Contacts of the helix formed by residues 1050 - 1057 (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 SER1050 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896A ASP* 2.5 25.9 + - - -
946A TYR* 2.9 18.7 + - - -
947A TYR* 3.5 7.6 + - - -
950A GLN* 5.7 3.4 - - - -
1049A PHE* 1.3 82.3 - - - +
1051A LYS* 1.3 64.4 + - - +
1052A LEU* 3.3 5.1 + - - +
1053A LEU 2.9 12.6 + - - -
1054A GLU* 3.0 19.2 + - - +
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Residues in contact with LYS1051 (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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1049A PHE 4.5 0.9 - - - +
1050A SER* 1.3 74.3 - - - +
1052A LEU* 1.3 64.3 + - - +
1054A GLU* 3.5 8.2 + - - +
1055A ALA* 3.2 20.8 + - - +
1255A ARG* 5.1 3.5 + - - +
1258A THR* 5.7 5.2 - - + -
1259A TRP* 4.1 27.7 - - + +
1262A GLN* 2.7 31.2 + - - +
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Residues in contact with LEU1052 (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* 4.1 7.9 - - + +
1050A SER* 3.2 7.0 + - - +
1051A LYS* 1.3 78.1 - - - +
1053A LEU* 1.3 59.6 + - - +
1055A ALA* 3.1 6.4 + - + +
1056A TYR* 3.0 52.9 + - + +
1176A VAL* 3.6 22.2 - - + +
1177A ASN* 5.1 2.5 - - + +
1256A PHE* 4.0 22.9 - - + -
1259A TRP* 3.3 68.3 - - + +
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Residues in contact with LEU1053 (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* 3.3 29.1 + - - +
899A MET* 3.8 16.2 - - + -
900A TYR* 3.6 35.4 - - + -
903A ILE* 5.3 2.0 - - + -
946A TYR* 3.8 10.3 - - + -
1049A PHE* 3.7 33.0 - - + -
1050A SER* 2.9 19.9 + - - +
1052A LEU* 1.3 73.6 - - - +
1054A GLU* 1.3 65.9 + - - +
1056A TYR* 3.3 7.6 + - + -
1057A LEU* 3.1 37.1 + - + +
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Residues in contact with GLU1054 (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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927A VAL* 5.5 5.0 - - - +
933A TYR* 5.4 6.0 - - - -
943A TYR* 4.8 1.2 + - - -
1048A SER* 3.3 18.5 - - - +
1049A PHE* 2.9 42.9 + - - +
1050A SER 3.0 20.9 + - - +
1051A LYS* 3.8 8.1 - - - +
1053A LEU* 1.3 78.1 - - - +
1055A ALA* 1.3 60.8 + - - +
1057A LEU* 3.8 17.7 + - - +
1058A LEU* 3.7 16.3 - - - +
1255A ARG* 3.7 22.1 + - - +
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Residues in contact with ALA1055 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1051A LYS 3.2 12.5 + - - +
1052A LEU* 3.1 10.4 + - + +
1054A GLU* 1.3 76.5 - - - +
1056A TYR* 1.3 65.4 + - - +
1058A LEU* 3.3 20.2 + - - +
1059A VAL* 4.1 1.2 - - - +
1252A LEU* 3.5 15.4 - - + +
1255A ARG* 4.1 26.0 - - + +
1256A PHE* 3.5 26.7 - - + -
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Residues in contact with TYR1056 (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* 4.3 17.7 - - + -
897A LEU* 4.8 2.7 - - - -
900A TYR* 3.1 33.0 - - + -
1052A LEU* 3.0 34.6 + - + +
1053A LEU* 3.3 17.9 + - + +
1055A ALA* 1.3 75.3 - - - +
1057A LEU* 1.3 54.5 + - - +
1058A LEU 3.0 0.2 - - - -
1059A VAL* 2.8 30.6 + - - +
1176A VAL* 3.6 16.4 + - + +
1178A LEU* 3.3 35.6 - - + +
1221A ILE* 3.9 15.5 - - + -
1225A LEU* 3.5 33.7 - - + -
1256A PHE* 3.8 24.7 - + - -
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Residues in contact with LEU1057 (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* 3.8 19.5 - - + -
903A ILE* 3.8 30.3 - - + -
904A SER* 4.5 4.3 - - - +
907A ARG* 5.5 4.4 - - - -
927A VAL* 3.6 40.7 - - + +
928A PHE* 4.8 7.4 - - + -
1049A PHE* 4.3 20.4 - - + -
1053A LEU* 3.1 36.7 + - + +
1054A GLU* 3.9 15.7 - - - +
1055A ALA 3.3 0.4 - - - -
1056A TYR* 1.3 79.2 - - - +
1058A LEU* 1.3 59.2 + - - +
1059A VAL 3.1 4.7 + - - +
1060A LYS* 4.4 8.0 - - - +
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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