASN 2.7 18.6 + - - +
913B MET* 3.1 23.0 + - - +
915B GLN* 1.3 84.0 - - + +
917B ASP* 1.3 64.3 + - - +
923B ARG* 3.6 0.6 + - - +
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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