Contacts of the strand formed by residues 1059 - 1066 (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 VAL1059 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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900A TYR* 2.7 27.5 + - - +
904A SER* 4.7 2.4 + - - -
1055A ALA 4.1 6.3 - - - +
1056A TYR* 2.8 15.6 + - - +
1057A LEU 4.2 2.6 - - - +
1058A LEU* 1.3 80.1 - - + +
1060A LYS* 1.3 62.9 + - - +
1061A TRP* 3.5 20.0 - - + +
1222A LEU* 3.6 22.4 - - + -
1225A LEU* 4.0 14.1 - - + -
1242A LEU* 3.7 14.8 - - + -
1244A ASP 3.4 4.0 - - - +
1245A ILE* 4.5 4.3 - - + +
1252A LEU* 3.8 28.9 - - + -
1256A PHE* 5.8 0.4 - - + -
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Residues in contact with LYS1060 (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* 4.5 31.6 - - - +
926A THR* 3.3 34.5 + - - +
927A VAL* 5.1 0.6 - - - +
1057A LEU 4.4 6.5 - - - +
1058A LEU 3.3 29.4 - - - +
1059A VAL* 1.3 75.0 - - - +
1061A TRP* 1.3 69.8 + - - +
1242A LEU* 3.6 5.0 - - - +
1243A GLU* 3.1 23.3 + - + +
1244A ASP* 2.7 50.5 + - + +
1246A HIS* 4.6 1.3 - - - -
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Residues in contact with TRP1061 (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 29.2 + - - -
904A SER* 5.8 0.2 - - - -
1059A VAL* 3.5 20.0 - - + +
1060A LYS* 1.3 80.5 - - - +
1062A ARG* 1.3 66.8 + - - +
1063A MET* 4.2 2.1 + - - +
1197A VAL* 3.6 25.6 - - + -
1198A LYS 3.9 4.0 - - - -
1199A LEU* 3.9 10.3 - - + -
1222A LEU* 3.0 33.2 - - + -
1225A LEU* 4.0 7.3 - - + +
1226A GLY* 3.4 14.0 - - - +
1229A MET* 3.7 22.3 - - + +
1240A ILE* 3.5 29.4 - - + -
1241A TYR 3.4 8.1 - - - -
1242A LEU* 3.4 37.0 - - + -
1243A GLU* 3.8 5.8 - - - +
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Residues in contact with ARG1062 (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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1061A TRP* 1.3 74.5 - - - +
1063A MET* 1.3 62.6 + - - +
1064A CYS* 3.7 13.6 + - - -
1202A LYS* 3.5 39.0 - - - +
1203A ASP* 4.0 20.2 + - - +
1240A ILE* 3.6 1.4 - - - -
1241A TYR* 2.7 47.0 + - + +
1242A LEU 6.0 0.2 - - - -
1243A GLU* 2.9 46.9 + - + +
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Residues in contact with MET1063 (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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905A LEU* 3.1 39.0 - - + +
1061A TRP 4.4 1.3 + - - +
1062A ARG* 1.3 74.8 - - - +
1064A CYS* 1.3 64.1 + - - +
1229A MET* 3.2 33.7 - - + +
1230A VAL* 5.0 2.5 - - - -
1233A ALA* 4.9 7.0 - - + -
1238A VAL* 3.9 16.4 - - + -
1239A ASP 3.9 4.7 - - - -
1240A ILE* 3.8 21.3 - - + -
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Residues in contact with CYS1064 (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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1062A ARG* 3.8 20.0 - - - -
1063A MET* 1.3 80.0 - - - +
1065A GLU* 1.3 93.3 + - - +
1066A ALA 3.4 0.3 + - - -
1202A LYS* 4.0 18.8 - - - -
1238A VAL* 3.3 16.3 - - - +
1239A ASP 2.9 14.7 + - - +
1241A TYR* 3.6 23.6 - - + -
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Residues in contact with GLU1065 (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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1064A CYS* 1.3 95.1 - - - +
1066A ALA* 1.3 68.9 + - - +
1202A LYS* 2.7 34.2 + - - -
1239A ASP* 3.0 41.3 + - - +
1241A TYR* 3.7 16.3 + - - -
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Residues in contact with ALA1066 (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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1064A CYS 3.4 1.6 + - - -
1065A GLU* 1.3 80.7 - - - +
1067A ARG* 1.3 68.2 + - - +
1068A GLU* 3.9 4.2 + - - +
1236A VAL* 3.4 30.7 - - + -
1237A ALA 3.9 0.2 - - - -
1238A VAL* 3.5 14.1 - - + +
1239A ASP* 4.9 1.3 - - - +
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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