Contacts of the strand formed by residues 141 - 148 (chain H) in PDB entry 5CZV


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 LEU 141 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127H  LEU      3.7    10.8    -      -       -      +
    129H  PRO*     4.0     9.2    -      -       +      -
    140H  ALA*     1.3    74.2    -      -       -      +
    142H  GLY*     1.3    59.0    +      -       -      +
    157H  TRP*     3.7    26.5    -      -       +      -
    184H  VAL*     3.3     3.8    -      -       -      +
    185H  VAL*     3.1    45.0    +      -       +      +
    187H  VAL*     3.5    32.3    -      -       +      -
    192H  LEU*     4.7     5.4    -      -       +      -
    197H  TYR*     3.8    31.6    -      -       +      +
    214H  VAL*     3.7    30.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 142 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127H  LEU*     3.0    44.4    +      -       -      +
    141H  LEU*     1.3    74.7    -      -       -      +
    143H  CYS*     1.3    59.2    +      -       -      +
    157H  TRP*     3.7     4.6    -      -       -      -
    183H  SER      3.4    10.5    -      -       -      -
    184H  VAL*     3.6    10.7    -      -       -      +
    214H  VAL*     3.4    15.6    -      -       -      +
    118L  PHE*     3.8     1.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 143 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124H  VAL*     3.7    19.1    -      -       +      -
    125H  PHE      3.9     6.5    -      -       -      -
    126H  PRO*     4.8     5.2    -      -       -      -
    127H  LEU*     3.8     5.8    -      -       -      +
    142H  GLY*     1.3    74.1    -      -       -      -
    144H  LEU*     1.3    60.4    -      -       -      +
    145H  VAL*     5.3     3.6    -      -       +      +
    155H  VAL*     5.7     1.6    -      -       +      -
    157H  TRP*     3.8     6.5    -      -       +      -
    182H  SER*     3.7     3.6    -      -       -      -
    183H  SER*     2.9    35.3    +      -       -      +
    199H  CYS*     2.0    54.5    -      -       +      -
    212H  LYS*     4.5     5.8    -      -       -      -
    214H  VAL*     4.9     4.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 144 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123H  SER      3.6     0.3    -      -       -      +
    124H  VAL*     3.1     9.6    -      -       -      +
    125H  PHE*     2.8    59.3    +      -       +      +
    127H  LEU*     4.6    10.3    -      -       +      -
    143H  CYS*     1.3    74.9    -      -       -      +
    145H  VAL*     1.3    66.3    +      -       -      +
    146H  LYS*     3.7    39.9    -      -       +      -
    180H  SER*     6.1     2.9    -      -       -      -
    181H  LEU      4.2     1.6    -      -       -      -
    182H  SER*     3.4    21.8    -      -       -      +
    124L  GLN*     4.8     1.8    -      -       -      +
    131L  SER*     4.6    14.4    -      -       -      -
    133L  VAL*     3.9    25.8    -      -       +      -
    178L  THR*     5.0     6.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 145 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122H  PRO*     3.7    26.9    -      -       +      -
    123H  SER      3.7     3.1    -      -       -      -
    124H  VAL*     4.6     4.0    -      -       +      -
    143H  CYS*     5.3     4.3    -      -       +      +
    144H  LEU*     1.3    77.9    -      -       -      +
    146H  LYS*     1.3    58.5    +      -       -      +
    148H  TYR*     3.8    17.5    -      -       +      -
    153H  VAL*     4.4     6.5    -      -       +      -
    155H  VAL*     5.4     7.0    -      -       +      -
    180H  SER*     3.4     6.6    +      -       -      -
    181H  LEU*     2.9    52.9    +      -       +      +
    182H  SER*     5.5     0.4    -      -       -      -
    183H  SER*     6.5     0.2    -      -       -      -
    199H  CYS*     6.1     0.7    -      -       -      -
    201H  VAL*     3.9    37.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 146 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122H  PRO*     3.6     1.4    -      -       -      +
    123H  SER*     2.9    38.7    +      -       -      +
    125H  PHE*     4.6     8.5    -      -       +      -
    144H  LEU*     3.7    18.8    -      -       +      -
    145H  VAL*     1.3    74.2    -      -       -      +
    147H  ASP*     1.3    93.7    +      -       -      +
    148H  TYR*     3.8     1.6    -      -       -      -
    174H  GLN*     2.8    26.2    +      -       -      -
    179H  TYR      4.3     0.2    -      -       -      -
    180H  SER*     3.2    16.2    -      -       -      +
    124L  GLN*     3.4    23.3    -      -       -      +
    129L  THR*     5.0    13.7    +      -       -      +
    131L  SER*     3.3    21.1    -      -       -      +
    178L  THR*     6.2     0.4    -      -       -      -
    180L  THR*     4.8    15.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 147 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120H  LYS*     4.7     1.9    -      -       -      +
    121H  GLY      3.0    17.8    -      -       -      +
    123H  SER*     5.6     2.2    -      -       -      -
    125H  PHE*     5.7     1.6    -      -       -      -
    146H  LYS*     1.3   111.3    +      -       -      +
    148H  TYR*     1.4    57.1    +      -       -      +
    174H  GLN*     3.3    20.7    +      -       -      +
    176H  SER*     4.3     4.2    +      -       -      -
    178H  LEU*     3.5    33.2    -      -       +      +
    179H  TYR      3.5     0.4    +      -       -      -
    180H  SER*     3.4     9.3    +      -       -      -
    129L  THR*     5.7     0.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 148 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120H  LYS      3.9     5.6    -      -       -      +
    121H  GLY      4.1     0.2    -      -       -      -
    122H  PRO*     3.5    31.9    -      -       +      -
    145H  VAL*     3.8    32.1    -      -       +      -
    147H  ASP*     1.4    74.6    -      -       -      +
    149H  PHE*     1.3    62.1    +      -       -      +
    150H  PRO      3.2    28.3    -      -       -      -
    151H  GLU*     3.4    12.1    +      -       +      -
    153H  VAL*     3.2    32.8    -      -       +      +
    171H  ALA*     3.0    26.0    -      -       -      +
    178H  LEU*     3.6     3.1    -      -       -      -
    179H  TYR*     2.9    67.0    +      -       +      +
    181H  LEU*     3.8     9.5    -      -       -      +
    203H  HIS*     3.8     7.9    -      -       +      -
----------------------------------------------------------
 Back to top of page


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