Contacts of the strand formed by residues 129 - 135 (chain A) in PDB entry 5CVE


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 TYR 129 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  CYS*     3.7     6.3    -      -       +      -
     65A  ALA      3.7    20.4    -      -       -      -
     66A  LEU*     3.7    36.0    -      -       +      +
     88A  ASP*     2.6    37.9    +      -       -      +
    112A  ARG*     4.0     9.9    -      -       -      -
    115A  PHE*     3.7    14.4    -      -       -      -
    122A  PHE*     5.2     0.9    -      -       -      -
    124A  PRO*     4.1     7.6    -      -       +      -
    125A  GLU*     4.3     7.7    +      -       +      +
    128A  SER*     1.3    95.7    -      -       -      +
    130A  ASP*     1.3    62.8    +      -       -      +
    131A  VAL      3.9     5.6    -      -       -      +
    132A  ILE*     3.8    18.8    -      -       +      -
    156A  SER*     3.0    29.4    +      -       -      +
    157A  LEU*     3.4     8.7    -      -       -      +
    158A  ARG*     2.8    26.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 130 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  THR*     3.5     2.1    -      -       +      +
     61A  GLY*     3.2    36.9    +      -       -      +
     63A  SER*     2.5    41.0    +      -       -      -
     64A  CYS      2.8    14.3    +      -       -      +
     84A  PHE*     4.2     2.7    -      -       +      -
    129A  TYR*     1.3    73.9    -      -       -      +
    131A  VAL*     1.3    62.7    +      -       -      +
    158A  ARG*     2.5    37.1    +      -       -      +
    159A  PRO      4.7     2.6    -      -       -      +
    161A  GLY*     3.1     9.5    -      -       -      -
    162A  ILE      3.0    25.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  LEU*     4.0    15.0    -      -       +      -
     53A  LEU*     4.5     0.2    -      -       +      -
     60A  THR*     3.7    16.6    -      -       +      -
     64A  CYS      3.5     2.6    +      -       -      -
     65A  ALA*     3.2     7.5    -      -       +      +
     66A  LEU      2.9    24.9    +      -       -      +
     80A  LEU*     5.0     1.3    -      -       +      -
     84A  PHE*     3.4    33.0    -      -       +      -
    129A  TYR*     3.9     1.0    -      -       -      +
    130A  ASP*     1.3    86.5    -      -       -      +
    132A  ILE*     1.3    75.6    +      -       -      +
    133A  TRP*     4.2    25.6    -      -       +      +
    162A  ILE*     3.3    18.8    -      -       +      +
    164A  VAL*     4.8     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  LEU*     3.5    11.9    -      -       +      -
     68A  CYS*     3.7    26.2    -      -       -      -
    124A  PRO*     4.8     0.2    -      -       +      -
    129A  TYR*     3.8    20.6    -      -       +      -
    131A  VAL*     1.3    75.7    -      -       -      +
    133A  TRP*     1.3    60.0    +      -       -      +
    134A  ILE*     4.1     7.2    -      -       +      -
    153A  CYS*     3.5    51.1    -      -       +      +
    156A  SER*     3.9    18.2    -      -       -      +
    157A  LEU*     3.8    13.0    -      -       +      -
    162A  ILE      3.0     6.3    +      -       -      -
    163A  ILE*     3.3     9.4    -      -       +      +
    164A  VAL      2.8    28.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  SER*     3.5    37.0    -      -       -      -
     48A  PHE*     4.6     6.3    -      +       -      -
     49A  LEU*     4.1    21.1    -      -       +      -
     66A  LEU      2.8    14.1    +      -       -      +
     67A  ASP*     3.7     4.0    -      -       -      +
     68A  CYS*     2.8    32.7    +      -       -      +
     75A  ILE*     3.9    21.8    -      -       +      +
     79A  LEU*     3.6    26.0    -      -       +      -
     80A  LEU*     4.3    15.5    -      -       +      -
    131A  VAL*     3.9    15.2    -      -       +      -
    132A  ILE*     1.3    72.6    -      -       -      +
    134A  ILE*     1.3    61.4    +      -       -      +
    135A  GLN*     2.8    35.9    +      -       +      +
    164A  VAL*     3.6    47.3    -      -       +      -
    166A  LYS*     4.4     7.2    -      -       +      -
    219A  SER*     5.7     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  CYS*     3.9    21.1    -      -       +      -
    119A  LEU*     4.7     6.1    -      -       +      -
    132A  ILE*     4.1     8.7    -      -       +      +
    133A  TRP*     1.3    77.3    -      -       -      +
    135A  GLN*     1.3    59.9    +      -       -      +
    136A  TRP      4.4     0.2    -      -       -      -
    137A  VAL*     3.6    24.0    -      -       +      -
    138A  ILE*     3.8    18.4    -      -       +      -
    146A  LEU*     5.9     0.9    -      -       +      -
    149A  PHE*     3.8    17.9    -      -       +      -
    150A  LEU*     3.8    21.3    -      -       +      -
    153A  CYS*     4.4     1.6    -      -       -      -
    163A  ILE*     3.7    25.4    -      -       +      -
    164A  VAL      2.7    13.3    +      -       -      +
    165A  ILE*     3.3     8.1    -      -       +      +
    166A  LYS      2.9    24.4    +      -       -      +
    167A  ASP*     4.9     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 135 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  ASP*     2.8    30.1    +      -       -      +
     45A  SER*     4.1     2.4    +      -       -      -
     68A  CYS      3.9     7.5    +      -       -      +
     74A  ARG*     4.1     0.4    -      -       -      -
     75A  ILE*     3.3    26.0    -      -       +      +
    133A  TRP*     2.8    33.2    +      -       +      +
    134A  ILE*     1.3    76.2    -      -       -      +
    136A  TRP*     1.3    96.1    +      -       +      +
    137A  VAL*     3.3     6.8    +      -       -      +
    166A  LYS*     3.1    32.0    -      -       +      +
    301A  SAH      2.8    27.0    +      -       -      -
----------------------------------------------------------
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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