Contacts of the strand formed by residues 137 - 147 (chain B) in PDB entry 1TJJ


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 GLY 137 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59B  LYS*     4.0     9.6    -      -       -      -
    135B  THR      3.4     1.6    +      -       -      -
    136B  THR*     1.3    79.9    -      -       -      +
    138B  ASN*     1.3    66.2    +      -       -      +
    139B  TYR*     3.6     7.7    -      -       -      -
    160B  SER*     3.4     3.3    -      -       -      -
    161B  LEU      2.8    35.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 138 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  SER*     3.3    26.7    +      -       -      +
     59B  LYS*     3.4     7.1    -      -       -      +
     60B  GLU*     2.7    59.5    +      -       +      +
     65B  TRP*     3.4    12.9    -      -       +      -
    137B  GLY*     1.3    76.2    -      -       -      -
    139B  TYR*     1.3    61.6    +      -       -      +
    159B  ALA      3.9     3.1    -      -       -      +
    160B  SER*     2.7    27.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 139 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57B  LEU*     4.5     2.2    -      -       +      -
     58B  GLU      3.3    15.7    -      -       -      +
     59B  LYS*     3.5    27.1    -      -       +      +
     65B  TRP*     3.7     6.8    -      -       -      -
     68B  ILE*     4.0     8.7    -      -       +      -
    134B  LEU      3.2    15.9    +      -       -      -
    135B  THR*     2.7    33.2    +      -       -      -
    137B  GLY*     3.6    20.0    -      -       -      -
    138B  ASN*     1.3    77.6    -      -       -      +
    140B  ARG*     1.3    61.9    +      -       -      +
    158B  ALA*     3.4     5.9    -      -       -      +
    159B  ALA      2.9    34.3    +      -       -      +
    161B  LEU*     3.7    20.2    -      -       +      -
   2484B  PFS      3.0    61.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 140 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56B  VAL      3.7     0.9    -      -       -      +
     57B  LEU*     3.4     4.7    -      -       -      +
     58B  GLU*     2.9    49.0    +      -       -      +
     65B  TRP*     3.4    60.5    -      -       +      +
    139B  TYR*     1.3    78.2    -      -       -      +
    141B  ILE*     1.3    60.2    +      -       -      +
    157B  ILE      3.3     9.4    -      -       -      +
    158B  ALA*     4.4    11.8    -      -       +      +
   2484B  PFS      3.3     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  LEU*     4.4    26.7    -      -       +      -
     56B  VAL      3.2    12.1    -      -       -      +
     57B  LEU*     4.1    18.4    -      -       +      -
     75B  GLY      5.3     2.0    -      -       -      +
    140B  ARG*     1.3    76.0    -      -       -      +
    142B  GLU*     1.3    70.9    +      -       -      +
    143B  SER*     5.0     2.7    -      -       -      +
    155B  ILE      4.0     0.3    -      -       -      +
    156B  LYS*     3.2     4.6    -      -       -      +
    157B  ILE*     2.8    63.3    +      -       +      -
   2484B  PFS      3.8    26.0    -      -       +      +
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Residues in contact with GLU 142 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  CYS*     5.0     0.2    -      -       -      +
     54B  ASP      3.7     1.2    -      -       -      +
     55B  LEU*     3.3     3.8    -      -       -      -
     56B  VAL*     2.9    56.5    +      -       +      +
    141B  ILE*     1.3    76.9    -      -       -      +
    143B  SER*     1.3    63.8    +      -       -      +
    144B  VAL*     4.0    13.4    -      -       +      +
    151B  ARG*     5.4     1.0    +      -       -      -
    154B  CYS*     3.9    20.4    -      -       -      -
    155B  ILE      3.4    10.3    -      -       -      +
    156B  LYS*     2.7    38.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 143 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53B  VAL*     3.9     4.0    -      -       -      +
     54B  ASP      3.5     3.8    -      -       -      -
     55B  LEU*     3.0    26.7    -      -       -      +
    141B  ILE*     4.2     4.0    -      -       -      +
    142B  GLU*     1.3    73.2    -      -       -      +
    144B  VAL*     1.3    60.0    +      -       -      +
    154B  CYS*     3.2     2.4    -      -       -      -
    155B  ILE*     2.9    39.0    +      -       -      -
   2485B  LPE      2.6    51.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 144 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  LYS      3.5     1.6    -      -       -      +
     53B  VAL*     3.4     4.9    -      -       -      +
     54B  ASP*     2.8    50.8    +      -       +      +
    142B  GLU*     4.0    17.0    -      -       -      +
    143B  SER*     1.3    75.6    +      -       -      +
    145B  LEU*     1.3    69.4    +      -       -      +
    146B  SER*     4.1     7.3    +      -       -      +
    151B  ARG*     3.6    39.0    -      -       +      +
    153B  GLY      3.5     6.3    -      -       -      +
    154B  CYS*     3.7    21.8    -      -       -      -
   2485B  LPE      3.6     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 145 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  ALA*     4.6     3.6    -      -       +      -
     47B  LEU*     3.9    32.5    -      -       +      -
     51B  LEU*     3.4    33.0    -      -       +      -
     52B  LYS      3.4    11.4    -      -       -      +
     53B  VAL*     3.9    15.3    -      -       +      +
    144B  VAL*     1.3    71.7    -      -       -      +
    146B  SER*     1.3    63.1    +      -       -      +
    151B  ARG*     3.7     2.8    -      -       -      +
    152B  LEU*     2.7    31.7    +      -       +      -
    153B  GLY      2.8    21.5    +      -       -      +
   2485B  LPE      3.1    42.5    +      -       -      +
   3322B  ACT      4.0     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 146 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  LEU*     3.6     4.9    -      -       -      +
     52B  LYS*     2.7    61.8    +      -       -      +
     54B  ASP*     4.7     2.4    +      -       -      -
    144B  VAL*     4.8     7.8    +      -       -      +
    145B  LEU*     1.3    77.6    -      -       -      +
    147B  SER*     1.3    62.8    +      -       -      +
    149B  GLY*     4.8     7.6    +      -       -      -
    150B  LYS      3.2    23.1    -      -       -      -
    151B  ARG*     4.0     4.0    -      -       -      -
    152B  LEU*     3.9     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 147 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  SER      3.9     8.9    +      -       -      -
     49B  SER      4.7     0.2    +      -       -      -
     50B  PRO*     2.7    31.4    +      -       -      +
     51B  LEU*     4.7     0.9    -      -       -      -
     52B  LYS*     5.6     0.4    -      -       -      -
    146B  SER*     1.3    76.3    -      -       -      +
    148B  SER*     1.3    71.8    +      -       -      +
    149B  GLY      3.1     0.2    -      -       -      -
    150B  LYS*     3.0    24.9    +      -       -      +
    152B  LEU*     3.6    21.1    -      -       -      +
----------------------------------------------------------
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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