Contacts of the strand formed by residues 109 - 115 (chain A) in PDB entry 9U65


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 THR 109 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  PRO*     5.4     0.2    -      -       +      -
    106A  PRO*     4.5    23.0    -      -       +      +
    107A  LYS      3.3     1.3    -      -       -      -
    108A  SER*     1.3    79.4    -      -       -      +
    110A  THR*     1.3    75.8    +      -       -      +
    111A  VAL*     3.3     1.6    +      -       -      +
    140A  GLU      3.2    18.6    +      -       -      +
    141A  VAL*     4.1     4.5    -      -       -      -
    142A  VAL*     3.5    34.1    -      -       +      +
    188A  GLY      2.9     8.2    +      -       -      +
    189A  GLY*     3.8     0.2    -      -       -      -
    190A  ASP*     3.1    23.1    +      -       -      +
    193A  THR*     5.6     0.2    -      -       -      -
    478A  LYS*     5.9     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  THR*     1.3    75.1    +      -       -      +
    111A  VAL*     1.3    68.0    +      -       -      +
    112A  MET*     4.6     3.4    -      -       +      -
    141A  VAL*     3.3    21.2    -      -       +      +
    142A  VAL      3.0    23.2    +      -       -      -
    193A  THR*     4.1    16.0    -      -       +      +
    474A  ALA      4.7     1.3    -      -       -      +
    477A  ALA*     3.5    43.3    -      -       +      +
    478A  LYS*     3.4    33.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  THR      3.3     2.0    +      -       -      +
    110A  THR*     1.3    75.8    -      -       -      +
    112A  MET*     1.3    70.2    +      -       -      +
    113A  VAL*     4.2    10.1    -      -       +      -
    142A  VAL*     3.4    16.2    -      -       +      +
    144A  VAL*     4.2     5.4    -      -       +      -
    180A  VAL*     4.2     4.0    -      -       +      -
    184A  ILE*     3.7    23.3    -      -       +      -
    189A  GLY*     3.5    31.6    -      -       -      -
    190A  ASP      3.5    12.8    -      -       -      +
    193A  THR      3.2     8.6    +      -       -      +
    194A  VAL*     4.0    25.4    -      -       +      -
    195A  THR*     3.0    24.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  THR*     4.6     4.0    -      -       +      -
    111A  VAL*     1.3    79.6    -      -       -      +
    113A  VAL*     1.3    57.8    +      -       -      +
    135A  LEU*     4.3    21.1    -      -       +      -
    141A  VAL*     4.5    17.0    -      -       +      -
    142A  VAL      3.1     9.4    +      -       -      +
    143A  LEU*     3.5    18.3    -      -       +      +
    144A  VAL      2.8    30.7    +      -       -      +
    195A  THR*     3.3    10.3    -      -       +      +
    197A  PHE*     4.1    11.2    -      -       +      -
    223A  ILE*     4.2    12.3    -      -       +      -
    473A  TRP*     3.1    42.8    -      -       +      +
    474A  ALA*     4.4     9.4    -      -       -      -
    477A  ALA*     3.5    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  VAL*     4.2     2.0    -      -       +      -
    112A  MET*     1.3    72.4    -      -       -      +
    114A  TRP*     1.3    62.1    +      -       -      +
    115A  ILE*     4.4     2.2    -      -       +      +
    144A  VAL*     3.3    27.4    -      -       +      +
    146A  LEU*     3.8    32.5    -      -       +      -
    177A  LEU*     4.1    16.8    -      -       +      -
    180A  VAL*     4.2    20.0    -      -       +      -
    194A  VAL*     3.6    26.2    -      -       +      -
    195A  THR      2.9     9.5    +      -       -      +
    196A  ILE*     3.4     5.5    -      -       +      +
    197A  PHE*     2.9    29.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  VAL*     1.3    72.8    -      -       -      +
    115A  ILE*     1.3    62.1    +      -       -      +
    116A  TYR*     3.6    28.9    +      +       +      +
    117A  GLY      4.8     0.2    -      -       -      -
    125A  SER*     5.6     1.3    -      -       -      -
    130A  TYR*     3.3    51.5    -      +       +      -
    143A  LEU*     4.7     3.1    -      -       +      -
    144A  VAL      2.7    15.8    +      -       -      +
    145A  SER*     4.4    14.6    -      -       -      -
    146A  LEU*     3.3    27.9    +      -       -      +
    197A  PHE*     3.2    66.3    -      +       +      -
    198A  GLY*     3.4    16.8    -      -       -      -
    199A  GLU*     3.5    27.4    -      -       +      -
    225A  GLN*     4.0    10.5    -      -       -      -
    444A  ILE*     4.1     7.4    -      -       +      -
    448A  PHE*     3.5    23.8    -      +       +      -
----------------------------------------------------------
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Residues in contact with ILE 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  VAL*     4.4     5.6    -      -       +      +
    114A  TRP*     1.3    79.6    -      -       -      +
    116A  TYR*     1.3    64.0    +      -       -      +
    117A  GLY      3.7     0.3    +      -       -      -
    146A  LEU*     3.8    26.2    -      -       +      -
    148A  TYR*     3.5    13.7    -      -       +      -
    173A  GLN*     3.2    41.3    -      -       +      +
    177A  LEU*     5.3     2.0    -      -       +      -
    196A  ILE*     4.8    10.8    -      -       +      -
    197A  PHE      2.8    15.6    +      -       -      +
    198A  GLY*     3.2    12.0    -      -       -      -
    199A  GLU      3.8     0.5    +      -       -      -
    202A  GLY*     3.2    17.6    -      -       -      +
    205A  SER*     4.1    12.8    -      -       -      -
    206A  VAL*     4.7    10.8    -      -       +      -
    209A  HIS*     4.2    17.3    -      -       +      +
----------------------------------------------------------
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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