Contacts of the strand formed by residues 144 - 152 (chain A) in PDB entry 1SZ7


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.
For CSU analysis of other PDB entry

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 MET 144 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  CYS      5.0     1.3    -      -       -      +
     69A  HIS*     3.8    33.7    -      -       +      +
     71A  PHE*     3.8    28.9    -      -       +      +
     74A  THR*     3.6    25.8    -      -       -      -
    136A  ARG      4.8     0.3    -      -       -      +
    139A  LEU*     3.0    41.6    +      -       +      +
    140A  GLU*     3.4     4.7    +      -       -      +
    142A  VAL*     3.6    17.5    -      -       +      +
    143A  GLN*     1.3    80.3    -      -       -      +
    145A  ALA*     1.3    60.7    +      -       -      +
    146A  VAL*     3.5     7.9    +      -       +      -
    167A  PHE*     3.7    32.8    -      -       +      -
    169A  ARG      4.0     2.9    -      -       -      -
    170A  ARG*     5.4     0.9    -      -       -      -
    171A  ILE*     3.9     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140A  GLU*     5.5     1.6    -      -       -      +
    144A  MET*     1.3    68.4    -      -       -      +
    146A  VAL*     1.3    63.7    +      -       -      +
    167A  PHE*     4.0     1.7    -      -       -      -
    168A  ILE*     2.8    35.3    +      -       +      +
    169A  ARG*     2.9    42.5    +      -       +      +
    171A  ILE*     3.7    19.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  PHE*     4.2    18.8    -      -       +      -
    136A  ARG*     3.4    46.3    -      -       +      +
    139A  LEU*     3.8    35.2    -      -       +      -
    144A  MET*     3.5    14.4    +      -       +      +
    145A  ALA*     1.3    78.4    -      -       -      +
    147A  GLU*     1.3    64.4    +      -       -      +
    148A  ALA      4.9     0.4    -      -       -      +
    165A  MET*     3.9    15.3    -      -       +      -
    166A  ARG      3.2    15.0    -      -       -      +
    167A  PHE*     4.3     3.1    -      -       +      -
    168A  ILE*     3.7     9.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  ARG*     5.1     2.9    -      -       -      +
    146A  VAL*     1.3    75.7    -      -       -      +
    148A  ALA*     1.3    69.8    +      -       -      +
    149A  LYS*     3.7    34.3    +      -       +      +
    164A  ARG*     3.7     2.4    -      -       -      +
    165A  MET*     3.3     5.0    -      -       -      +
    166A  ARG*     2.8    77.3    +      -       -      +
    168A  ILE*     3.8     6.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  CYS*     3.4    42.6    -      -       +      +
    135A  LEU*     4.2    13.0    -      -       +      -
    136A  ARG*     5.0    10.8    +      -       +      +
    146A  VAL*     4.2     2.1    +      -       +      +
    147A  GLU*     1.3    78.1    -      -       -      +
    149A  LYS*     1.3    62.9    +      -       -      +
    163A  ILE*     4.3     2.2    -      -       +      -
    164A  ARG      3.4     4.7    -      -       -      -
    165A  MET*     3.8    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  ASN*     5.7     0.2    -      -       -      -
    132A  CYS*     3.7     9.1    -      -       -      -
    147A  GLU*     3.7    30.3    +      -       +      +
    148A  ALA*     1.3    76.4    -      -       -      +
    150A  PHE*     1.3    65.1    +      -       -      +
    151A  VAL*     3.5    25.2    +      -       +      -
    163A  ILE*     3.4     3.9    -      -       -      +
    164A  ARG*     2.8    48.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107A  LEU*     5.6     0.7    -      -       +      -
    110A  ASN*     4.7     3.8    -      -       -      -
    111A  PRO*     6.4     0.4    -      -       +      -
    126A  ILE*     3.5    32.0    -      -       +      +
    128A  SER*     3.3    48.5    -      -       -      -
    129A  ASN*     3.9     1.7    +      -       -      -
    131A  LEU*     4.5     5.8    -      -       +      -
    132A  CYS*     3.5    25.3    -      -       -      -
    149A  LYS*     1.3    75.9    -      -       -      +
    151A  VAL*     1.3    63.3    +      -       -      +
    152A  GLN      3.8    19.7    -      -       -      +
    153A  ASP*     4.9     9.4    -      -       +      -
    161A  THR*     3.5    24.0    -      -       +      -
    162A  GLU      3.4     2.2    -      -       -      -
    163A  ILE*     3.7    26.5    -      -       +      +
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Residues in contact with VAL 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  LYS*     3.5    28.9    +      -       +      -
    150A  PHE*     1.3    77.9    -      -       -      +
    152A  GLN*     1.3    66.6    +      -       +      +
    158A  ASP*     4.6     1.6    -      -       -      +
    162A  GLU*     2.8    50.4    +      -       +      +
    164A  ARG*     4.0    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  ILE*     4.9     1.4    -      -       -      +
    150A  PHE*     3.8     6.2    -      -       -      -
    151A  VAL*     1.3    82.5    -      -       +      +
    153A  ASP*     1.3    64.3    +      -       -      +
    158A  ASP*     3.3    27.5    -      -       -      +
    159A  GLY      4.2     4.7    +      -       -      -
    160A  VAL*     3.4    32.8    -      -       -      +
    161A  THR*     3.4     5.7    -      -       -      +
    162A  GLU*     2.9    55.3    +      -       +      +
----------------------------------------------------------
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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
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
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