Contacts of the strand formed by residues 200 - 206 (chain L) in PDB entry 3KYM


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 TYR 200 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122C  ASP*     5.3     1.7    +      -       -      +
    144L  LEU*     3.6    30.3    -      -       +      -
    160L  TRP*     4.6    14.4    -      +       +      -
    161L  ASN*     3.8     1.8    -      -       -      -
    165L  LEU*     4.3    21.1    -      -       +      -
    188L  VAL*     4.2    13.5    -      -       +      -
    190L  VAL*     3.4    44.6    -      -       +      +
    194L  ASN      3.7     8.0    +      -       -      -
    195L  PHE*     3.6    41.4    -      +       -      -
    198L  GLN*     4.3    10.4    -      -       +      +
    199L  THR*     1.3    87.1    +      -       -      +
    201L  THR*     1.3    60.5    +      -       -      +
    202L  CYS      4.3     0.2    -      -       -      -
    216L  THR*     3.4     2.8    -      -       -      -
    217L  VAL*     2.8    40.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 201 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126C  LYS*     3.5    32.9    +      -       +      +
    160L  TRP*     3.4    16.0    -      -       -      -
    161L  ASN*     3.3    43.7    +      -       +      +
    199L  THR*     3.7    10.3    -      -       +      -
    200L  TYR*     1.3    75.8    -      -       -      +
    202L  CYS*     1.3    74.0    +      -       -      +
    203L  ASN*     3.9     6.6    +      -       -      -
    214L  ASP*     4.8     2.9    +      -       -      +
    215L  LYS      3.5     6.0    +      -       -      -
    216L  THR*     3.7    18.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 202 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127L  VAL*     4.0    11.4    -      -       +      -
    146L  CYS*     2.0    51.6    -      -       -      -
    158L  VAL*     4.2     9.0    -      -       -      -
    159L  SER      3.9     3.8    -      -       -      -
    160L  TRP*     3.6    12.0    -      -       -      -
    201L  THR*     1.3    93.1    +      -       -      +
    203L  ASN*     1.3    66.2    +      -       -      +
    204L  VAL*     4.1    11.7    -      -       +      -
    214L  ASP*     3.5     1.3    -      -       -      -
    215L  LYS*     2.8    33.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 203 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157L  THR      3.4     2.8    -      -       -      +
    158L  VAL*     3.3     6.9    -      -       -      -
    159L  SER*     3.0    48.6    +      -       -      +
    161L  ASN*     3.3     2.8    -      -       -      -
    162L  SER*     2.4    43.7    +      -       -      +
    201L  THR*     3.9     5.6    +      -       -      -
    202L  CYS*     1.3    86.4    +      -       -      +
    204L  VAL*     1.3    62.0    +      -       -      +
    205L  ASP*     5.6     0.2    -      -       -      +
    214L  ASP*     3.2    28.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 204 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125L  PRO*     4.0    21.8    -      -       +      -
    127L  VAL*     3.6    42.6    -      -       +      -
    148L  VAL*     4.1    14.8    -      -       +      -
    156L  VAL*     4.6     6.7    -      -       +      -
    157L  THR      3.8     1.8    -      -       -      -
    158L  VAL*     4.2    14.6    -      -       +      -
    202L  CYS*     4.1    11.9    -      -       +      -
    203L  ASN*     1.3    77.7    -      -       -      +
    205L  ASP*     1.3    66.1    +      -       -      +
    206L  HIS      4.7     0.2    -      -       -      +
    211L  THR      3.6     1.0    -      -       -      +
    212L  LYS*     3.2     7.8    -      -       -      +
    213L  VAL*     3.0    31.7    +      -       +      +
    214L  ASP*     3.9     8.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 205 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156L  VAL*     3.3     7.1    -      -       -      +
    157L  THR*     2.9    55.8    +      -       +      +
    204L  VAL*     1.3    74.9    -      -       -      +
    206L  HIS*     1.3    63.8    +      -       -      +
    207L  LYS*     3.1    39.6    +      -       -      +
    211L  THR      3.3    14.2    +      -       -      +
    212L  LYS*     4.6    11.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 206 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122L  THR*     4.7     0.4    +      -       -      -
    124L  GLY*     4.0    11.7    -      -       -      -
    125L  PRO*     3.7    21.5    -      -       +      -
    151L  TYR*     3.9     6.7    -      +       +      -
    152L  PHE      2.9    24.5    +      -       -      -
    153L  PRO*     2.7    35.1    +      -       -      +
    156L  VAL*     3.5    23.4    +      -       +      +
    204L  VAL*     4.1     1.6    -      -       -      +
    205L  ASP*     1.3    73.6    +      -       -      +
    207L  LYS*     1.3    63.8    +      -       -      +
    208L  PRO*     3.6    16.4    -      -       +      +
    209L  SER*     3.1    38.3    +      -       -      -
    210L  ASN      3.0    17.2    +      -       -      -
    211L  THR      3.2    12.0    +      -       -      +
----------------------------------------------------------
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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