Contacts of the strand formed by residues 105 - 113 (chain A) in PDB entry 4TZQ


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 LEU 105 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  ILE*     4.5     2.0    -      -       +      -
     96A  ALA*     3.2    30.1    -      -       +      +
     99A  ALA*     3.8    16.6    +      -       +      -
    100A  THR*     4.0     9.9    -      -       +      -
    103A  GLY      3.4     0.6    -      -       -      -
    104A  PHE*     1.3    77.5    -      -       -      +
    106A  LYS*     1.3    60.4    +      -       -      +
    107A  GLU      3.4    28.3    -      -       -      +
    108A  VAL*     4.2     7.2    -      -       +      +
    129A  PHE*     3.4    34.6    -      -       +      +
    131A  TYR*     2.5    32.5    +      -       -      +
    199A  LEU*     4.3    11.7    -      -       +      -
    200A  GLU      3.9     5.6    -      -       -      +
    202A  THR*     4.1     2.5    -      -       -      -
    211A  ILE*     4.4    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  PHE      3.9     0.8    +      -       -      -
    105A  LEU*     1.3    71.7    -      -       -      +
    107A  GLU*     1.3    65.3    +      -       +      +
    128A  LYS*     3.5     2.4    -      -       -      +
    129A  PHE*     2.8    31.4    +      -       -      +
    142A  SER*     3.3     9.6    -      -       -      +
    143A  THR      3.1    23.4    +      -       -      -
    144A  ASP*     5.2     1.6    -      -       -      +
    150A  ASP*     2.8    29.4    +      -       -      +
    152A  HIS*     4.1    14.4    -      -       +      -
    200A  GLU*     2.9    42.9    +      -       +      +
    201A  TYR      3.8    20.6    +      -       -      +
    202A  THR*     3.8    18.1    -      -       +      +
    203A  ASN*     4.3    11.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105A  LEU*     3.4     6.7    -      -       -      +
    106A  LYS*     1.3    88.5    -      -       +      +
    108A  VAL*     1.3    62.6    +      -       -      +
    109A  SER*     2.8    19.8    +      -       -      +
    126A  SER*     3.7     3.3    -      -       -      -
    127A  MET      3.3    12.3    -      -       -      +
    128A  LYS*     3.7    27.5    +      -       +      +
    129A  PHE*     4.3     1.6    -      -       -      -
    199A  LEU*     3.1     7.6    -      -       -      +
    200A  GLU*     3.0    32.8    +      -       +      +
    220A  PHE*     3.4    26.4    -      -       +      -
    221A  TYR*     2.6    30.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  ILE*     4.1    13.0    -      -       +      -
     50A  PHE*     3.7    19.1    -      -       +      -
     93A  LEU*     4.8     7.6    -      -       +      -
     96A  ALA*     4.3    17.0    -      -       +      -
    105A  LEU*     4.3    11.2    -      -       +      -
    107A  GLU*     1.3    74.7    -      -       -      +
    109A  SER*     1.3    64.9    +      -       -      +
    127A  MET*     3.0    32.1    +      -       +      +
    129A  PHE*     3.8    24.8    -      -       +      -
    197A  PHE*     4.4    17.3    -      -       +      -
    198A  ARG      3.9     3.6    -      -       -      +
    199A  LEU*     4.2     8.5    -      -       +      -
    214A  PHE*     4.9     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  PHE*     4.2     1.8    -      -       -      -
    107A  GLU*     2.8    27.6    +      -       -      +
    108A  VAL*     1.3    82.7    +      -       -      +
    110A  LEU*     1.3    60.6    +      -       -      +
    111A  VAL*     3.7     2.8    +      -       -      +
    124A  VAL*     4.0    13.7    -      -       -      -
    125A  PHE      3.3    10.8    -      -       -      -
    126A  SER*     3.2    12.6    -      -       -      -
    197A  PHE*     3.2    10.1    -      -       -      -
    198A  ARG      2.9    39.2    +      -       -      -
    221A  TYR*     4.2     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  PHE*     3.7    12.3    -      -       +      -
     53A  VAL*     4.2    16.2    -      -       +      -
     54A  LEU*     4.0    17.9    -      -       +      -
     59A  ILE*     3.7    29.2    -      -       +      -
    109A  SER*     1.3    69.4    -      -       -      +
    111A  VAL*     1.3    62.1    +      -       -      +
    112A  ILE*     4.0    11.8    +      -       +      +
    123A  GLU      3.9     0.9    -      -       -      +
    124A  VAL*     3.5     6.2    -      -       -      +
    125A  PHE*     3.1    33.9    +      -       +      +
    195A  ALA*     4.3     7.9    -      -       +      -
    196A  ASN*     3.4    24.9    -      -       -      +
    197A  PHE*     3.6    35.0    -      -       +      -
    496B  ILE*     5.6     2.2    -      -       +      -
----------------------------------------------------------
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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  SER*     4.0     7.4    -      -       -      +
    110A  LEU*     1.3    76.8    -      -       -      +
    112A  ILE*     1.3    62.5    +      -       -      +
    113A  THR*     4.1     3.6    -      -       +      -
    121A  ALA*     3.7    24.0    -      -       +      -
    123A  GLU      3.9     2.0    -      -       -      -
    124A  VAL*     4.5     2.7    -      -       +      -
    194A  THR      3.5     2.3    -      -       -      +
    195A  ALA*     3.3     2.6    -      -       -      -
    196A  ASN*     2.6    35.8    +      -       -      +
    198A  ARG*     3.6    60.4    +      -       +      +
    221A  TYR*     3.8    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  ILE*     3.9    23.8    -      -       +      -
    110A  LEU*     4.7    10.5    -      -       +      +
    111A  VAL*     1.3    78.0    -      -       -      +
    113A  THR*     1.3    59.7    +      -       -      +
    121A  ALA*     3.5     3.5    -      -       -      -
    122A  ILE*     2.7    37.0    +      -       +      -
    123A  GLU*     2.9    50.0    +      -       +      +
    125A  PHE*     4.8     3.1    -      -       +      -
    189A  LEU*     4.3    18.8    -      -       +      -
    193A  PHE*     3.8    34.1    -      -       +      -
    194A  THR      3.4     2.9    -      -       -      +
    195A  ALA*     4.2    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  VAL*     4.1     4.9    -      -       +      -
    112A  ILE*     1.3    79.2    -      -       -      +
    114A  ASN*     1.3    60.1    +      -       -      +
    115A  ASN      2.6    25.8    +      -       -      -
    116A  GLU*     4.4     1.0    -      -       -      -
    118A  ASP*     3.8    14.3    -      -       -      +
    120A  GLU      3.6    19.3    -      -       -      +
    121A  ALA*     3.9     6.3    -      -       -      -
    122A  ILE*     3.5    12.3    -      -       -      +
    193A  PHE*     3.3     8.7    -      -       -      +
    194A  THR*     2.8    39.4    +      -       -      +
    198A  ARG*     3.7    26.2    +      -       -      +
----------------------------------------------------------
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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