Contacts of the strand formed by residues 325 - 333 (chain B) in PDB entry 5LK5


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 325 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66B  LEU      3.4     2.3    -      -       -      +
     67B  GLN*     3.1     4.0    -      -       -      -
     68B  THR*     3.1    27.3    +      -       -      -
     97B  VAL*     3.9    10.1    -      -       +      -
     98B  LYS      3.3     9.6    -      -       -      +
     99B  HIS*     2.7    37.7    +      -       +      +
    101B  GLN*     3.0    10.5    +      -       -      +
    320B  GLN*     2.9    24.2    +      -       -      +
    324B  GLY*     1.3    76.5    -      -       -      +
    326B  ILE*     1.3    62.0    +      -       -      +
    327B  PHE*     3.8    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 326 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  SER      3.5    19.7    -      -       -      +
     53B  SER*     3.8     7.0    -      -       -      +
     54B  GLY*     3.8    21.5    -      -       -      +
     63B  ASP      4.4     6.5    -      -       -      +
     65B  GLY*     3.8    29.8    -      -       -      +
     66B  LEU      3.3     2.2    -      -       -      -
     67B  GLN*     3.9    20.2    -      -       +      +
     96B  THR*     3.8     1.2    +      -       -      +
     97B  VAL*     3.6     3.5    +      -       -      -
     98B  LYS*     2.9    57.7    +      -       +      +
    100B  GLU*     4.4     3.6    -      -       -      +
    324B  GLY      3.7    11.0    -      -       -      +
    325B  THR*     1.3    75.5    -      -       -      +
    327B  PHE*     1.3    65.2    +      -       -      +
    328B  ASP*     4.2     3.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 327 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  PHE*     3.8     4.5    -      -       -      -
     49B  PHE*     4.0    25.8    -      +       -      -
     65B  GLY*     3.2     3.6    -      -       -      -
     66B  LEU*     2.9    43.4    +      -       +      +
     68B  THR*     4.5     4.9    -      -       +      -
     95B  PHE*     4.5     7.0    -      +       -      -
     96B  THR      3.4     4.3    -      -       -      +
     97B  VAL*     4.0    17.3    -      -       +      -
    107B  GLY      4.4     2.2    -      -       -      -
    108B  GLY*     3.5    39.0    -      -       -      -
    316B  LEU*     4.1    23.6    -      -       +      -
    318B  LEU*     3.9    15.7    -      -       +      -
    325B  THR*     3.8    27.1    -      -       +      -
    326B  ILE*     1.3    72.9    -      -       -      +
    328B  ASP*     1.3    60.4    +      -       -      +
    330B  PHE*     3.6    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 328 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  GLN*     3.0    14.2    -      -       -      +
     27B  PHE*     3.5     6.9    -      -       -      -
     62B  LYS      3.2     7.8    -      -       -      +
     63B  ASP*     3.7    13.0    -      -       -      +
     64B  LYS      3.1    12.3    -      -       -      +
     65B  GLY*     4.3     2.0    -      -       -      -
     95B  PHE*     3.8     4.2    -      -       -      +
     96B  THR*     2.9    41.0    +      -       -      +
    326B  ILE*     4.2     5.1    +      -       +      +
    327B  PHE*     1.3    75.0    -      -       -      +
    329B  ASN*     1.3    91.4    +      -       -      +
    330B  PHE*     3.2     6.9    +      -       -      -
    500B   CA      2.3    32.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 329 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  GLU      3.2    11.8    +      -       -      -
     26B  GLN*     3.6    20.8    +      -       -      +
     62B  LYS      5.2     1.8    +      -       -      -
     63B  ASP*     5.2     2.9    -      -       -      +
     94B  GLN*     3.7     3.6    +      -       -      +
     95B  PHE*     3.5    12.0    +      -       -      -
     96B  THR*     3.5    16.6    +      -       +      +
    171B  LEU*     5.4     1.5    -      -       +      +
    328B  ASP*     1.3   112.7    +      -       -      +
    330B  PHE*     1.3    64.9    +      -       -      +
    331B  LEU*     3.6     1.7    +      -       -      +
    342B  PHE*     3.9    10.2    -      -       +      -
    346B  THR*     3.3    46.7    -      -       +      +
    350B  THR*     5.3     1.6    +      -       -      -
    500B   CA      4.4     1.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 330 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  PHE*     4.1    22.0    -      +       +      -
     24B  LYS*     3.4     9.2    -      -       -      +
     25B  GLU*     3.0    41.6    +      -       +      +
     27B  PHE*     3.9    26.0    -      +       -      -
     37B  TRP*     4.1     8.5    -      +       -      -
     66B  LEU*     4.7     0.7    -      -       +      -
     94B  GLN      3.4     7.0    -      -       -      +
     95B  PHE*     3.6    18.8    -      +       +      -
    110B  VAL*     3.8    23.8    -      -       +      -
    314B  LEU*     3.9    26.9    -      -       +      -
    316B  LEU*     4.1    16.4    -      -       +      -
    327B  PHE*     3.6    32.5    -      -       +      -
    328B  ASP      4.0     3.6    -      -       -      -
    329B  ASN*     1.3    76.3    -      -       -      +
    331B  LEU*     1.3    60.2    +      -       -      +
    342B  PHE*     4.1     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 331 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  VAL*     4.0    19.5    -      -       +      -
     23B  PHE      3.3    14.1    -      -       -      +
     24B  LYS*     4.3    11.4    -      -       +      -
     92B  VAL*     3.6     2.6    -      -       -      +
     93B  VAL*     4.7     0.2    -      -       -      +
     94B  GLN*     2.8    47.1    +      -       +      +
    314B  LEU*     6.2     0.2    -      -       -      +
    329B  ASN      4.6     0.7    -      -       -      +
    330B  PHE*     1.3    75.9    -      -       -      +
    332B  ILE*     1.3    69.7    +      -       -      +
    333B  THR*     3.8    18.2    -      -       +      -
    338B  TYR*     4.1    15.5    -      -       +      -
    339B  ALA*     3.8    30.1    -      -       +      -
    342B  PHE*     3.7    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 332 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  VAL*     3.7     1.9    -      -       -      -
     22B  TYR*     2.9    28.3    +      -       +      -
     23B  PHE*     2.8    34.7    +      -       +      +
     81B  PHE*     4.4    19.3    -      -       +      -
     84B  PHE*     3.9    16.4    -      -       +      -
     91B  LEU*     3.8    22.2    -      -       +      -
     92B  VAL      3.3     9.6    -      -       -      +
     93B  VAL*     4.8     5.8    -      -       +      -
    112B  LEU*     4.2    21.5    -      -       +      -
    314B  LEU*     3.8    28.0    -      -       +      -
    331B  LEU*     1.3    77.1    -      -       -      +
    333B  THR*     1.3    64.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 333 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  PRO*     4.4     0.7    -      -       -      +
     20B  ALA      2.6    23.7    +      -       -      -
     21B  VAL*     4.5     0.8    -      -       -      -
     22B  TYR*     4.0     7.0    -      -       -      -
     91B  LEU*     3.7     7.4    -      -       -      +
     92B  VAL*     2.8    45.0    +      -       +      +
    331B  LEU*     3.8    31.0    -      -       +      -
    332B  ILE*     1.3    76.1    -      -       -      +
    334B  ASN*     1.3    64.1    +      -       -      +
    335B  ASP*     3.5    28.5    +      -       -      +
    338B  TYR*     4.0    13.0    -      -       +      -
    339B  ALA*     4.2     2.9    -      -       +      +
----------------------------------------------------------
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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