Contacts of the strand formed by residues 75 - 86 (chain B) in PDB entry 5TX4


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 LYS 75 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  GLU*     6.2     4.9    -      -       +      -
     71B  TYR*     3.5     1.9    -      -       -      -
     72B  VAL*     3.0    36.3    +      -       +      +
     73B  GLY*     3.3     0.6    -      -       -      -
     74B  ARG*     1.3    90.0    -      -       +      +
     76B  PRO*     1.3    70.1    -      -       +      +
     77B  LYS*     3.8    13.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 76 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69B  VAL*     4.5    10.1    -      -       +      -
     70B  TYR      3.5     6.5    -      -       -      +
     71B  TYR*     3.7    31.9    -      -       +      +
     74B  ARG      3.6     8.5    -      -       -      +
     75B  LYS*     1.3    86.6    -      -       +      +
     77B  LYS*     1.3    65.4    +      -       -      +
     78B  VAL*     5.6     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 77 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  ILE      3.8     0.5    -      -       -      +
     69B  VAL*     3.2     6.9    -      -       -      +
     70B  TYR*     2.7    77.8    +      -       +      +
     72B  VAL*     4.2    22.9    -      -       +      +
     75B  LYS*     4.0    15.3    -      -       +      +
     76B  PRO*     1.3    79.9    -      -       -      +
     78B  VAL*     1.3    65.8    +      -       -      +
     79B  GLU*     5.6     3.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 78 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  THR*     3.9    19.5    -      -       +      -
     68B  ILE      3.3    10.3    -      -       -      +
     69B  VAL*     4.0    20.6    -      -       +      -
     76B  PRO*     5.6     2.5    -      -       +      +
     77B  LYS*     1.3    78.5    -      -       -      +
     79B  GLU*     1.3    67.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 79 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  THR*     3.5     3.1    -      -       -      -
     68B  ILE*     2.8    39.4    +      -       +      +
     70B  TYR*     3.7    34.3    +      -       +      -
     77B  LYS*     5.6     3.4    +      -       +      +
     78B  VAL*     1.3    78.2    -      -       -      +
     80B  GLN*     1.3    77.6    +      -       -      +
     81B  LEU*     5.6     5.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 80 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65B  PRO*     3.2    34.8    -      -       +      +
     66B  LEU      3.6     5.2    -      -       -      +
     67B  THR*     3.7    20.9    +      -       +      +
     79B  GLU*     1.3    89.0    -      -       -      +
     81B  LEU*     1.3    62.6    +      -       -      +
     82B  SER*     3.9     4.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 81 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  PHE*     5.0     0.2    -      -       +      -
     30B  TRP*     4.1    17.0    -      -       +      -
     32B  TRP*     4.5    10.1    -      -       +      -
     33B  ILE*     4.3     4.5    -      -       +      -
     65B  PRO*     3.1     5.5    -      -       -      +
     66B  LEU      2.9    34.6    +      -       -      +
     68B  ILE*     3.6    42.6    -      -       +      -
     79B  GLU*     3.8     5.4    +      -       +      +
     80B  GLN*     1.3    72.1    -      -       -      +
     82B  SER*     1.3    64.9    +      -       -      +
     84B  MET*     3.3    34.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 82 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65B  PRO*     4.1     9.7    -      -       -      +
     80B  GLN*     3.9     4.2    +      -       -      +
     81B  LEU*     1.3    77.4    -      -       -      +
     83B  ASN*     1.3    88.5    +      -       -      +
     84B  MET*     3.3     8.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 83 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63B  LEU*     3.7    40.4    -      -       +      +
     64B  GLU      3.7    11.3    +      -       -      -
     82B  SER*     1.3    90.0    +      -       -      +
     84B  MET*     1.3    63.1    +      -       -      +
     85B  ILE      3.7     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 84 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  PHE*     3.7    26.5    -      -       +      -
     28B  LEU*     5.0     3.4    -      -       +      -
     30B  TRP*     4.1    20.0    -      -       +      -
     39B  TYR*     2.7    48.8    +      -       +      +
     41B  ALA*     3.8     6.2    -      -       -      +
     63B  LEU*     5.9     0.2    -      -       -      -
     64B  GLU      3.1     6.1    +      -       -      +
     66B  LEU*     4.0    19.7    -      -       +      -
     81B  LEU*     3.3    40.2    -      -       +      +
     82B  SER      3.5     9.6    -      -       -      +
     83B  ASN*     1.3    81.2    -      -       -      +
     85B  ILE*     1.3    60.2    +      -       +      +
     86B  VAL*     4.3     1.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 85 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  TYR*     3.6    28.3    -      -       +      -
     40B  ASN      3.6    19.5    -      -       -      +
     41B  ALA      3.6     4.0    -      -       -      +
     42B  ASN*     4.1     4.3    -      -       -      +
     63B  LEU*     3.1     9.2    -      -       -      +
     64B  GLU*     2.8    39.1    +      -       +      +
     65B  PRO      3.6    21.8    -      -       -      +
     66B  LEU*     4.5     9.4    -      -       +      -
     83B  ASN      3.7     0.2    -      -       -      -
     84B  MET*     1.3    80.2    -      -       +      +
     86B  VAL*     1.3    75.6    +      -       -      +
     87B  LYS*     4.0    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 86 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  LEU*     3.6    15.3    -      -       +      +
     41B  ALA*     2.8    11.3    +      -       +      +
     42B  ASN*     3.2    41.3    +      -       -      +
     43B  PHE*     4.3     6.1    -      -       -      -
     44B  CYS*     3.5    30.7    -      -       -      -
     60B  SER*     3.6    14.4    -      -       -      -
     63B  LEU*     3.7    15.9    -      -       +      -
     84B  MET      5.6     1.8    -      -       -      +
     85B  ILE*     1.3    74.0    -      -       -      +
     87B  LYS*     1.3    59.1    +      -       -      +
     88B  SER      3.5    14.6    -      -       -      +
----------------------------------------------------------
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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