Contacts of the strand formed by residues 146 - 152 (chain L) in PDB entry 1G9N


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 ALA 146 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138L  LEU*     4.1    14.1    -      -       +      -
    141L  PHE*     3.3    35.9    -      -       +      -
    144L  ARG      3.1     6.4    +      -       -      +
    145L  GLU*     1.3    73.8    -      -       -      +
    147L  LYS*     1.3    63.5    +      -       -      +
    148L  VAL*     3.4     1.5    +      -       +      -
    163L  GLU*     3.9     3.6    -      -       -      +
    177L  LEU*     3.3    19.8    -      -       +      +
    198L  VAL*     5.1     1.1    -      -       +      -
    199L  THR      4.2     3.6    -      -       -      -
    200L  HIS*     3.8    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 147 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145L  GLU      4.1     1.2    -      -       -      -
    146L  ALA*     1.3    70.3    -      -       -      +
    148L  VAL*     1.3    67.3    +      -       -      +
    149L  GLN*     3.6    29.0    +      -       +      -
    163L  GLU*     5.2     0.4    -      -       -      -
    197L  GLU      3.7     0.5    -      -       -      +
    199L  THR*     2.8    53.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 148 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138L  LEU*     3.7    18.6    -      -       +      -
    146L  ALA      3.4     1.9    +      -       -      +
    147L  LYS*     1.3    81.6    -      -       -      +
    149L  GLN*     1.3    72.5    +      -       -      +
    150L  TRP*     5.0     2.4    -      -       -      +
    163L  GLU*     4.1    14.5    +      -       -      +
    177L  LEU*     3.4    28.7    -      -       +      -
    179L  SER*     4.1    19.5    +      -       -      +
    196L  CYS*     3.5    27.1    -      -       -      -
    197L  GLU      3.1     9.6    -      -       -      +
    198L  VAL*     4.1     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 149 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147L  LYS*     3.6    32.0    +      -       +      -
    148L  VAL*     1.3    81.7    -      -       -      +
    150L  TRP*     1.3    64.4    +      -       -      +
    151L  LYS*     3.7    15.2    +      -       +      +
    156L  LEU*     3.1    41.1    -      -       +      +
    196L  CYS*     3.4     5.9    -      -       -      -
    197L  GLU*     2.7    56.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 150 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119L  ILE*     3.5    19.5    -      -       +      -
    134L  VAL*     3.5    48.5    -      -       +      -
    136L  CYS*     3.4    23.3    -      -       +      -
    148L  VAL*     5.1     2.0    -      -       +      -
    149L  GLN*     1.3    76.4    -      -       -      +
    151L  LYS*     1.3    62.9    +      -       -      +
    152L  VAL*     3.7     5.6    +      -       +      +
    155L  ALA      3.4     3.1    -      -       -      +
    156L  LEU      4.3     1.5    -      -       -      -
    157L  GLN      2.8    30.4    +      -       -      +
    158L  SER*     5.8     4.3    -      -       -      +
    161L  SER*     3.6    22.9    -      -       -      +
    179L  SER*     3.0    31.9    +      -       -      -
    180L  THR      3.9     0.6    -      -       -      +
    181L  LEU*     3.6    42.8    -      -       +      +
    194L  TYR*     4.8     7.6    -      -       +      -
    195L  ALA      3.0    29.8    -      -       -      -
    196L  CYS*     3.9     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 151 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149L  GLN*     3.7    19.9    +      -       +      +
    150L  TRP*     1.3    73.7    -      -       -      +
    152L  VAL*     1.3    62.7    +      -       -      +
    153L  ASP      3.8     1.8    +      -       -      -
    154L  ASN*     4.2    20.3    +      -       -      +
    155L  ALA      3.1    17.7    -      -       -      +
    156L  LEU*     3.5    30.6    -      -       +      +
    193L  VAL*     4.2     0.5    -      -       -      +
    194L  TYR      3.8     0.3    -      -       -      -
    195L  ALA*     2.9    50.7    +      -       +      +
    197L  GLU*     5.0    14.4    +      -       +      +
    208L  THR*     5.9     2.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 152 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150L  TRP*     4.4     7.6    -      -       +      +
    151L  LYS*     1.3    71.4    -      -       -      +
    153L  ASP*     1.3    70.2    +      -       -      +
    155L  ALA*     2.8    33.3    +      -       +      +
    157L  GLN*     5.0    13.5    -      -       +      +
    181L  LEU*     4.1    35.0    -      -       +      -
    183L  LEU*     4.7     4.7    -      -       +      -
    191L  HIS*     3.3    43.7    +      -       +      +
    193L  VAL      3.8     3.1    -      -       -      -
    194L  TYR*     3.4    22.0    -      -       +      -
----------------------------------------------------------
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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