Contacts of the strand formed by residues 135 - 140 (chain H) in PDB entry 1K22


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 LYS 135 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133H  GLY      3.9     2.5    -      -       -      +
    134H  TYR*     1.3    73.1    -      -       -      +
    136H  GLY*     1.3    59.1    +      -       -      +
    159H  ASN*     4.9     1.6    -      -       +      -
    160H  LEU      3.4     7.9    -      -       -      +
    161H  PRO*     3.8    20.9    -      -       +      -
    184H  TYR*     3.2    28.4    +      -       -      +
    186H  LYS*     4.2    12.1    -      -       -      -
    201H  MET*     3.4     3.8    -      -       -      +
     14L  SER*     2.7   126.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 136 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135H  LYS*     1.3    74.2    -      -       -      +
    137H  ARG*     1.3    60.3    +      -       -      -
    159H  ASN*     3.2     6.1    -      -       -      +
    160H  LEU      2.9    32.7    +      -       -      -
    199H  PHE*     3.4    27.0    -      -       -      -
    200H  VAL      3.1    12.8    -      -       -      -
    201H  MET*     3.7     2.5    -      -       -      -
     14L  LEU*     4.1     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 137 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26H  MET*     3.8    15.8    +      -       -      +
     27H  SER*     4.9     4.9    -      -       -      -
    136H  GLY*     1.3    73.5    -      -       -      -
    138H  VAL*     1.3    64.8    +      -       -      +
    139H  THR*     4.3    10.4    +      -       +      -
    157H  VAL*     3.4    28.5    -      -       +      +
    158H  VAL      3.5     3.1    -      -       -      +
    159H  ASN*     3.1    16.0    +      -       -      +
    198H  PRO      3.3     2.6    -      -       -      +
    199H  PHE*     3.3     3.4    -      -       -      -
    200H  VAL*     2.6    52.7    +      -       +      +
    207H  TRP*     3.4    24.2    -      -       -      -
      4L  ARG*     3.7     7.7    -      -       -      +
     14L  LEU*     2.9    85.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 138 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16H  ILE*     4.0    16.9    -      -       +      +
    136H  GLY      5.3     0.2    -      -       -      -
    137H  ARG*     1.3    73.9    -      -       -      +
    139H  THR*     1.3    66.6    +      -       -      +
    157H  VAL*     3.5     1.4    -      -       -      +
    158H  VAL*     2.9    44.8    +      -       +      +
    160H  LEU*     4.4     8.3    -      -       +      -
    190H  ALA*     4.2     6.3    -      -       +      -
    198H  PRO      3.5     5.2    -      -       -      +
    199H  PHE*     3.3    35.4    -      -       +      -
    213H  VAL*     3.5    30.7    -      -       +      -
    228H  TYR*     3.5    17.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 139 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16H  ILE*     4.0     6.2    -      -       -      +
     22H  ALA*     5.5     1.3    -      -       +      -
     27H  SER*     3.6    23.1    +      -       -      +
     30H  GLN*     2.5    39.6    +      -       -      +
    137H  ARG*     4.3     6.5    +      -       +      -
    138H  VAL*     1.3    84.0    -      -       -      +
    140H  GLY*     1.3    59.4    +      -       -      +
    155H  LEU*     4.4     7.9    -      -       +      -
    156H  GLN      3.2    14.1    -      -       -      +
    157H  VAL*     3.7    20.2    -      -       +      -
    194H  ASP*     4.7     3.6    -      -       -      +
    197H  GLY*     4.4     7.3    -      -       -      -
    198H  PRO*     3.7    17.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 140 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16H  ILE*     3.8     2.8    -      -       -      +
     30H  GLN*     4.2     6.1    -      -       -      -
    139H  THR*     1.3    77.0    -      -       -      +
    141H  TRP*     1.3    60.1    +      -       -      -
    142H  GLY      3.8     0.3    +      -       -      -
    155H  LEU*     3.6    13.9    -      -       -      +
    156H  GLN*     3.1    36.8    +      -       -      +
    194H  ASP*     3.3    22.4    -      -       -      -
----------------------------------------------------------
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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