Contacts of the strand formed by residues 146 - 152 (chain A) in PDB entry 4C3P


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 ASN 146 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138A  PRO*     5.3     8.1    -      -       +      +
    140A  GLY      3.5     8.7    +      -       -      +
    141A  LYS*     3.4    35.4    -      -       -      +
    145A  GLY*     1.3    80.9    -      -       -      -
    147A  VAL*     1.3    65.7    +      -       -      +
    148A  TYR*     3.7    27.1    +      -       +      +
    162A  LYS*     5.2     0.4    -      -       -      -
    163A  VAL*     3.1    32.2    +      -       -      +
    165A  PHE*     5.2     5.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138A  PRO*     3.5     4.9    -      -       -      +
    139A  LEU*     2.7    38.0    +      -       +      -
    140A  GLY      3.1    10.2    +      -       -      +
    142A  GLY*     5.5     1.3    -      -       -      +
    145A  GLY      5.6     0.4    -      -       -      +
    146A  ASN*     1.3    76.3    -      -       -      +
    148A  TYR*     1.3    65.4    +      -       -      +
    160A  ALA*     4.0    17.7    -      -       +      -
    161A  LEU      3.8    11.7    -      -       -      +
    162A  LYS*     4.1    23.3    -      -       +      +
    210A  LEU*     5.4     0.7    -      -       +      -
   1389A  ACP      3.5    56.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  ILE*     4.0    19.1    -      -       +      -
    136A  GLY      3.9    17.0    -      -       -      -
    137A  ARG      3.6     2.5    -      -       -      +
    138A  PRO*     4.1    22.9    -      -       +      -
    139A  LEU*     3.9     4.7    -      -       -      -
    146A  ASN*     3.7    34.2    +      -       +      +
    147A  VAL*     1.3    76.6    -      -       -      +
    149A  LEU*     1.3    70.7    +      -       -      +
    160A  ALA*     3.2     7.6    -      -       -      +
    161A  LEU*     2.9    44.9    +      -       +      +
    163A  VAL*     4.1    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  ILE*     3.8     1.2    -      -       -      -
    136A  GLY*     3.1    22.3    +      -       -      -
    137A  ARG*     2.9    47.2    +      -       +      +
    139A  LEU*     3.6    11.3    -      -       +      +
    148A  TYR*     1.3    78.7    -      -       -      +
    150A  ALA*     1.3    73.7    +      -       -      +
    158A  ILE*     3.8    24.5    -      -       +      -
    159A  LEU      3.7    11.0    -      -       -      +
    212A  TYR*     3.6    41.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  PHE*     4.7     4.5    -      -       +      -
    134A  GLU      3.4    13.9    -      -       -      +
    135A  ILE*     4.4     7.2    -      -       +      +
    136A  GLY      4.5     0.9    -      -       -      +
    149A  LEU*     1.3    82.9    -      -       -      +
    151A  ARG*     1.3    62.5    +      -       -      +
    158A  ILE*     3.4     9.6    -      -       -      +
    159A  LEU*     2.8    53.5    +      -       +      +
    161A  LEU*     4.1    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  PHE*     3.1     9.9    -      -       -      -
    134A  GLU*     3.0    61.3    +      -       +      +
    150A  ALA*     1.3    76.8    -      -       -      +
    152A  GLU*     1.3    62.4    +      -       -      +
    153A  LYS*     4.9     0.9    -      -       -      -
    156A  LYS*     3.4    46.9    +      -       -      +
    157A  PHE      3.2     5.2    -      -       -      +
    158A  ILE*     3.1    35.2    -      -       +      +
    159A  LEU*     4.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  TRP*     5.1     1.3    -      -       -      +
    132A  ASP*     3.4    14.2    -      -       +      +
    133A  PHE*     4.0    18.3    -      -       +      -
    151A  ARG*     1.3    72.7    -      -       -      +
    153A  LYS*     1.3    59.6    +      -       -      +
    154A  GLN*     2.9    26.1    +      -       -      +
    155A  SER*     2.9    41.2    +      -       -      +
    156A  LYS*     2.7    34.7    +      -       -      -
    157A  PHE      3.0    11.5    +      -       -      +
    159A  LEU*     4.7     1.7    -      -       +      +
     16B  PHE*     3.3    34.6    -      -       +      -
     17B  ILE      4.7     0.5    -      -       -      +
     18B  ASN*     6.0     0.2    -      -       -      -
     19B  PHE*     4.1    27.7    +      -       +      -
----------------------------------------------------------
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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