Contacts of the strand formed by residues 381 - 390 (chain C) in PDB entry 1K3B


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 HIS 381 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228B  GLN*     3.6    10.7    +      -       -      -
    234B  CYS*     3.4    27.1    -      -       +      +
    349B  ALA*     3.2     5.5    -      -       -      +
    350B  PHE*     3.1    37.8    +      -       +      +
    352B  VAL*     3.5    32.4    -      -       +      +
    379C  THR*     4.8     0.4    -      -       -      -
    380C  ASN*     1.3    83.3    +      -       -      +
    382C  ALA*     1.3    61.4    +      -       -      +
    383C  VAL*     3.4    17.7    -      -       +      +
    403C  ASN*     2.7    31.4    +      -       -      -
    404C  SER*     4.1     0.2    +      -       -      -
    405C  TRP*     3.3    32.8    +      +       -      -
----------------------------------------------------------
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Residues in contact with ALA 382 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234B  CYS*     3.5    28.7    -      -       -      +
    235B  TYR*     3.7    31.2    -      -       +      +
    238B  ALA*     3.9     9.4    -      -       +      +
    277B  GLY      5.7     0.4    -      -       -      +
    279B  PRO*     4.1    14.1    -      -       +      -
    348B  VAL      3.4     9.0    -      -       -      +
    349B  ALA*     4.2     5.8    -      -       +      +
    381C  HIS*     1.3    73.6    +      -       -      +
    383C  VAL*     1.3    66.9    +      -       -      +
    404C  SER*     4.5     3.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 383 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238B  ALA*     3.6    12.1    -      -       -      +
    347B  ALA*     3.4     5.9    -      -       -      -
    348B  VAL*     2.8    47.4    +      -       +      +
    350B  PHE*     3.8    23.6    -      -       +      -
    381C  HIS*     3.4    28.9    -      -       +      +
    382C  ALA*     1.3    80.0    -      -       -      +
    384C  LEU*     1.3    60.4    +      -       -      +
    401C  VAL*     3.3    21.8    -      -       +      -
    402C  LYS      3.5    13.7    -      -       -      +
    403C  ASN*     3.6    13.9    -      -       -      +
    404C  SER      4.9     0.9    -      -       -      +
    415C  PHE*     4.2     2.5    -      -       +      -
    426C  ILE*     5.0     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 384 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222B  VAL*     4.6     6.3    -      -       +      -
    238B  ALA*     4.2     9.2    -      -       -      +
    241B  GLY*     3.9    18.2    -      -       -      +
    242B  MET*     3.7    24.5    -      -       +      +
    245B  ALA*     5.0     0.4    -      -       +      -
    345B  PRO*     3.6    23.8    -      -       +      -
    346B  MET      3.3    26.7    -      -       -      +
    347B  ALA*     4.1     0.4    -      -       -      +
    383C  VAL*     1.3    75.8    -      -       -      +
    385C  LEU*     1.3    63.0    +      -       -      +
    386C  VAL*     3.5    26.1    +      -       +      +
    401C  VAL*     3.3     3.7    -      -       -      +
    402C  LYS*     2.8    58.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 385 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336B  MET*     3.8    22.0    -      -       +      -
    340B  LEU*     3.6    11.8    -      -       +      +
    345B  PRO*     3.1    28.4    -      -       -      +
    346B  MET*     2.9    39.3    +      -       +      +
    348B  VAL*     4.0    14.2    -      -       +      +
    383C  VAL      4.2     1.0    +      -       -      -
    384C  LEU*     1.3    71.4    -      -       -      +
    386C  VAL*     1.3    58.6    +      -       -      +
    387C  GLY      3.8     2.5    -      -       -      +
    399C  TRP*     3.4    60.1    -      -       +      -
    400C  ILE      3.8    10.8    -      -       -      +
    401C  VAL*     4.2     9.1    -      -       +      +
    426C  ILE*     5.8     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 386 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212B  ASP*     4.5     7.0    -      -       -      +
    213B  TRP*     2.9    35.4    +      -       +      +
    214B  ARG*     4.6     1.6    -      -       -      +
    222B  VAL*     4.1    28.5    -      -       +      -
    340B  LEU*     4.0     9.0    -      -       -      -
    345B  PRO*     4.1     4.9    -      -       +      -
    384C  LEU*     3.6    31.6    -      -       +      +
    385C  LEU*     1.3    79.3    -      -       -      +
    387C  GLY*     1.3    58.7    +      -       -      +
    400C  ILE*     2.9    32.1    +      -       +      +
    402C  LYS*     4.3     4.5    -      -       +      -
    414C  TYR*     3.7    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 387 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211B  TRP      3.0    14.6    -      -       -      -
    212B  ASP*     4.1     1.1    -      -       -      -
    340B  LEU*     3.5    16.2    -      -       -      +
    385C  LEU*     3.8     1.1    -      -       -      +
    386C  VAL*     1.3    80.9    -      -       -      +
    388C  TYR*     1.3    64.1    +      -       -      +
    399C  TRP*     3.5    10.7    -      -       -      -
    400C  ILE*     2.8    33.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 388 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207B  LEU*     4.0     4.2    -      -       -      +
    208B  PRO*     2.7    42.7    +      -       -      +
    209B  THR      3.5    24.9    -      -       -      -
    210B  SER*     3.5     5.6    +      -       -      -
    211B  TRP*     2.7    51.3    +      -       +      +
    337B  LYS*     3.6    39.0    -      -       +      -
    340B  LEU*     4.0    12.8    -      -       +      -
    341B  VAL*     3.7    14.0    -      -       +      +
    387C  GLY*     1.3    73.3    -      -       -      +
    389C  GLY*     1.3    60.2    +      -       -      +
    398C  TYR*     3.3    18.6    -      -       -      +
    399C  TRP*     3.8     9.9    -      +       +      +
    400C  ILE*     4.1     6.3    -      -       -      +
    419C  ARG*     3.6    22.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 389 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209B  THR      4.3     5.2    -      -       -      -
    210B  SER*     3.9    12.8    -      -       -      -
    388C  TYR*     1.3    76.2    -      -       -      +
    390C  THR*     1.3    63.0    +      -       -      -
    397C  ASP*     3.5     0.2    -      -       -      -
    398C  TYR*     2.9    41.2    +      -       -      -
    419C  ARG*     2.8    19.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 390 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209B  THR*     4.3     8.7    +      -       -      -
    210B  SER*     5.0     0.6    +      -       -      -
    389C  GLY*     1.3    73.0    -      -       -      -
    391C  ASP*     1.3    69.5    +      -       -      +
    392C  SER*     3.1     7.1    +      -       -      -
    395C  GLY*     3.7    24.5    -      -       -      +
    396C  MET      3.6     4.3    -      -       -      +
    397C  ASP*     2.7    24.7    +      -       -      +
    398C  TYR*     3.5     9.0    +      -       -      -
    419C  ARG*     3.8     3.8    +      -       -      -
----------------------------------------------------------
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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