Contacts of the helix formed by residues 906 - 917 (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 ILE 906 (chain A).
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Specific contacts
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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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Residues in contact with ARG 907 (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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903A ILE* 2.7 20.6 + - + +
904A SER* 3.6 14.4 + - - +
906A ILE* 1.3 71.3 - - - +
908A PRO* 1.3 94.8 - - + +
910A MET* 3.0 10.6 + - - +
911A THR* 3.0 26.9 + - - -
926A THR 5.5 0.2 + - - -
927A VAL* 3.0 43.8 + - + +
928A PHE* 4.4 14.0 - - + +
1057A LEU* 5.5 4.5 - - - -
1060A LYS* 4.5 30.0 - - - +
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Residues in contact with PRO 908 (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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904A SER 4.6 4.5 - - - +
905A LEU 5.0 1.3 - - - +
906A ILE* 3.6 4.9 - - - -
907A ARG* 1.3 119.7 - - + +
909A LEU* 1.3 57.5 + - - +
911A THR* 3.2 6.6 + - - +
912A ARG* 2.9 30.0 + - - +
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Residues in contact with LEU 909 (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 5.1 0.4 - - - +
881A PHE* 3.4 21.8 - - + +
882A GLY 4.0 7.9 - - - +
883A SER* 3.5 35.9 - - - +
884A ASP 5.0 0.4 - - - +
906A ILE* 3.1 25.7 + - + +
908A PRO* 1.3 80.3 - - - +
910A MET* 1.3 57.8 + - + +
912A ARG* 3.2 39.6 + - - +
913A TRP* 2.8 31.3 + - + +
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Residues in contact with MET 910 (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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881A PHE* 3.6 50.9 - - + -
902A TRP* 3.9 13.7 - - + -
903A ILE* 3.9 40.4 - - + +
906A ILE* 2.8 33.2 + - + +
907A ARG* 3.0 7.2 + - - +
909A LEU* 1.3 71.2 - - - +
911A THR* 1.3 63.9 + - - +
913A TRP* 3.2 2.1 + - - +
914A MET* 2.9 39.5 + - + +
928A PHE* 4.4 14.1 - - + -
937A PHE* 4.4 14.1 - - + -
942A LEU* 5.0 1.6 - - + -
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Residues in contact with THR 911 (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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907A ARG* 3.0 16.8 + - - -
908A PRO* 3.5 10.8 - - - -
910A MET* 1.3 75.7 - - - +
912A ARG* 1.3 65.9 + - - +
914A MET* 3.1 13.4 + - - +
915A VAL* 3.2 20.1 + - + +
927A VAL 4.2 2.4 + - - -
928A PHE* 3.1 45.1 + - - +
929A GLY* 4.8 1.6 - - - +
930A ASN* 4.9 4.0 - - + +
931A ALA* 4.0 14.4 - - + +
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Residues in contact with ARG 912 (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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881A PHE 5.3 1.0 + - - -
882A GLY* 4.9 6.9 + - - -
908A PRO 2.9 16.8 + - - +
909A LEU* 3.5 35.4 - - - +
911A THR* 1.3 79.0 - - - +
913A TRP* 1.3 63.2 + - - +
915A VAL* 3.7 4.7 + - - +
916A ALA* 3.2 24.9 + - + +
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Residues in contact with TRP 913 (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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21A ASP* 4.7 6.2 + - - -
881A PHE* 3.6 54.3 - + + +
882A GLY* 4.3 3.6 - - - -
909A LEU* 2.8 16.6 + - + +
910A MET 3.5 3.8 - - - +
911A THR 3.1 0.2 - - - -
912A ARG* 1.3 78.8 - - - +
914A MET* 1.3 72.5 + - + +
916A ALA* 3.4 5.7 + - + +
917A ASN* 3.1 48.2 + - + +
919A TYR* 3.9 20.4 - + - -
936A CYS* 3.7 25.4 - - - -
940A LEU* 4.1 15.3 - - + -
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Residues in contact with MET 914 (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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881A PHE* 4.9 2.5 - - + -
910A MET* 2.9 37.3 + - + +
911A THR 3.1 4.0 + - - +
913A TRP* 1.3 84.7 - - + +
915A VAL* 1.3 55.9 + - - +
917A ASN 3.2 5.2 + - - -
919A TYR* 2.7 46.9 + - + +
928A PHE* 3.8 28.0 - - + -
931A ALA* 3.8 17.9 - - + -
933A TYR* 3.6 27.4 - - - -
936A CYS* 3.7 21.5 - - - -
937A PHE* 3.7 22.9 - - + -
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Residues in contact with VAL 915 (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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911A THR* 3.2 20.5 + - + +
912A ARG* 4.0 3.8 - - - +
914A MET* 1.3 72.2 - - - +
916A ALA* 1.3 60.8 + - - +
917A ASN 2.8 10.8 + - - -
918A GLY* 2.9 14.4 + - - -
919A TYR 3.8 16.2 - - - +
920A VAL* 4.4 19.1 - - + +
930A ASN* 4.0 21.3 - - + +
931A ALA* 4.2 5.2 - - + +
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Residues in contact with ALA 916 (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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912A ARG* 3.2 17.9 + - + +
913A TRP* 3.6 9.0 - - + +
915A VAL* 1.3 80.9 - - - +
917A ASN* 1.3 64.8 + - - +
918A GLY 3.5 0.4 - - - -
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Residues in contact with ASN 917 (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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913A TRP* 3.1 54.7 + - + +
914A MET 3.2 2.9 + - - +
915A VAL 2.9 1.6 - - - -
916A ALA* 1.3 84.7 + - - +
918A GLY* 1.3 58.2 + - - +
919A TYR* 3.4 26.1 + - + -
935A ARG* 5.2 2.6 + - - -
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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