Contacts of the strand formed by residues 121 - 131 (chain A) in PDB entry 3K3K


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 121 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  TYR*     4.3    11.8    +      -       +      -
     95A  ARG*     5.3     2.7    -      -       -      +
     97A  ASP*     3.4    27.9    +      -       -      +
     98A  ILE*     4.5     7.9    -      -       -      +
    107A  GLY      5.9     0.2    -      -       -      -
    108A  PHE      3.3     7.6    -      -       -      +
    109A  SER*     3.5    15.7    -      -       -      +
    119A  ASN      3.6     2.4    +      -       -      +
    120A  TYR*     1.3    78.0    -      -       -      +
    122A  SER*     1.3    65.8    +      -       -      +
    123A  VAL*     4.4    17.4    -      -       -      +
    143A  TYR*     3.1     4.2    -      -       -      +
    144A  VAL*     2.9    50.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  TYR*     4.3     0.7    -      -       -      -
    107A  GLY*     3.0     3.7    -      -       -      -
    108A  PHE*     2.8    55.1    +      -       -      +
    120A  TYR*     3.8    22.2    -      -       -      -
    121A  LYS*     1.3    76.7    +      -       -      +
    123A  VAL*     1.3    69.2    +      -       -      +
    124A  THR*     4.5     1.4    +      -       -      -
    141A  GLU*     3.4    23.9    +      -       -      +
    142A  SER      3.1    14.8    +      -       -      -
    143A  TYR*     4.0     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  PHE*     3.8    25.4    -      -       +      +
     21A  HIS*     3.2    13.3    -      -       +      -
     23A  TYR*     3.6    17.5    +      -       +      +
     98A  ILE*     4.1    20.6    -      -       +      -
    105A  VAL*     3.8    21.8    -      -       +      -
    106A  THR      3.4    11.4    -      -       -      +
    121A  LYS*     4.4    12.6    -      -       -      +
    122A  SER*     1.3    81.2    +      -       -      +
    124A  THR*     1.3    67.2    +      -       -      +
    125A  THR*     4.2     3.1    -      -       +      -
    141A  GLU*     3.3     2.3    -      -       -      +
    142A  SER*     2.8    33.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 124 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  TRP*     4.9     1.0    -      -       -      -
     49A  VAL*     3.7    24.5    -      -       +      -
     58A  TYR*     4.7     8.4    +      -       +      +
    104A  ARG      4.1     0.5    -      -       -      +
    105A  VAL*     3.5     2.1    -      -       -      -
    106A  THR*     2.8    48.1    +      -       -      +
    107A  GLY*     4.7     0.6    -      -       -      -
    108A  PHE*     6.1     0.3    -      -       -      -
    122A  SER*     4.5     1.6    +      -       -      -
    123A  VAL*     1.3    70.6    -      -       -      +
    125A  THR*     1.3    66.2    +      -       -      +
    126A  VAL*     4.9     0.2    -      -       +      -
    139A  VAL*     3.7    27.8    -      -       +      -
    140A  LEU      3.3     4.3    -      -       -      +
    141A  GLU*     3.4    29.0    -      -       +      +
    168A  LEU*     5.6     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 125 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  PHE*     3.8    17.0    -      -       +      -
     21A  HIS*     2.8    30.2    +      -       +      +
    103A  ARG      5.6     0.2    -      -       -      -
    104A  ARG      3.4     7.2    -      -       -      -
    105A  VAL*     3.6    31.4    -      -       +      -
    123A  VAL*     4.2     0.7    -      -       +      -
    124A  THR*     1.3    79.0    -      -       -      +
    126A  VAL*     1.3    63.5    +      -       -      +
    127A  HIS*     2.6    32.3    +      -       -      -
    139A  VAL*     3.5     5.2    -      -       -      +
    140A  LEU*     2.9    34.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  PRO*     3.7    28.5    -      -       +      +
     45A  VAL*     4.1    17.9    -      -       +      -
     46A  TRP*     4.0    21.1    -      -       +      +
     49A  VAL*     4.2    16.6    -      -       +      -
    103A  ARG      4.5     3.5    -      -       -      +
    104A  ARG*     3.1    36.5    +      -       +      +
    125A  THR*     1.3    76.8    -      -       -      +
    127A  HIS*     1.3    69.7    +      -       -      +
    137A  THR*     3.6    22.7    -      -       +      -
    138A  VAL      3.8     2.9    -      -       -      -
    139A  VAL*     4.3     5.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 127 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  LEU*     3.4    28.6    -      -       +      +
     16A  SER*     3.2    34.1    +      -       -      -
     20A  PHE*     6.0     0.2    -      +       -      -
     42A  PRO*     4.5     3.8    -      -       -      -
    103A  ARG      6.2     0.2    -      -       -      -
    125A  THR*     2.6    40.8    +      -       -      -
    126A  VAL*     1.3    80.6    +      -       -      +
    128A  ARG*     1.3    61.0    +      -       -      +
    129A  PHE*     4.0    10.2    -      -       +      -
    137A  THR*     3.1     9.9    -      -       -      +
    138A  VAL      2.9    45.0    +      -       -      +
    140A  LEU*     3.7    15.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 128 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  GLU*     5.6     2.9    -      -       -      +
     41A  PRO*     6.2     0.2    -      -       -      +
     42A  PRO*     3.6    29.0    -      -       +      +
     43A  GLU*     3.5    32.5    +      -       -      -
    104A  ARG*     4.3    16.6    -      -       -      +
    126A  VAL      4.5     0.4    +      -       -      -
    127A  HIS*     1.3    71.8    -      -       -      +
    129A  PHE*     1.3    81.0    +      -       -      +
    130A  GLU*     5.1     8.4    +      -       +      +
    135A  ILE*     4.1    29.8    -      -       +      +
    136A  TRP      3.8     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 129 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  GLU*     4.4     2.0    -      -       +      -
      9A  GLU*     3.7    37.9    -      -       +      -
     12A  GLU*     3.6    35.2    -      -       +      -
     13A  LEU*     4.0     9.9    -      -       +      -
    127A  HIS*     4.0    19.3    -      -       +      -
    128A  ARG*     1.3    79.1    -      -       -      +
    130A  GLU*     1.3    60.9    +      -       -      +
    135A  ILE*     3.2     8.5    -      -       -      +
    136A  TRP*     2.8    63.5    +      +       +      +
    138A  VAL*     3.6    38.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 130 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  ARG*     5.1     9.5    +      -       +      +
    129A  PHE*     1.3    76.4    -      -       -      +
    131A  LYS*     1.3    81.8    +      -       -      +
    132A  GLU      3.9    10.4    -      -       -      +
    133A  ASN*     3.4    18.7    -      -       -      +
    134A  ARG      3.1     7.9    -      -       -      +
    135A  ILE*     3.7    24.5    -      -       +      +
    136A  TRP*     4.0     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  GLU*     1.3    83.4    -      -       -      +
    132A  GLU*     1.3    82.3    +      -       +      +
    134A  ARG*     2.7    39.1    +      -       +      +
    136A  TRP*     3.6    20.9    -      -       +      -
----------------------------------------------------------
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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