Contacts of the strand formed by residues 391 - 400 (chain B) in PDB entry 3U1K


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 THR 391 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    368B  ARG*     4.2     0.7    +      -       -      -
    386B  PHE*     3.7     1.0    -      -       -      +
    387B  GLN*     3.2     7.8    +      -       -      -
    388B  ARG*     2.9    42.7    +      -       -      +
    390B  GLN*     1.3    77.8    -      -       -      +
    392B  GLN*     1.3    62.8    +      -       -      +
    393B  VAL*     4.5     3.8    -      -       +      -
    478B  GLU      3.4     7.6    -      -       -      +
    479B  SER*     5.0     0.2    -      -       -      -
    480B  ASN      2.9    22.7    +      -       -      +
    481B  GLY      2.8    29.8    +      -       -      +
    482B  SER      4.3     0.4    -      -       -      +
    483B  SER*     4.2    23.8    -      -       -      -
    486B  ALA*     4.2    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 392 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    385B  LEU*     3.9    21.6    -      -       +      +
    386B  PHE      3.6     3.4    -      -       -      +
    387B  GLN*     3.1    22.3    +      -       -      +
    391B  THR*     1.3    72.9    -      -       -      +
    393B  VAL*     1.3    62.8    +      -       -      +
    476B  VAL      3.6     0.2    -      -       -      -
    477B  LEU*     2.7    45.8    +      -       +      +
    478B  GLU*     2.8    44.2    +      -       +      +
     62C  LYS      3.0    24.2    +      -       -      -
     63C  LEU*     3.5    14.4    -      -       -      +
     64C  ALA      2.9    25.8    +      -       -      -
     65C  ARG*     3.6     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 393 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    385B  LEU*     3.6     6.2    -      -       -      +
    386B  PHE*     2.9    37.5    +      -       +      +
    391B  THR*     4.5     7.2    -      -       +      -
    392B  GLN*     1.3    77.9    -      -       -      +
    394B  LEU*     1.3    64.3    +      -       -      +
    395B  CYS*     3.7    26.9    +      -       -      -
    475B  GLU      3.4    15.0    -      -       -      +
    476B  VAL*     4.2    15.5    -      -       +      +
    483B  SER*     3.9    11.0    -      -       -      +
    486B  ALA*     3.7    29.2    -      -       +      +
    487B  SER*     3.8    17.3    -      -       -      +
    490B  GLY*     5.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 394 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    376B  MET*     4.2    20.9    -      -       +      -
    377B  PHE*     4.8     7.4    -      -       +      -
    383B  SER*     5.3     2.7    -      -       -      -
    384B  ALA      3.5    16.4    -      -       -      +
    385B  LEU*     4.1    12.8    -      -       +      +
    393B  VAL*     1.3    71.6    -      -       -      +
    395B  CYS*     1.3    67.7    +      -       -      +
    396B  THR*     4.7     8.6    -      -       +      +
    473B  THR      3.7     0.7    -      -       -      +
    474B  SER*     3.6     1.2    -      -       -      -
    475B  GLU*     2.9    54.4    +      -       +      +
    477B  LEU*     3.8    23.8    -      -       +      +
     63C  LEU*     6.0     3.6    -      -       +      -
    105C  LYS*     4.6     4.0    -      -       -      +
    155C  ASN*     5.2     0.2    -      -       -      +
    157C  LEU*     3.7    34.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 395 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    383B  SER*     3.2     5.0    -      -       -      -
    384B  ALA      2.9    34.3    +      -       -      +
    393B  VAL*     3.7    21.1    +      -       -      -
    394B  LEU*     1.3    73.0    -      -       -      +
    396B  THR*     1.3    64.6    +      -       -      +
    472B  VAL*     4.7     2.2    -      -       +      -
    473B  THR      3.1     5.4    -      -       -      +
    474B  SER*     3.3    24.7    -      -       -      -
    487B  SER      3.7     4.0    -      -       -      -
    490B  GLY*     3.5    45.3    -      -       -      +
    491B  GLY*     3.5     6.5    -      -       -      +
    494B  ALA*     3.8     4.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 396 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    380B  LEU*     4.3    22.7    -      -       +      +
    382B  GLY      3.4    10.3    -      -       -      -
    383B  SER*     4.6     1.1    -      -       -      -
    394B  LEU*     4.7    13.7    -      -       +      +
    395B  CYS*     1.3    78.9    -      -       -      +
    397B  VAL*     1.3    63.8    +      -       -      +
    398B  THR*     3.5    17.2    +      -       -      -
    471B  ARG      3.5     0.7    -      -       -      +
    472B  VAL*     3.4     4.1    -      -       -      +
    473B  THR*     2.8    48.1    +      -       -      +
    475B  GLU*     4.7    13.0    -      -       -      +
    494B  ALA*     4.6     0.4    -      -       -      -
    105C  LYS*     4.7     9.0    -      -       +      +
    157C  LEU      5.1     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 397 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    380B  LEU*     5.1     0.7    -      -       -      +
    381B  HIS*     3.4     8.3    +      -       +      +
    382B  GLY      2.9    27.1    +      -       -      +
    396B  THR*     1.3    73.3    +      -       -      +
    398B  THR*     1.3    69.6    +      -       -      +
    399B  PHE*     4.0    19.7    -      -       +      -
    470B  ILE*     4.6     5.8    -      -       +      -
    471B  ARG      3.3     8.3    -      -       -      +
    472B  VAL*     4.6    11.0    -      -       +      -
    494B  ALA*     3.2    41.3    -      -       +      +
    495B  LEU*     3.6    15.5    -      -       +      +
    498B  SER*     3.4    26.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 398 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    380B  LEU*     6.0     1.4    -      -       -      +
    381B  HIS*     3.6    12.3    +      -       +      +
    396B  THR*     3.5    12.5    +      -       -      -
    397B  VAL*     1.3    79.0    +      -       -      +
    399B  PHE*     1.3    72.1    +      -       -      +
    400B  ASP      3.8     0.5    +      -       -      -
    470B  ILE      4.1     0.2    -      -       -      -
    471B  ARG*     2.9    39.8    +      -       -      +
    473B  THR*     5.4     2.9    +      -       -      -
    110C  GLY      6.0     2.0    -      -       -      +
    111C  ARG      5.9     0.2    -      -       -      +
    113C  PRO*     3.7    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 399 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381B  HIS*     2.8    50.3    +      +       +      +
    397B  VAL*     4.0     8.1    -      -       +      -
    398B  THR*     1.3    80.7    -      -       -      +
    400B  ASP*     1.3    59.3    +      -       -      +
    466B  PHE*     3.4    34.3    -      +       -      -
    468B  PHE*     4.0    13.0    -      +       +      -
    469B  THR      3.4     9.0    -      -       -      -
    470B  ILE*     4.1     7.0    -      -       +      -
    498B  SER*     3.6    38.6    -      -       -      -
    500B  VAL*     3.6    16.2    -      -       +      -
    600B  ARG*     4.1    14.8    -      -       +      -
    604B  GLY*     5.9     0.7    -      -       -      -
    605B  PRO*     3.7    28.7    -      -       +      -
    650B  PHE*     4.2     7.8    -      -       -      -
    652B  PRO*     5.2     3.6    -      -       -      +
    113C  PRO*     4.9     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 400 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    398B  THR      3.8     0.2    +      -       -      -
    399B  PHE*     1.3    73.9    -      -       -      +
    401B  SER*     1.3    69.4    +      -       -      +
    404B  SER*     3.3    26.0    +      -       -      +
    468B  PHE*     3.4     9.7    -      -       -      +
    469B  THR*     2.9    32.7    +      -       -      +
    471B  ARG*     2.7    34.0    +      -       -      +
    638B  THR*     5.6     0.9    +      -       -      -
    650B  PHE*     3.4    13.0    -      -       -      -
    111C  ARG      5.1     0.9    -      -       -      +
    112C  ILE*     5.4     6.3    -      -       -      +
    113C  PRO*     3.2    34.5    -      -       +      +
    116C  TYR*     4.5     0.5    +      -       -      -
----------------------------------------------------------
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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