Contacts of the strand formed by residues 97 - 104 (chain G) in PDB entry 6ALG


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 GLU 97 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95G  LYS*     3.6    16.2    -      -       -      +
     96G  ASP*     1.3    80.1    -      -       +      +
     98G  VAL*     1.3    67.0    +      -       -      +
     99G  ILE*     6.0     5.2    -      -       +      +
    145G  LYS*     3.3    30.6    +      -       -      -
    146G  VAL      3.4     5.4    -      -       -      +
    147G  GLN*     4.0    19.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 98 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92G  VAL*     4.1    10.5    -      -       +      -
     95G  LYS*     3.6    32.3    -      -       +      +
     96G  ASP      5.4     0.9    -      -       -      +
     97G  GLU*     1.3    80.4    -      -       -      +
     99G  ILE*     1.3    69.1    +      -       -      +
    100G  LEU*     3.7    21.3    -      -       +      -
    118G  ASP*     5.1     5.4    -      -       -      +
    121G  VAL*     3.7    23.8    -      -       +      -
    144G  ILE      3.7     0.3    -      -       -      +
    145G  LYS*     3.4     4.9    -      -       -      +
    146G  VAL*     2.9    48.1    +      -       +      +
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Residues in contact with ILE 99 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97G  GLU*     6.0     5.2    -      -       -      +
     98G  VAL*     1.3    81.2    -      -       -      +
    100G  LEU*     1.3    73.2    +      -       -      +
    101G  THR*     4.5     4.5    +      -       -      +
    118G  ASP*     4.3    10.4    -      -       -      +
    143G  ARG*     4.3    23.8    -      -       +      -
    144G  ILE      3.3     6.1    -      -       -      +
    145G  LYS*     4.4    21.3    -      -       +      -
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Residues in contact with LEU 100 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88G  LEU*     5.1     2.2    -      -       +      -
     90G  VAL*     4.8     1.6    -      -       +      -
     98G  VAL*     3.7    32.5    -      -       +      -
     99G  ILE*     1.3    75.9    -      -       -      +
    101G  THR*     1.3    68.4    +      -       -      +
    115G  ILE*     3.6    28.7    -      -       +      -
    116G  THR      4.7     4.9    -      -       -      +
    118G  ASP*     5.0     7.9    -      -       -      +
    121G  VAL*     3.7    28.5    -      -       +      -
    123G  ILE*     4.6    13.7    -      -       +      -
    143G  ARG*     3.4     3.5    -      -       -      -
    144G  ILE*     2.5    50.8    +      -       +      +
    146G  VAL*     4.2    20.6    -      -       +      -
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Residues in contact with THR 101 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99G  ILE*     4.5     6.2    +      -       -      +
    100G  LEU*     1.3    80.1    +      -       -      +
    102G  LEU*     1.3    63.1    +      -       -      +
    103G  ASN*     3.4    29.4    +      -       -      +
    115G  ILE*     4.6     3.7    -      -       -      +
    116G  THR*     2.9    44.7    +      -       -      +
    118G  ASP*     5.7     0.2    +      -       -      -
    141G  SER      6.0     0.2    -      -       -      -
    142G  MET      3.6    11.9    -      -       -      +
    143G  ARG*     4.2    13.6    -      -       +      +
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Residues in contact with LEU 102 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101G  THR*     1.3    71.8    -      -       -      +
    103G  ASN*     1.3    73.1    +      -       -      +
    104G  LYS*     4.5     6.1    -      -       +      -
    110G  VAL*     3.7    24.5    -      -       +      -
    111G  THR      4.7     1.6    -      -       -      +
    114G  ASP      3.9    13.7    -      -       -      +
    115G  ILE*     3.7    26.9    -      -       +      -
    130G  ILE*     4.4    17.3    -      -       +      -
    140G  ILE*     3.7    33.4    -      -       +      -
    141G  SER*     3.4     2.8    -      -       -      -
    142G  MET*     3.1    43.7    +      -       +      +
    144G  ILE*     4.6    12.7    -      -       +      +
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Residues in contact with ASN 103 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101G  THR*     3.4    26.6    +      -       -      +
    102G  LEU*     1.3    80.9    -      -       -      +
    104G  LYS*     1.3    63.9    +      -       -      +
    114G  ASP*     3.9    10.4    +      -       -      +
    116G  THR*     5.4     2.4    +      -       -      -
    139G  SER*     5.6     0.7    -      -       -      +
    140G  ILE      4.1     3.1    -      -       -      -
    141G  SER*     3.3    22.6    -      -       -      -
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Residues in contact with LYS 104 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102G  LEU*     4.5     3.3    -      -       +      +
    103G  ASN*     1.3    76.3    -      -       -      +
    105G  SER*     1.3    74.1    +      -       -      +
    106G  GLY      5.2     1.8    +      -       -      -
    108G  GLY*     5.3     3.6    -      -       -      -
    109G  PRO      3.2    19.6    +      -       -      -
    110G  VAL*     3.8    26.9    -      -       +      +
    114G  ASP*     3.0    45.6    +      -       +      +
    133G  LEU*     3.4    11.3    -      -       +      +
    139G  SER*     2.5    26.6    +      -       -      -
    140G  ILE*     3.7    10.7    +      -       +      +
----------------------------------------------------------
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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