Contacts of the strand formed by residues 144 - 154 (chain H) in PDB entry 3KDM


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 144 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141H  SER*     2.7    47.3    +      -       -      -
    143H  GLY*     1.3    80.0    -      -       -      +
    145H  ALA*     1.3    63.4    +      -       -      +
    192H  THR*     3.3    36.6    -      -       +      +
    193H  VAL      3.4     8.7    -      -       -      +
    195H  SER*     3.6     3.8    +      -       -      -
    120L  PHE*     4.1     5.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 145 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135H  PRO*     5.1     2.2    -      -       +      -
    139H  SER      5.7     1.3    -      -       -      -
    140H  THR*     6.3     1.3    -      -       -      +
    141H  SER      5.3     1.6    -      -       -      +
    144H  THR*     1.3    75.5    -      -       -      +
    146H  ALA*     1.3    62.6    +      -       -      +
    192H  THR*     3.0     5.5    -      -       -      -
    193H  VAL*     2.4    51.6    +      -       +      +
    195H  SER*     3.9     9.8    +      -       -      +
    198H  LEU*     3.8    38.1    -      -       +      -
    120L  PHE*     4.3     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 146 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135H  PRO*     3.4    13.7    -      -       -      +
    136H  SER      4.5     1.0    +      -       -      -
    145H  ALA*     1.3    76.3    -      -       -      +
    147H  LEU*     1.3    66.3    +      -       -      +
    191H  VAL      3.3     8.3    -      -       -      +
    192H  THR*     4.1     3.4    -      -       +      -
    120L  PHE*     3.7    44.0    -      -       +      -
    122L  PHE*     3.3    17.7    -      -       +      -
    139L  LEU*     3.8    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 147 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133H  LEU      3.2    15.3    -      -       -      +
    135H  PRO*     3.2    33.4    -      -       +      -
    146H  ALA*     1.3    77.4    -      -       -      +
    148H  GLY*     1.3    61.8    +      -       -      +
    163H  TRP*     3.7    13.7    -      -       +      -
    190H  VAL*     3.3     5.8    -      -       -      +
    191H  VAL*     2.9    49.7    +      -       +      +
    193H  VAL*     4.8     4.3    -      -       +      -
    198H  LEU*     3.8     9.4    -      -       +      -
    203H  TYR*     3.7    27.1    -      -       +      -
    220H  ALA*     3.6    25.8    -      -       +      +
    122L  PHE*     3.8     9.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 148 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133H  LEU*     2.8    37.2    +      -       -      +
    147H  LEU*     1.3    78.0    -      -       -      +
    149H  CYS*     1.3    71.2    +      -       -      -
    163H  TRP*     3.5    10.8    -      -       -      -
    189H  SER      3.0    14.1    -      -       -      -
    190H  VAL*     4.0     1.3    -      -       -      -
    220H  ALA*     3.5     7.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 149 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130H  VAL*     4.2     7.9    -      -       +      -
    131H  PHE      3.3     9.6    -      -       -      +
    132H  PRO*     4.7     2.9    -      -       -      -
    133H  LEU*     3.9     5.8    -      -       -      +
    148H  GLY*     1.3    80.2    -      -       -      -
    150H  LEU*     1.3    60.1    +      -       -      +
    151H  VAL*     4.0     7.6    +      -       +      +
    161H  VAL*     5.5     0.2    -      -       +      -
    163H  TRP*     3.8     5.6    -      -       +      -
    188H  SER*     3.1     5.4    -      -       -      -
    189H  SER*     2.9    34.4    +      -       -      +
    205H  CYS*     2.0    53.6    -      -       +      -
    207H  VAL*     5.1     0.7    -      -       +      -
    218H  LYS*     4.1    14.4    -      -       -      -
    220H  ALA*     4.9     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 150 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129H  SER      3.4     2.3    -      -       -      +
    130H  VAL*     3.3     6.8    -      -       -      +
    131H  PHE*     2.8    57.0    +      -       +      +
    133H  LEU*     4.1    12.9    -      -       +      +
    149H  CYS*     1.3    71.2    -      -       -      +
    151H  VAL*     1.3    60.8    +      -       -      +
    152H  LYS*     4.1    13.2    -      -       +      -
    186H  SER*     3.7    17.3    -      -       -      +
    187H  LEU      3.6    11.2    -      -       -      +
    188H  SER*     3.5    18.8    -      -       -      +
    128L  GLN*     4.3     2.0    -      -       -      +
    135L  SER*     3.4    37.0    -      -       -      +
    137L  VAL*     4.9     8.3    -      -       +      -
    182L  THR*     5.2     8.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 151 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128H  PRO*     3.5    24.2    -      -       +      -
    129H  SER      3.7     3.1    -      -       -      -
    130H  VAL*     4.4     5.2    -      -       +      +
    149H  CYS*     4.4     8.1    -      -       +      +
    150H  LEU*     1.3    75.0    -      -       -      +
    152H  LYS*     1.3    57.2    -      -       -      +
    154H  TYR*     3.7    12.3    -      -       +      -
    159H  VAL*     4.0    24.0    -      -       +      -
    161H  VAL*     4.1    13.5    -      -       +      -
    186H  SER*     3.3     4.9    -      -       -      -
    187H  LEU*     2.7    44.9    +      -       +      +
    189H  SER      5.4     0.4    -      -       -      +
    207H  VAL*     3.9    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 152 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128H  PRO*     3.5     2.0    -      -       -      +
    129H  SER*     3.0    37.7    +      -       -      +
    131H  PHE*     4.6     7.6    -      -       +      -
    150H  LEU*     4.1    13.5    -      -       +      -
    151H  VAL*     1.3    72.3    -      -       -      +
    153H  ASP*     1.3    96.2    +      -       -      +
    154H  TYR      3.7     1.1    -      -       -      -
    180H  GLN*     2.8    27.7    +      -       -      +
    186H  SER*     3.4    16.2    -      -       -      +
    128L  GLN*     4.0    13.9    -      -       -      +
    133L  THR*     4.3    13.0    -      -       -      +
    135L  SER*     3.7    24.7    -      -       -      +
    182L  THR*     6.3     1.3    -      -       +      -
    184L  THR*     4.6    16.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 153 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126H  LYS*     3.0    35.3    +      -       -      +
    127H  GLY      3.3     4.2    -      -       -      +
    129H  SER*     5.7     2.5    +      -       -      +
    152H  LYS*     1.3   104.8    +      -       -      +
    154H  TYR*     1.3    57.1    +      -       -      +
    180H  GLN*     3.0    21.1    +      -       -      -
    182H  SER*     4.6     2.1    +      -       -      -
    184H  LEU*     3.7    26.7    -      -       +      +
    185H  TYR      2.9    17.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 154 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126H  LYS      3.0    12.3    -      -       -      +
    128H  PRO*     3.6    23.8    -      -       +      -
    151H  VAL*     3.7    31.9    -      -       +      -
    153H  ASP*     1.3    79.7    -      -       -      +
    155H  PHE*     1.3    63.8    +      -       -      +
    156H  PRO      3.4    19.7    -      -       -      -
    157H  GLU*     2.9    29.8    +      -       -      -
    159H  VAL*     3.5    32.7    -      -       +      +
    177H  ALA*     3.2    16.8    -      -       -      +
    184H  LEU*     3.8     2.4    -      -       -      -
    185H  TYR*     2.9    55.0    +      +       +      +
    186H  SER*     4.1     3.4    -      -       -      -
    187H  LEU*     3.6     4.5    -      -       +      +
    209H  HIS*     3.8    10.3    -      +       -      +
----------------------------------------------------------
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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