Contacts of the helix formed by residues 207 - 221 (chain B) in PDB entry 3LKB


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 VAL 207 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  THR*     3.8    35.9    -      -       +      +
     22B  ASP*     4.6     3.8    -      -       +      -
     23B  ALA*     4.0    16.8    -      -       +      +
    151B  HIS*     4.8     5.6    -      -       +      -
    155B  PHE*     4.0    10.4    -      -       +      -
    206B  ASN*     1.3    90.4    +      -       -      +
    208B  ALA*     1.3    67.5    +      -       -      +
    209B  GLY      3.4     0.9    +      -       -      -
    210B  PRO*     3.5    18.6    -      -       +      +
    211B  VAL*     3.4    15.4    -      -       -      +
    232B  TYR*     3.3    10.8    -      -       +      +
    233B  THR*     4.2     1.8    -      -       -      -
    393B  VAL      4.5     1.3    -      -       -      +
   4571B  IPA      3.6    35.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 208 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  ASP*     4.8     8.2    +      -       +      +
    207B  VAL*     1.3    77.8    -      -       -      +
    209B  GLY*     1.3    58.3    +      -       -      +
    211B  VAL*     3.4     3.1    +      -       -      +
    212B  ALA*     2.9    32.6    +      -       -      +
    232B  TYR      3.4     5.6    +      -       -      +
    233B  THR      3.6    24.0    -      -       -      +
    234B  GLY      5.1     1.3    -      -       -      +
    237B  ASP*     4.2    15.5    -      -       +      +
    238B  LEU*     4.0    24.9    -      -       -      +
    241B  LEU*     4.7     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 209 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  ASP*     3.4    20.6    +      -       -      -
    182B  SER*     6.1     0.2    -      -       -      -
    208B  ALA*     1.3    78.5    -      -       -      +
    210B  PRO*     1.4    68.9    -      -       -      +
    212B  ALA*     3.2     6.4    +      -       -      +
    213B  ASN*     3.1    28.7    +      -       -      -
    241B  LEU*     4.7    10.1    -      -       -      -
   4571B  IPA      5.5     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 210 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151B  HIS*     5.1     1.1    -      -       +      -
    180B  VAL*     4.2     4.0    -      -       +      +
    181B  GLY*     3.7    33.7    -      -       -      +
    182B  SER*     3.9    15.9    -      -       -      +
    184B  ASN*     3.1    25.5    +      -       -      +
    206B  ASN*     3.8    28.0    -      -       -      +
    207B  VAL*     3.5    22.4    -      -       +      +
    209B  GLY*     1.4    84.6    -      -       -      +
    211B  VAL*     1.3    64.3    +      -       -      +
    213B  ASN      3.2     1.2    +      -       -      -
    214B  ILE*     3.1    22.3    +      -       +      +
   4571B  IPA      4.5     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 211 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204B  HIS*     3.7    37.7    -      -       +      +
    206B  ASN*     3.8    16.6    -      -       +      -
    207B  VAL      3.4    15.9    +      -       -      +
    208B  ALA*     3.4     8.5    +      -       -      +
    209B  GLY      3.3     0.4    -      -       -      -
    210B  PRO*     1.3    74.4    -      -       -      +
    212B  ALA*     1.3    65.5    +      -       -      +
    214B  ILE*     3.0     6.4    +      -       -      +
    215B  LEU*     2.9    30.6    +      -       +      +
    233B  THR*     4.0     9.6    -      -       +      +
    238B  LEU*     4.4     6.3    -      -       +      -
    249B  PHE*     3.6    33.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 212 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208B  ALA      2.9    17.9    +      -       -      +
    209B  GLY      3.5     4.0    -      -       -      +
    211B  VAL*     1.3    76.5    -      -       -      +
    213B  ASN*     1.3    63.9    +      -       -      +
    215B  LEU*     3.2     5.2    +      -       -      +
    216B  LYS*     3.1    29.6    +      -       +      +
    238B  LEU*     4.6     4.2    -      -       +      +
    241B  LEU*     3.5    34.3    -      -       +      +
    242B  ALA*     3.6    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 213 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216A  LYS*     5.3     5.9    +      -       -      -
    183B  GLY      4.9     4.2    -      -       -      +
    184B  ASN*     3.0    50.2    +      -       -      +
    185B  LEU*     4.6    10.6    -      -       -      +
    187B  ASN*     3.6     7.9    +      -       -      +
    209B  GLY      3.1    18.3    +      -       -      +
    210B  PRO      3.2     1.5    +      -       -      +
    212B  ALA*     1.3    77.4    -      -       -      +
    214B  ILE*     1.3    61.0    +      -       -      +
    216B  LYS*     3.4    24.2    +      -       -      +
    217B  ASP*     3.2    21.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 214 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149B  VAL*     4.1    22.0    -      -       +      -
    180B  VAL*     4.3     8.3    -      -       +      -
    184B  ASN*     3.7     7.4    -      -       -      +
    187B  ASN*     3.6    30.3    -      -       +      +
    190B  LEU*     4.3     7.9    -      -       +      -
    191B  LEU*     4.0    25.5    -      -       +      +
    194B  PHE*     6.3     0.2    -      -       +      -
    202B  VAL*     5.8     1.1    -      -       +      -
    204B  HIS*     4.1    24.7    -      -       +      +
    206B  ASN*     5.9     0.4    -      -       -      +
    210B  PRO*     3.1    16.3    +      -       +      +
    211B  VAL      3.0     7.4    +      -       -      +
    213B  ASN*     1.3    72.5    -      -       -      +
    215B  LEU*     1.3    67.6    +      -       -      +
    216B  LYS      3.2     0.2    +      -       -      -
    217B  ASP*     3.3     1.7    +      -       -      +
    218B  ALA*     2.9    22.2    +      -       -      +
    227B  HIS*     4.1    15.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 215 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204B  HIS*     4.8     0.4    -      -       +      -
    211B  VAL*     2.9    27.1    +      -       +      +
    212B  ALA      3.8     5.6    -      -       -      +
    214B  ILE*     1.3    76.2    -      -       -      +
    216B  LYS*     1.3    57.4    +      -       -      +
    218B  ALA*     3.8     3.6    -      -       -      +
    219B  LYS*     2.9    29.1    +      -       -      +
    227B  HIS*     3.3    47.3    -      -       +      +
    238B  LEU*     4.2     8.7    -      -       +      -
    242B  ALA*     4.4     4.5    -      -       +      -
    245B  ALA*     3.4    22.6    -      -       +      +
    246B  ALA*     3.9    26.0    -      -       +      -
    249B  PHE*     3.8    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 216 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  LEU*     4.4    22.4    -      -       -      +
    213A  ASN*     5.4     4.9    +      -       -      -
    216A  LYS*     5.4     8.7    -      -       -      +
    212B  ALA*     3.1    21.6    +      -       -      +
    213B  ASN*     3.6    22.4    +      -       -      +
    214B  ILE      3.2     0.2    -      -       -      -
    215B  LEU*     1.3    74.3    -      -       -      +
    217B  ASP*     1.3    61.6    +      -       -      +
    219B  LYS*     3.4     5.0    +      -       +      +
    220B  ARG*     3.0    31.9    +      -       -      +
    241B  LEU      3.6    25.8    +      -       -      +
    242B  ALA*     4.1     8.3    -      -       -      +
    245B  ALA*     3.8    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 217 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185B  LEU      3.6    13.7    -      -       -      +
    186B  ASP*     4.6     6.0    -      -       -      +
    187B  ASN*     2.7    45.3    +      -       +      +
    188B  THR*     4.9     0.9    -      -       -      +
    191B  LEU*     3.9    15.0    -      -       +      -
    213B  ASN      3.2    10.4    +      -       -      +
    214B  ILE      3.8     3.6    -      -       -      +
    216B  LYS*     1.3    79.5    -      -       -      +
    218B  ALA*     1.3    56.0    +      -       -      +
    220B  ARG*     3.1    10.4    +      -       -      +
    221B  LEU*     2.9    35.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 218 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191B  LEU*     3.5    18.4    -      -       +      +
    214B  ILE      2.9    21.0    +      -       -      +
    215B  LEU*     3.8     4.5    -      -       +      +
    217B  ASP*     1.3    72.6    -      -       -      +
    219B  LYS*     1.3    59.5    +      -       -      +
    221B  LEU      3.5     0.5    +      -       -      -
    222B  GLY      3.4     2.6    +      -       -      -
    223B  LEU*     3.1    47.5    +      -       +      +
    227B  HIS*     4.0    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 219 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215B  LEU      2.9    18.5    +      -       -      +
    216B  LYS*     3.6     6.3    -      -       +      +
    217B  ASP      3.3     0.4    -      -       -      -
    218B  ALA*     1.3    73.3    -      -       -      +
    220B  ARG*     1.3    77.7    +      -       -      +
    222B  GLY*     3.2    13.4    +      -       -      -
    244B  ASP*     4.3    18.9    +      -       -      +
    245B  ALA*     4.0    32.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 220 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186A  ASP*     5.2     8.9    +      -       -      -
    217A  ASP*     5.3     6.3    +      -       -      -
    220A  ARG*     4.3    38.8    -      -       +      +
    216B  LYS      3.0    15.1    +      -       -      +
    217B  ASP*     3.1    15.5    +      -       -      +
    219B  LYS*     1.3    87.0    -      -       -      +
    221B  LEU*     1.3    61.6    +      -       +      +
    222B  GLY      3.2     1.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 221 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188B  THR*     4.3    20.9    -      -       -      +
    191B  LEU*     4.0    18.6    -      -       +      -
    192B  LYS*     4.0    32.7    +      -       +      +
    217B  ASP*     2.9    20.9    +      -       +      +
    218B  ALA      4.1     0.4    -      -       -      +
    219B  LYS      3.1     0.8    -      -       -      -
    220B  ARG*     1.3    79.1    -      -       +      +
    222B  GLY*     1.3    61.7    +      -       -      +
    223B  LEU*     3.3    35.5    +      -       +      +
----------------------------------------------------------
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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