Contacts of the strand formed by residues 127 - 134 (chain A) in PDB entry 1IXB


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 GLY 127 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123A  ARG*     4.0     3.6    -      -       -      -
    125A  GLY      4.0     1.4    +      -       -      -
    126A  SER*     1.3    76.4    -      -       -      +
    128A  TRP*     1.3    60.8    -      -       -      -
    143A  THR      3.2    12.6    -      -       -      -
    145A  ASN      3.5    14.4    -      -       -      -
    168A  VAL*     2.9    38.0    +      -       -      +
    169A  TRP*     3.4    13.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 128 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  ASN*     3.5    43.5    -      -       +      +
     81A  HIS*     3.8     9.9    -      +       -      -
     83A  LEU*     5.7     0.4    -      -       +      -
     84A  PHE*     3.8    25.6    -      +       +      -
    123A  ARG*     4.3     1.0    -      -       -      +
    127A  GLY*     1.3    74.1    -      -       -      -
    129A  ALA*     1.3    58.9    +      -       -      +
    130A  TRP*     3.4    39.7    -      +       +      +
    142A  SER*     3.1     8.9    -      -       -      -
    143A  THR*     2.9    31.4    +      -       -      +
    145A  ASN      3.2    22.0    +      -       -      -
    146A  GLN*     2.9    21.9    +      -       -      -
    147A  ASP      4.4     3.6    -      -       -      -
    165A  GLY      4.8     1.6    -      -       -      -
    166A  LEU      3.4    13.7    -      -       -      -
    167A  ASP*     3.5    52.7    -      -       +      -
    168A  VAL*     4.0     5.1    -      -       -      +
    169A  TRP*     3.9     4.9    -      -       -      +
    206A  MH2      3.8     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 129 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116A  PHE*     3.8    18.0    -      -       +      +
    119A  ALA*     4.4     5.6    -      -       +      +
    120A  ALA*     3.7    41.1    -      -       +      +
    128A  TRP*     1.3    72.8    -      -       -      +
    130A  TRP*     1.3    64.4    +      -       -      +
    141A  VAL      3.7     6.3    -      -       -      +
    142A  SER*     4.2     0.7    -      -       -      -
    165A  GLY*     3.1     3.6    -      -       -      -
    166A  LEU*     2.8    35.6    +      -       +      +
    168A  VAL*     4.8     1.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 130 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  ASN*     3.4    34.5    -      -       +      -
     83A  LEU*     4.1    22.7    -      -       +      -
    116A  PHE*     3.7     6.5    -      -       -      -
    128A  TRP*     3.4    40.6    -      +       +      +
    129A  ALA*     1.3    76.7    -      -       -      +
    131A  LEU*     1.3    60.4    +      -       -      +
    132A  VAL*     3.9    17.4    +      -       +      -
    140A  VAL*     3.3     9.2    -      -       -      +
    141A  VAL*     2.8    45.1    +      -       +      +
    142A  SER*     4.1     1.1    -      -       -      -
    143A  THR*     2.9    27.5    +      -       +      -
    147A  ASP      4.0     4.3    -      -       -      -
    148A  SER*     4.8     1.3    -      -       -      -
    149A  PRO*     3.5    28.0    -      -       +      +
    162A  PRO*     3.7    26.0    -      -       +      -
    164A  MET      3.6    15.3    -      -       -      +
    165A  GLY*     3.9     8.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  LEU*     4.7     4.9    -      -       +      -
    102A  ILE*     4.2    24.0    -      -       +      -
    106A  PHE*     4.2     9.0    -      -       +      -
    112A  PHE*     3.9    27.4    -      -       +      -
    116A  PHE*     3.9     2.8    -      -       -      -
    130A  TRP*     1.3    71.3    -      -       -      +
    132A  VAL*     1.3    53.6    +      -       -      +
    138A  LEU*     4.1    25.6    -      -       +      -
    139A  ALA      3.5    15.0    -      -       -      +
    140A  VAL*     4.8     0.4    -      -       -      +
    162A  PRO*     3.6     1.7    -      -       -      +
    163A  ILE*     2.8    55.0    +      -       +      +
    164A  MET*     3.1    36.1    +      -       +      +
    194A  TRP*     4.7     3.8    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
    130A  TRP*     3.9     5.1    -      -       +      -
    131A  LEU*     1.3    76.9    -      -       -      +
    133A  LEU*     1.3    60.1    +      -       -      +
    134A  LYS*     4.1     9.0    -      -       +      -
    138A  LEU*     3.2    10.6    -      -       -      +
    139A  ALA*     2.8    56.6    +      -       +      +
    141A  VAL*     3.8    20.2    -      -       +      -
    149A  PRO*     3.7    33.4    -      -       +      -
    159A  SER      3.5    19.1    -      -       -      +
    160A  GLY      4.0     4.5    -      -       -      +
    161A  PHE      3.1    11.2    -      -       -      +
    162A  PRO*     4.0     2.2    -      -       +      -
    163A  ILE*     4.4     0.9    -      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
    104A  ARG*     5.5     2.0    -      -       -      +
    132A  VAL*     1.3    72.7    -      -       -      +
    134A  LYS*     1.3    61.2    +      -       -      +
    135A  GLY      3.5    26.5    +      -       -      +
    136A  ASP*     4.2     2.2    -      -       -      -
    137A  LYS*     3.8    23.8    -      -       -      +
    138A  LEU*     3.9    17.0    -      -       +      +
    160A  GLY*     3.4     1.6    -      -       -      -
    161A  PHE*     2.9    38.2    +      -       +      +
    163A  ILE*     4.2     8.7    -      -       +      +
    201A  PHE*     4.2    15.3    -      -       +      -
    204A  LYS*     3.6    41.3    -      -       +      +
    205A  LYS*     4.0     8.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  VAL*     4.1     7.6    -      -       +      -
    133A  LEU*     1.3    77.0    -      -       -      +
    135A  GLY*     1.3    58.3    +      -       -      +
    136A  ASP      3.0     9.7    +      -       -      -
    137A  LYS*     2.9    27.1    +      -       +      +
    139A  ALA*     4.0    21.4    -      -       +      +
    141A  VAL*     4.3    13.2    -      -       -      +
    153A  GLU*     4.3    12.7    +      -       -      -
    159A  SER*     3.6    33.8    -      -       -      +
    160A  GLY*     4.1     4.5    -      -       -      -
----------------------------------------------------------
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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