Contacts of the strand formed by residues 137 - 148 (chain L) in PDB entry 5D4D


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 ARG 137 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59L  GLU*     3.0    35.0    +      -       -      +
     60L  ASP*     5.5     2.8    +      -       -      -
     68L  ILE*     4.4    15.1    -      -       -      +
     69L  PRO      4.9     3.9    +      -       -      +
     70L  GLY*     4.7     3.2    +      -       -      -
     71L  VAL*     4.5     1.2    -      -       -      +
    102L  LYS*     6.1     1.0    -      -       -      +
    103L  ALA      3.9     3.2    +      -       -      +
    104L  GLU*     3.7    31.4    +      -       +      +
    132L  LEU*     3.6     5.8    -      -       -      +
    135L  GLY      4.1     2.1    +      -       -      +
    136L  GLY*     1.3    72.1    -      -       -      +
    138L  LEU*     1.3    61.9    +      -       -      +
    139L  ASN*     4.2    21.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 138 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58L  ILE*     4.2     7.0    -      -       +      -
     68L  ILE*     4.0    25.6    -      -       +      -
     71L  VAL*     4.1    10.5    -      -       +      -
     78L  ILE*     4.5     3.1    -      -       +      -
    101L  LEU*     3.6    27.6    -      -       +      +
    102L  LYS*     3.6     1.9    -      -       -      -
    103L  ALA*     2.9    41.3    +      -       +      +
    109L  VAL*     4.5     6.5    -      -       +      -
    129L  ILE*     4.9     4.3    -      -       +      -
    130L  ALA*     4.5    11.4    -      -       +      -
    132L  LEU*     3.5    28.0    -      -       +      +
    137L  ARG*     1.3    75.6    +      -       -      +
    139L  ASN*     1.3    61.7    +      -       -      +
    140L  MET*     3.7    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 139 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57L  TYR*     5.4     0.2    -      -       -      -
     58L  ILE*     3.8     2.3    -      -       -      +
     59L  GLU*     2.8    66.0    +      -       +      +
    100L  LEU*     6.0     0.2    -      -       -      +
    101L  LEU      3.3     2.0    -      -       -      +
    102L  LYS*     3.3    39.6    -      -       +      +
    137L  ARG*     4.2    22.0    +      -       -      +
    138L  LEU*     1.3    75.0    -      -       -      +
    140L  MET*     1.3    67.7    +      -       -      +
    141L  GLU*     5.5     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 140 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56L  VAL*     4.2     7.4    -      -       +      -
     57L  TYR*     3.2    15.5    -      -       -      +
     58L  ILE*     3.6    28.7    -      -       +      -
     78L  ILE*     3.7    16.6    -      -       +      -
     82L  LEU*     4.3    11.9    -      -       -      -
     99L  LEU      3.9     0.3    -      -       -      +
    100L  LEU*     3.6     2.6    -      -       -      +
    101L  LEU*     2.9    51.6    +      -       +      +
    114L  PHE*     5.1     5.6    -      -       +      -
    129L  ILE*     5.0     3.4    -      -       +      -
    138L  LEU*     3.7    33.0    -      -       +      -
    139L  ASN*     1.3    79.2    +      -       -      +
    141L  GLU*     1.3    66.9    +      -       -      +
    142L  VAL*     4.2    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 141 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55L  SER      4.2     0.2    -      -       -      +
     56L  VAL*     3.4     2.8    -      -       -      -
     57L  TYR*     2.9    44.1    +      -       +      +
     98L  THR*     4.1    19.0    -      -       +      +
     99L  LEU      3.3     6.5    -      -       -      +
    100L  LEU*     3.9    30.1    -      -       +      +
    139L  ASN*     5.5     3.1    -      -       -      +
    140L  MET*     1.3    78.4    -      -       -      +
    142L  VAL*     1.3    64.7    +      -       -      +
    161L  ARG*     3.2    38.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 142 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53L  VAL*     4.4    11.9    -      -       +      -
     55L  SER      3.4     5.6    -      -       -      +
     56L  VAL*     3.6    24.9    -      -       +      -
     82L  LEU*     3.7    21.1    -      -       +      -
     85L  LEU*     5.0     0.9    -      -       +      -
     98L  THR*     3.6     5.7    -      -       -      -
     99L  LEU*     2.9    65.1    +      -       +      +
    114L  PHE*     4.0    14.6    -      -       +      -
    140L  MET*     4.2    10.3    -      -       -      -
    141L  GLU*     1.3    80.1    -      -       -      +
    143L  ARG*     1.3    60.9    +      -       -      +
    144L  VAL*     3.6     9.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 143 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53L  VAL*     3.2     4.0    -      -       -      -
     54L  THR*     2.7    50.1    +      -       -      +
     55L  SER*     2.8    27.0    +      -       -      +
     96L  THR*     2.9    27.7    +      -       -      +
     97L  VAL      3.7     4.5    -      -       -      -
     98L  THR*     4.7     6.5    -      -       -      +
    142L  VAL*     1.3    70.1    -      -       -      +
    144L  VAL*     1.3    56.7    +      -       -      +
    145L  ASP*     2.5    30.1    +      -       -      +
    158L  ILE*     3.5    23.8    -      -       +      +
    159L  LYS      5.4     0.6    -      -       -      -
    160L  ASP*     2.8    47.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 144 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51L  THR*     4.3     8.3    -      -       -      +
     52L  ALA      3.3    11.0    -      -       -      +
     53L  VAL*     3.7    22.7    -      -       +      -
     85L  LEU*     5.1     0.4    -      -       +      -
     87L  VAL*     4.2    19.7    -      -       +      -
     89L  PHE*     3.5    29.2    -      -       +      -
     96L  THR*     3.3     2.4    -      -       -      -
     97L  VAL*     2.9    41.8    +      -       +      +
     99L  LEU*     4.2    23.6    -      -       +      -
    142L  VAL*     4.2     9.6    -      -       +      +
    143L  ARG*     1.3    74.3    -      -       -      +
    145L  ASP*     1.3    62.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 145 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51L  THR*     3.4     2.3    -      -       -      -
     52L  ALA      2.8    34.6    +      -       -      -
     54L  THR*     3.1    30.2    +      -       +      +
     89L  PHE*     4.5     2.5    -      -       -      -
     95L  GLN*     3.3     7.1    -      -       -      +
     96L  THR*     3.2    19.3    -      -       -      +
    143L  ARG*     2.5    44.1    +      -       -      +
    144L  VAL*     1.3    73.2    -      -       -      +
    146L  ARG*     1.3    65.3    +      -       -      +
    158L  ILE*     4.0     1.9    -      -       -      +
    171L  PHE*     3.3     9.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 146 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49L  PRO*     5.3     9.0    -      -       +      -
     50L  GLY      3.3    19.1    -      -       -      +
     51L  THR*     4.3     7.1    -      -       -      +
     89L  PHE*     3.4    40.2    +      -       +      +
     92L  PRO*     2.7    43.4    +      -       -      +
     93L  SER      4.0     0.4    -      -       -      -
     94L  LEU*     3.1    29.2    +      -       -      +
     95L  GLN*     3.0    33.4    +      -       -      +
    145L  ASP*     1.3    78.2    -      -       -      +
    147L  GLY*     1.3    62.9    +      -       -      +
    171L  PHE*     3.8     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 147 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49L  PRO*     3.7     0.7    -      -       -      +
     50L  GLY      2.9    32.4    +      -       -      +
    146L  ARG*     1.3    77.9    -      -       -      +
    148L  VAL*     1.3    65.1    +      -       -      +
    171L  PHE*     3.3    22.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 148 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29K  GLU*     6.2     2.7    -      -       -      +
     46L  SER      3.5    12.6    -      -       -      +
     47L  SER*     3.8    18.2    -      -       -      +
     48L  ILE      3.8     3.8    -      -       -      +
     49L  PRO*     3.7    23.3    -      -       +      -
    147L  GLY*     1.3    80.1    -      -       -      +
    149L  GLY*     1.3    68.9    +      -       -      +
    150L  TYR      3.5     1.4    +      -       -      -
    151L  VAL*     4.4     7.3    -      -       -      +
    171L  PHE*     3.5    15.1    -      -       -      +
----------------------------------------------------------
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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