Contacts of the strand formed by residues 129 - 139 (chain D) in PDB entry 6IAP


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 129 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124D  GLN*     3.0    42.8    +      -       +      +
    125D  LEU*     3.7     5.7    -      -       -      +
    127D  SER*     3.2    24.4    -      -       -      +
    128D  GLY*     1.3    79.6    -      -       -      +
    130D  ALA*     1.3    65.4    +      -       -      +
    180D  THR*     5.0     4.0    +      -       -      -
    181D  LEU      4.0     7.1    +      -       -      -
    182D  SER*     4.7     1.3    -      -       -      +
    183D  LYS*     4.3     1.1    -      -       -      +
    126E  PHE*     5.2     1.8    -      -       +      -
    147E  LYS*     3.5    26.8    +      -       +      +
    148E  ASP*     5.1     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 130 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120D  PRO*     3.9    18.2    -      -       +      -
    124D  GLN*     3.8     5.2    -      -       -      -
    125D  LEU*     4.1     7.2    -      -       +      -
    129D  THR*     1.3    79.4    +      -       -      +
    131D  SER*     1.3    62.2    +      -       -      +
    132D  VAL*     4.3     1.3    -      -       -      -
    179D  LEU      3.8     0.5    -      -       -      +
    180D  THR*     3.7     1.9    +      -       -      -
    181D  LEU*     2.7    45.5    +      -       +      +
    182D  SER      4.3     3.8    -      -       -      +
    183D  LYS      4.4     0.2    -      -       -      +
    186D  TYR*     3.9    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 131 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118D  PHE      4.3     0.2    -      -       -      +
    119D  PRO      4.3     1.4    -      -       -      +
    120D  PRO*     3.6    19.4    -      -       -      +
    124D  GLN*     2.8    33.8    +      -       -      +
    130D  ALA*     1.3    75.4    -      -       -      +
    132D  VAL*     1.3    63.4    +      -       -      +
    133D  VAL*     4.0     5.6    +      -       -      +
    178D  THR*     3.7    24.0    -      -       -      -
    179D  LEU      3.3     5.6    -      -       -      -
    180D  THR*     4.5     7.2    -      -       -      -
    128E  LEU*     5.4     3.1    -      -       -      +
    145E  LEU*     3.2    20.6    -      -       -      +
    147E  LYS*     4.3     5.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 132 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117D  ILE*     4.1     3.1    -      -       +      -
    118D  PHE      3.4    12.8    -      -       -      +
    120D  PRO*     3.8    22.4    -      -       +      -
    130D  ALA      5.5     0.2    -      -       -      -
    131D  SER*     1.3    73.1    -      -       -      +
    133D  VAL*     1.3    60.2    +      -       -      +
    148D  TRP*     3.7    23.7    -      -       +      -
    177D  SER      3.6     1.4    -      -       -      +
    178D  THR*     3.4     3.8    -      -       -      -
    179D  LEU*     2.9    51.5    +      -       +      +
    181D  LEU*     4.9     3.1    -      -       +      -
    186D  TYR*     4.3     9.9    -      -       +      -
    192D  TYR*     4.4     4.7    -      -       +      -
    209D  PHE*     3.3    35.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 133 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117D  ILE*     3.4     5.2    -      -       -      +
    118D  PHE*     2.8    53.2    +      -       +      -
    131D  SER      4.6     3.1    -      -       -      +
    132D  VAL*     1.3    74.6    -      -       -      +
    134D  CYS*     1.3    67.7    +      -       -      +
    135D  LEU*     4.5     4.7    -      -       +      +
    148D  TRP*     4.2     2.9    -      -       -      -
    176D  SER*     4.7    12.6    -      -       -      -
    177D  SER      3.6     2.5    -      -       -      +
    178D  THR*     3.5    24.5    -      -       +      +
    128E  LEU*     3.9    31.9    -      -       +      -
    145E  LEU*     4.0    17.0    -      -       +      -
    183E  SER*     4.3     8.7    -      -       -      +
    185E  VAL*     5.6     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 134 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115D  VAL*     4.0     7.2    -      -       -      -
    116D  PHE      3.6     3.1    -      -       -      -
    117D  ILE*     4.7     0.4    -      -       -      +
    133D  VAL*     1.3    72.9    -      -       -      +
    135D  LEU*     1.3    59.3    +      -       -      +
    136D  LEU*     3.8    21.6    -      -       -      +
    146D  VAL*     3.8     6.5    -      -       -      -
    148D  TRP*     3.1    19.9    -      -       +      -
    175D  LEU      3.7     1.9    -      -       -      +
    176D  SER*     3.4     2.4    -      -       -      -
    177D  SER*     2.8    41.8    +      -       -      +
    194D  CYS*     2.0    47.8    -      -       +      -
    196D  VAL*     4.4     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 135 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114D  SER      3.3     4.3    -      -       -      +
    115D  VAL*     3.3     2.8    -      -       -      +
    116D  PHE*     2.8    64.6    +      -       +      +
    118D  PHE*     4.1    17.3    -      -       +      -
    133D  VAL*     3.9     5.8    -      -       +      -
    134D  CYS*     1.3    72.3    -      -       -      +
    136D  LEU*     1.3    66.4    +      -       -      +
    137D  ASN*     4.1    18.2    -      -       +      +
    174D  SER*     4.9     0.4    -      -       -      -
    175D  LEU      3.5     5.4    -      -       -      +
    176D  SER*     4.6     1.8    -      -       -      +
    141E  ALA*     4.0    16.6    -      -       +      -
    170E  PHE*     3.7    31.0    -      -       +      -
    185E  VAL*     3.7    26.7    -      -       +      -
    187E  THR*     5.6     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 136 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113D  PRO*     3.7    16.2    -      -       +      -
    114D  SER      3.4     5.2    -      -       -      -
    115D  VAL*     4.5     2.9    -      -       +      -
    134D  CYS*     3.8    20.0    -      -       -      +
    135D  LEU*     1.3    75.8    -      -       -      +
    137D  ASN*     1.3    59.6    +      -       -      +
    139D  PHE*     3.6    11.3    -      -       +      -
    144D  ALA*     4.1    18.6    -      -       +      -
    146D  VAL*     4.5     7.9    -      -       +      +
    174D  SER*     3.4     4.3    -      -       -      -
    175D  LEU*     2.8    63.7    +      -       +      +
    196D  VAL*     3.6    47.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 137 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113D  PRO*     3.7     0.2    -      -       -      +
    114D  SER*     2.7    47.2    +      -       -      +
    116D  PHE*     4.0    15.0    -      -       +      -
    135D  LEU*     4.1    15.8    -      -       +      +
    136D  LEU*     1.3    74.8    -      -       -      +
    138D  ASN*     1.3    85.2    +      -       -      +
    139D  PHE*     3.8     1.3    -      -       -      -
    174D  SER*     3.0    20.3    +      -       -      -
    168E  HIS*     3.2    21.0    +      -       -      -
    185E  VAL*     5.4     0.7    -      -       -      +
    187E  THR*     3.4    31.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 138 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111D  ALA*     4.3     7.8    -      -       -      +
    112D  ALA      3.6    11.3    -      -       -      +
    114D  SER*     5.2     0.8    +      -       -      +
    137D  ASN*     1.3    94.4    +      -       -      +
    139D  PHE*     1.3    59.2    +      -       -      +
    167D  ASP*     4.3     2.3    -      -       -      +
    170D  ASP*     3.8    16.5    +      -       -      +
    172D  THR*     3.2    26.9    +      -       +      +
    173D  TYR      3.4     5.7    +      -       -      -
    174D  SER*     3.2     9.9    +      -       -      -
    168E  HIS*     3.5    23.5    +      -       -      -
    187E  THR*     4.9     4.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 139 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111D  ALA*     3.3    15.9    -      -       -      +
    113D  PRO*     3.6    34.3    -      -       +      -
    136D  LEU*     3.6    13.9    -      -       +      -
    138D  ASN*     1.3    74.7    -      -       -      +
    140D  TYR*     1.3    62.6    +      -       -      +
    141D  PRO      3.2    20.0    -      -       -      -
    142D  ARG*     3.2    33.7    -      -       -      -
    144D  ALA*     4.4     9.0    -      -       +      -
    163D  VAL*     4.4     2.7    -      -       +      -
    172D  THR*     3.5     4.8    -      -       -      -
    173D  TYR*     2.8    60.8    +      -       +      +
    174D  SER      4.3     0.2    -      -       -      -
    175D  LEU*     3.5    41.7    -      -       +      -
    198D  HIS*     3.7     8.3    -      +       -      +
----------------------------------------------------------
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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