Contacts of the strand formed by residues 128 - 134 (chain A) in PDB entry 1UMZ


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 HIS 128 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  GLN*     3.2     5.5    -      -       -      -
     60A  MET      2.9    30.2    +      -       -      -
    121A  PHE*     3.3    53.1    -      +       +      +
    122A  ASP      4.6     2.4    +      -       -      -
    123A  PRO*     4.9     1.1    -      -       +      -
    126A  GLU*     3.2    40.1    -      -       -      +
    127A  PHE*     1.3    78.0    +      -       -      +
    129A  TYR*     1.3    63.6    +      -       -      +
    130A  TYR*     3.5    25.3    -      -       +      +
    144A  ASP*     2.8    28.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 129 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  PRO*     4.1    22.2    +      -       +      -
      8A  ASP*     3.0    23.6    +      -       -      -
     57A  SER*     3.4    20.6    -      -       -      +
     58A  MET      3.5     3.6    -      -       -      -
     59A  GLN*     3.3    39.5    +      -       +      -
    128A  HIS*     1.3    73.6    -      -       -      +
    130A  TYR*     1.3    63.0    +      -       -      +
    131A  SER*     4.5     4.7    -      -       -      +
    143A  VAL*     3.4     5.5    -      -       -      +
    144A  ASP*     2.8    52.6    +      -       -      +
    201A  SER*     3.8    17.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 130 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  SER*     3.4     0.3    -      -       -      -
     58A  MET      2.8    33.2    +      -       -      +
     60A  MET*     3.8    34.7    +      -       +      -
     62A  LEU*     4.5     2.0    -      -       +      +
     74A  PHE*     3.4    19.7    -      -       +      -
     88A  PHE*     4.2    17.5    -      +       +      -
     90A  PHE*     3.5    34.2    -      +       +      -
    101A  LEU*     4.3     3.4    -      -       +      -
    119A  LEU*     3.9     2.3    -      -       +      +
    121A  PHE*     3.5    25.4    -      +       -      -
    123A  PRO*     3.9    13.7    -      -       -      +
    128A  HIS*     3.5    28.4    -      -       +      +
    129A  TYR*     1.3    74.8    -      -       -      +
    131A  SER*     1.3    60.5    +      -       -      +
    142A  LEU      3.4     3.1    -      -       -      -
    143A  VAL*     3.8    32.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  PRO*     4.9     2.8    -      -       -      +
     55A  HIS*     4.3    13.1    +      -       -      -
     56A  PHE      3.2     9.6    -      -       -      -
     57A  SER*     2.8    25.1    +      -       -      -
     74A  PHE*     4.7     0.4    -      -       -      -
     88A  PHE*     3.4     9.5    -      -       -      -
    129A  TYR*     4.5     5.9    -      -       -      +
    130A  TYR*     1.3    74.3    +      -       -      +
    132A  VAL*     1.3    64.6    +      -       -      +
    140A  VAL      4.4     0.2    -      -       -      -
    141A  PHE*     3.6     0.7    -      -       -      -
    142A  LEU*     2.9    51.2    +      -       -      +
    144A  ASP      5.1     2.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  GLY      3.8     1.0    -      -       -      +
     55A  HIS*     3.5     7.9    -      -       -      -
     56A  PHE*     2.9    38.8    +      -       +      +
     74A  PHE*     4.9     4.5    -      -       +      -
     75A  TYR*     6.5     0.2    -      -       -      -
     76A  LEU*     4.2    21.3    -      -       +      -
     86A  ILE*     4.0    34.8    -      -       +      +
     88A  PHE*     3.7    22.9    -      -       +      -
    131A  SER*     1.3    77.8    -      -       -      +
    133A  LEU*     1.3    71.1    -      -       -      +
    134A  TRP*     4.2    11.0    -      -       +      -
    139A  ILE*     4.1    11.0    -      -       +      -
    140A  VAL      3.3     4.7    -      -       -      +
    141A  PHE*     4.9     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  GLY      3.6    12.6    -      -       -      +
     55A  HIS*     4.1    12.6    -      -       +      -
    131A  SER      4.3     0.2    -      -       -      -
    132A  VAL*     1.3    73.7    -      -       -      +
    134A  TRP*     1.3    60.1    +      -       -      +
    135A  ASN*     4.1    13.5    -      -       -      +
    138A  MET*     3.7     7.9    -      -       +      +
    139A  ILE*     3.2     4.7    -      -       -      +
    140A  VAL*     2.8    56.1    +      -       +      +
    142A  LEU*     4.5     7.9    -      -       +      +
    223A  TRP*     4.0    26.2    -      -       +      -
    224A  TRP*     4.1    14.4    -      -       +      -
    229A  PHE*     3.8    31.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  TYR      3.3    27.8    -      -       -      -
     52A  LEU*     3.8    22.2    -      -       +      -
     53A  PHE*     3.2    35.6    -      +       -      +
     54A  GLY      2.9    40.1    +      -       -      +
     56A  PHE*     4.1     6.5    -      +       +      -
     76A  LEU*     4.0    17.5    -      -       +      -
     86A  ILE*     4.2     1.6    -      -       +      -
    132A  VAL*     4.2    14.1    -      -       +      -
    133A  LEU*     1.3    73.7    -      -       -      +
    135A  ASN*     1.3    67.9    +      -       -      +
    138A  MET      3.7     2.2    -      -       -      -
    139A  ILE*     3.6    22.9    -      -       +      -
    161A  PHE*     4.4     0.2    -      +       -      -
    162A  PRO*     2.9    33.4    +      -       +      +
    165A  GLN      4.2     2.2    -      -       -      -
    167A  MET*     3.3    46.9    -      -       +      -
    224A  TRP*     4.4     1.4    -      -       -      -
----------------------------------------------------------
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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