Contacts of the strand formed by residues 129 - 139 (chain B) in PDB entry 1K4C


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 129 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124B  GLN*     3.0    37.6    +      -       -      +
    125B  LEU*     3.4     8.2    +      -       -      -
    127B  SER*     3.3     5.8    -      -       -      -
    128B  GLY*     1.3    81.2    -      -       -      +
    130B  ALA*     1.3    60.1    +      -       -      +
    180B  THR*     6.1     0.9    -      -       -      -
    181B  LEU      4.0     4.7    -      -       -      -
    182B  THR*     4.6     0.4    -      -       -      -
    183B  LYS      4.3     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 130 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120B  PRO*     4.0     6.3    -      -       +      -
    124B  GLN*     3.7     3.5    -      -       -      +
    125B  LEU*     3.8    12.8    -      -       +      -
    129B  GLY*     1.3    75.6    -      -       -      +
    131B  SER*     1.3    60.9    +      -       -      +
    132B  VAL*     4.1     2.2    +      -       -      +
    179B  LEU      3.8     1.9    -      -       -      +
    180B  THR*     3.5     2.8    -      -       -      +
    181B  LEU*     2.7    46.1    +      -       +      +
    182B  THR      4.2     2.5    -      -       -      +
    186B  TYR*     3.6    37.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 131 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  LEU*     5.8     1.6    -      -       -      +
    146A  LEU*     3.6    23.0    -      -       -      +
    148A  LYS*     4.1     5.9    -      -       -      +
    118B  PHE      4.3     0.2    -      -       -      +
    119B  PRO      4.2     0.5    -      -       -      -
    120B  PRO*     3.3    22.9    -      -       -      +
    124B  GLN*     2.8    32.3    +      -       -      +
    130B  ALA*     1.3    73.5    -      -       -      +
    132B  VAL*     1.3    61.6    +      -       -      +
    133B  VAL*     3.9     5.2    +      -       -      +
    178B  THR*     4.2     9.1    -      -       -      +
    179B  LEU      3.5     4.0    -      -       -      -
    180B  THR*     3.3    24.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 132 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117B  ILE*     4.3     3.4    -      -       +      -
    118B  PHE      3.7     6.1    -      -       -      +
    120B  PRO*     4.2    12.6    -      -       +      -
    130B  ALA      4.9     2.5    -      -       -      +
    131B  SER*     1.3    76.4    -      -       -      +
    133B  VAL*     1.3    60.4    +      -       -      +
    148B  TRP*     3.6    31.0    -      -       +      -
    178B  THR*     3.6     2.6    -      -       -      +
    179B  LEU*     2.8    45.0    +      -       +      +
    181B  LEU*     5.5     1.6    -      -       +      -
    186B  TYR*     4.5     8.1    -      -       +      -
    192B  TYR*     4.1    26.0    -      -       +      -
    209B  PHE*     3.5    31.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 133 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  LEU*     4.1    32.3    -      -       +      -
    146A  LEU*     4.3    21.1    -      -       +      -
    183A  SER*     4.2     4.9    -      -       -      +
    117B  ILE*     3.4     1.7    -      -       -      +
    118B  PHE*     2.7    44.7    +      -       +      +
    131B  SER      3.9     4.2    +      -       -      +
    132B  VAL*     1.3    77.0    -      -       -      +
    134B  CYS*     1.3    64.1    +      -       -      +
    135B  PHE*     3.7    31.0    -      -       +      -
    148B  TRP*     4.5     2.2    -      -       -      -
    176B  SER*     5.3     1.6    -      -       -      -
    177B  SER      3.8     2.0    -      -       -      +
    178B  THR*     4.1    24.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 134 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115B  VAL*     3.8    14.4    -      -       -      -
    116B  SER      3.2    11.7    -      -       -      +
    117B  ILE*     4.7     2.5    -      -       -      -
    133B  VAL*     1.3    77.5    -      -       -      +
    135B  PHE*     1.3    66.0    +      -       -      +
    136B  LEU*     3.6    14.4    -      -       +      +
    148B  TRP*     3.7     9.0    -      -       +      -
    176B  SER*     3.4     4.9    -      -       -      -
    177B  SER*     2.9    39.9    +      -       -      +
    194B  CYS*     2.7    47.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  LEU*     3.7    23.3    -      -       +      -
    142A  THR*     4.1     4.9    -      -       +      -
    143A  LEU      4.1     8.1    -      -       -      -
    171A  PHE*     3.5    26.7    -      +       -      -
    183A  SER*     3.8    12.1    -      -       -      -
    184A  SER      3.8    14.4    -      -       -      -
    185A  SER*     3.7    28.7    -      -       -      -
    114B  THR      3.2     1.1    -      -       -      +
    115B  VAL*     3.2     8.5    -      -       -      +
    116B  SER*     2.8    40.3    +      -       -      +
    118B  PHE*     3.4    27.6    -      +       -      -
    133B  VAL*     3.7    15.0    -      -       +      -
    134B  CYS*     1.3    79.2    -      -       -      +
    136B  LEU*     1.3    63.3    -      -       -      +
    137B  ASN*     3.7    17.7    -      -       -      +
    175B  MET      3.7     1.8    -      -       -      -
    176B  SER*     4.0     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113B  PRO*     4.4     3.6    -      -       +      -
    114B  THR      3.6     3.4    -      -       -      -
    115B  VAL*     3.3    37.7    -      -       +      -
    134B  CYS*     3.6    22.7    -      -       +      +
    135B  PHE*     1.3    75.1    -      -       -      +
    137B  ASN*     1.3    59.3    +      -       -      +
    139B  PHE*     3.3    18.0    -      -       +      -
    144B  ILE*     4.2    11.7    -      -       +      -
    146B  VAL*     4.5    15.7    -      -       +      -
    174B  SER*     3.3     3.5    -      -       -      -
    175B  MET*     2.8    56.7    +      -       +      +
    177B  SER*     4.7     4.5    -      -       -      -
    194B  CYS*     5.0     2.2    -      -       -      -
    196B  ALA*     3.3    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  THR*     4.2     8.6    +      -       -      +
    169A  HIS*     3.8    10.0    -      -       -      -
    171A  PHE*     3.5    27.7    -      -       -      -
    185A  SER*     2.9    24.3    +      -       -      -
    187A  THR*     5.0     2.7    +      -       -      +
    113B  PRO*     3.6     0.5    -      -       -      +
    114B  THR*     2.9    50.2    +      -       +      +
    135B  PHE*     3.7    17.4    -      -       -      +
    136B  LEU*     1.3    80.8    +      -       -      +
    138B  ASN*     1.3    82.4    +      -       -      +
    139B  PHE*     3.6     2.4    +      -       -      -
    174B  SER*     3.5     5.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 138 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  HIS*     3.0    36.1    +      -       -      -
    187A  THR*     5.6     4.0    +      -       -      -
    111B  ALA*     3.9    10.9    -      -       -      +
    112B  ALA      3.8     9.0    -      -       -      +
    114B  THR*     5.4     4.4    +      -       -      +
    137B  ASN*     1.3    83.1    -      -       -      +
    139B  PHE*     1.3    59.4    +      -       -      +
    170B  ASP*     3.1    17.3    -      -       -      +
    172B  THR*     3.1    27.5    +      -       +      +
    173B  TYR      3.1     6.2    +      -       -      -
    174B  SER*     2.9     9.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 139 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111B  ALA*     3.2    15.7    -      -       -      +
    113B  PRO*     3.6    33.7    -      -       +      -
    136B  LEU      3.3    26.0    -      -       -      -
    138B  ASN*     1.3    74.5    -      -       -      +
    140B  TYR*     1.3    63.0    +      -       -      +
    141B  PRO      3.2    13.2    -      -       -      -
    142B  LYS*     3.3    32.3    -      -       -      -
    144B  ILE*     3.4    30.7    -      -       +      -
    163B  TRP*     5.2     2.7    -      +       -      -
    172B  THR*     3.5     1.8    -      -       -      -
    173B  TYR*     2.8    52.3    +      -       +      +
    174B  SER*     3.7     9.9    -      -       -      -
    175B  MET*     3.8     7.2    -      -       +      -
    198B  HIS*     3.7     7.2    -      +       -      +
----------------------------------------------------------
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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