Contacts of the strand formed by residues 127 - 133 (chain A) in PDB entry 5IVK


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 ARG 127 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  THR*     3.5    19.5    +      -       -      -
    119A  ASN*     2.9    32.9    +      -       -      -
    120A  ASN*     3.9    21.7    +      -       -      +
    123A  PRO*     4.0    22.5    -      -       -      +
    125A  THR*     3.8     7.4    -      -       +      +
    126A  LYS*     1.3    79.2    -      -       -      +
    128A  PRO*     1.3    76.8    -      -       +      +
    157A  ASP*     3.1    50.9    +      -       +      +
    158A  VAL*     3.9     7.8    +      -       -      +
    159A  VAL*     4.5     5.4    -      -       +      +
    206A  GLY      2.9    11.3    +      -       -      +
    207A  GLY*     3.5     2.3    -      -       -      -
    208A  ASN*     2.7    27.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 128 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  LYS      4.6     1.1    -      -       -      +
    127A  ARG*     1.3    89.2    -      -       +      +
    129A  VAL*     1.3    59.0    +      -       -      +
    130A  LEU*     4.3     4.7    -      -       +      -
    157A  ASP      3.8    10.8    -      -       -      +
    158A  VAL*     3.6    11.1    -      -       +      +
    159A  VAL      3.1    23.7    +      -       -      -
    211A  ASN*     3.6    18.3    -      -       +      +
    508A  ALA*     4.2    26.0    -      -       +      +
    509A  THR*     3.4    35.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 129 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  ARG      3.7     3.8    -      -       -      +
    128A  PRO*     1.3    73.5    -      -       -      +
    130A  LEU*     1.3    58.5    +      -       -      +
    131A  VAL*     4.1    12.8    -      -       +      -
    159A  VAL*     3.5    13.0    -      -       +      +
    161A  ILE*     3.9    27.8    -      -       +      -
    198A  ILE*     4.2     8.7    -      -       +      -
    202A  CYS*     4.0    15.7    -      -       +      -
    207A  GLY*     3.6    31.2    -      -       -      -
    208A  ASN      3.7     7.6    -      -       -      +
    211A  ASN      3.0    10.2    +      -       -      +
    212A  ILE*     3.3     8.5    -      -       +      -
    213A  THR*     2.7    34.7    +      -       -      +
    508A  ALA*     5.4     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 130 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  PRO*     4.2     3.6    -      -       +      +
    129A  VAL*     1.3    76.0    -      -       -      +
    131A  VAL*     1.3    60.7    +      -       -      +
    132A  TYR      4.1     0.2    -      -       -      -
    153A  PHE*     4.0    29.8    -      -       +      -
    158A  VAL*     3.8    31.9    -      -       +      -
    159A  VAL      2.8     8.7    +      -       -      +
    160A  LEU*     3.4    13.7    -      -       +      +
    161A  ILE*     2.9    26.0    +      -       -      +
    213A  THR*     3.4    11.2    -      -       +      -
    215A  PHE*     3.9    21.3    -      -       +      -
    504A  TRP*     4.2    21.8    -      -       +      +
    505A  THR*     4.7     1.8    -      -       -      +
    508A  ALA*     3.5    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  VAL*     4.1     4.9    -      -       +      -
    130A  LEU*     1.3    75.8    -      -       -      +
    132A  TYR*     1.3    64.2    +      -       -      +
    133A  ILE*     4.9     5.2    -      -       +      -
    161A  ILE*     3.4    10.1    -      -       +      +
    163A  ILE*     4.1    12.8    -      -       +      -
    195A  LEU*     4.0    15.7    -      -       +      -
    198A  ILE*     3.5    42.4    -      -       +      -
    212A  ILE*     3.8    26.2    -      -       +      -
    213A  THR      2.8    11.6    +      -       -      +
    214A  VAL*     3.5     8.9    -      -       +      +
    215A  PHE*     2.9    28.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  LEU      4.1     0.4    -      -       -      -
    131A  VAL*     1.3    72.7    -      -       -      +
    133A  ILE*     1.3    68.4    +      -       -      +
    134A  HIS*     3.5    24.8    +      -       +      -
    135A  GLY      4.5     0.7    +      -       -      -
    148A  TYR*     3.7    22.1    +      +       -      -
    160A  LEU*     4.7     1.8    -      -       +      -
    161A  ILE      2.9    10.9    +      -       -      +
    162A  ASN*     3.8    25.6    -      -       +      +
    163A  ILE*     3.4    26.3    +      -       -      +
    215A  PHE*     3.3    43.6    -      +       +      -
    216A  GLY*     3.5    15.9    -      -       -      -
    217A  GLU*     3.3    29.3    +      -       +      +
    243A  MET*     4.8     3.4    -      -       -      -
    475A  LEU*     3.6    11.0    -      -       +      +
    479A  PHE*     3.6    25.1    -      +       +      -
----------------------------------------------------------
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Residues in contact with ILE 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131A  VAL*     4.7     3.8    -      -       +      +
    132A  TYR*     1.3    77.6    -      -       -      +
    134A  HIS*     1.3    66.8    +      -       -      +
    163A  ILE*     4.0    20.0    -      -       +      -
    165A  TYR*     3.7    24.0    -      -       +      -
    191A  GLN*     3.8    22.7    -      -       +      +
    195A  LEU*     5.2     4.0    -      -       +      -
    214A  VAL*     3.7    31.9    -      -       +      -
    215A  PHE      2.9     7.6    +      -       -      +
    216A  GLY*     3.2    12.6    -      -       -      -
    220A  GLY*     3.2    18.8    -      -       -      +
    223A  SER*     3.6    24.0    -      -       -      -
    224A  THR*     4.1     8.3    -      -       -      +
    227A  MET*     4.3     9.6    -      -       +      -
----------------------------------------------------------
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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