Contacts of the helix formed by residues 894 - 906 (chain A) in PDB entry 1MWH
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 894 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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826A PHE* 5.0 2.6 - - - -
872A TYR 3.5 3.6 + - - -
873A TRP* 2.9 30.3 + - - -
874A GLY* 4.0 3.8 - - - -
893A PRO* 1.3 75.0 - - - +
895A GLY* 1.3 72.7 + - - +
896A ASP 3.6 0.2 + - - -
897A LEU* 3.5 8.1 + - - +
898A GLY* 3.2 8.4 + - - -
1181A PRO* 5.1 5.1 - - + +
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Residues in contact with GLY 895 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872A TYR* 2.8 50.7 + - - -
894A THR* 1.3 81.0 - - - +
896A ASP* 1.3 65.4 + - - -
898A GLY* 3.5 0.2 - - - -
899A MET* 2.9 24.3 + - - +
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Residues in contact with ASP 896 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872A TYR* 3.9 7.9 + - - -
895A GLY* 1.3 71.4 - - - -
897A LEU* 1.3 58.7 + - - +
899A MET* 3.2 4.2 + - - +
900A TYR* 2.8 32.3 + - - +
946A TYR* 2.7 31.6 + - - -
1050A SER* 2.5 28.6 + - - -
1052A LEU* 4.1 7.7 - - + +
1053A LEU* 3.3 19.5 + - + +
1056A TYR* 4.3 13.7 - - + -
1178A LEU* 6.3 0.2 - - + -
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Residues in contact with LEU 897 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893A PRO* 3.5 27.6 - - + -
894A THR 3.5 4.8 + - - +
895A GLY 3.2 1.0 + - - -
896A ASP* 1.3 78.4 - - - +
898A GLY* 1.3 58.1 + - - +
900A TYR* 3.6 5.3 - - + +
901A SER* 3.0 30.6 + - - +
1056A TYR* 4.8 3.6 - - - -
1178A LEU* 4.0 19.9 - - + +
1179A ALA 4.8 3.4 - - - +
1181A PRO* 4.6 10.1 - - + -
1184A TRP* 4.8 3.1 - - + -
1224A PHE* 3.8 47.1 - - + +
1225A LEU* 3.8 27.1 - - + -
1228A GLY* 4.6 3.8 - - - -
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Residues in contact with GLY 898 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871A VAL 6.1 0.2 - - - -
892A MET* 3.9 10.4 - - - +
893A PRO* 3.3 33.1 - - - +
894A THR 3.2 4.8 + - - -
895A GLY 3.0 5.8 + - - -
897A LEU* 1.3 76.0 - - - +
899A MET* 1.3 65.5 + - - +
901A SER* 3.0 2.8 + - - -
902A TRP* 3.0 30.9 + - - -
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Residues in contact with MET 899 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A TRP* 5.0 5.4 - - + +
871A VAL* 4.1 14.4 - - - +
872A TYR* 3.9 31.4 - - + -
895A GLY 2.9 19.7 + - - +
896A ASP 3.6 4.3 - - - +
898A GLY* 1.3 74.5 - - - +
900A TYR* 1.3 62.6 + - - +
902A TRP* 3.4 35.7 - - + +
903A ILE* 3.1 37.4 + - + +
942A LEU* 4.4 10.8 - - + +
946A TYR* 4.0 24.5 - - + -
1049A PHE* 4.3 14.6 - - + -
1053A LEU* 3.8 13.9 - - + -
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Residues in contact with TYR 900 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896A ASP 2.8 17.5 + - - +
897A LEU* 3.6 8.5 - - + +
899A MET* 1.3 78.4 - - - +
901A SER* 1.3 62.2 + - - +
903A ILE* 4.0 3.3 - - - +
904A SER* 2.9 55.4 + - - -
1053A LEU* 3.6 13.6 - - + +
1056A TYR* 3.1 43.5 - - + -
1057A LEU* 3.8 15.0 - - + -
1059A VAL* 2.7 23.6 + - - +
1061A TRP* 2.9 22.4 + - - -
1225A LEU* 3.6 45.1 - - + -
1229A MET* 4.3 6.5 - - + -
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Residues in contact with SER 901 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893A PRO* 4.0 2.3 - - - +
897A LEU 3.0 18.9 + - - -
898A GLY 3.0 6.0 + - - -
900A TYR* 1.3 85.2 - - - +
902A TRP* 1.3 64.3 + - - +
904A SER* 3.4 1.7 + - - -
905A LEU* 3.1 27.8 + - - +
1228A GLY* 2.7 36.4 - - - -
1229A MET* 3.2 6.4 + - - +
1232A THR* 3.1 23.7 + - - -
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Residues in contact with TRP 902 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868A TRP* 3.6 30.7 - + - -
871A VAL* 3.4 26.5 - - + +
877A LEU* 3.5 21.8 - - + -
881A PHE* 4.1 9.4 - + - -
888A PHE* 3.8 27.5 - + + -
892A MET* 3.9 13.7 - - - -
898A GLY 3.0 32.7 + - - -
899A MET* 3.4 35.1 - - + +
901A SER* 1.3 73.9 - - - +
903A ILE* 1.3 84.2 + - + +
905A LEU* 3.3 12.2 + - - +
906A ILE* 3.4 27.5 + - + +
910A MET* 3.9 26.5 - - + -
942A LEU* 4.2 9.2 - - + -
1232A THR* 4.2 1.3 - - + +
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Residues in contact with ILE 903 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899A MET* 3.1 29.7 + - + +
900A TYR* 4.0 2.2 - - - +
902A TRP* 1.3 109.3 - - + +
904A SER* 1.3 60.6 + - - +
906A ILE 3.0 4.3 + - - -
907A ARG* 2.7 31.3 + - + -
910A MET* 3.9 20.5 - - + +
928A PHE* 4.1 18.6 - - + -
937A PHE* 5.9 0.2 - - + -
942A LEU* 5.7 0.9 - - + -
1049A PHE* 4.4 28.0 - - + -
1053A LEU* 5.3 2.0 - - + -
1057A LEU* 3.8 25.8 - - + -
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Residues in contact with SER 904 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900A TYR* 2.9 47.5 + - - -
901A SER 3.8 2.2 - - - -
903A ILE* 1.3 77.6 - - - +
905A LEU* 1.3 62.7 - - - +
906A ILE 3.3 0.5 + - - -
907A ARG* 3.6 18.7 + - - +
908A PRO* 4.6 3.1 - - - +
1057A LEU* 4.5 4.2 - - - +
1059A VAL 4.7 2.4 + - - -
1229A MET* 3.4 33.1 - - - +
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Residues in contact with LEU 905 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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887A ILE* 4.9 2.2 - - + +
888A PHE* 3.7 22.7 - - + -
901A SER 3.1 14.8 + - - +
902A TRP 3.5 7.6 - - - +
903A ILE 3.1 0.4 - - - -
904A SER* 1.3 78.5 - - - +
906A ILE* 1.3 63.9 + - + +
908A PRO* 5.0 2.6 - - - +
1063A MET* 3.1 38.4 - - + +
1229A MET* 4.0 10.1 - - + +
1232A THR* 3.6 43.7 - - + -
1233A ALA* 3.9 17.9 - - + +
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Residues in contact with ILE 906 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880A ALA* 4.2 14.8 - - + +
881A PHE* 4.1 16.6 - - + -
883A SER* 4.1 1.6 - - - -
887A ILE* 3.7 27.1 - - + -
888A PHE* 3.8 20.2 - - + -
902A TRP* 3.5 21.8 - - + +
903A ILE 3.0 0.8 + - - -
905A LEU* 1.3 82.6 - - + +
907A ARG* 1.3 60.1 + - - +
908A PRO* 3.4 4.3 - - - -
909A LEU* 3.1 28.4 + - + -
910A MET* 2.8 48.6 + - + +
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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