Contacts of the strand formed by residues 96 - 101 (chain A) in PDB entry 1AMN


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 96 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  GLY*     2.9    29.2    -      -       -      -
     33A  ILE      3.4     5.2    -      -       -      +
     34A  PRO*     3.6    25.4    -      -       +      +
     35A  PHE*     3.3    13.0    -      -       -      -
     38A  PRO*     4.8     5.2    -      -       +      +
     58A  TRP*     4.0    17.3    -      +       -      -
     64A  PRO*     3.6    36.3    -      -       +      -
     65A  ASN      5.7     0.7    -      -       -      -
     93A  ASP*     2.9    47.7    +      -       -      -
     94A  CYS*     2.9    16.3    +      -       -      +
     95A  LEU*     1.3    79.9    -      -       -      +
     97A  LEU*     1.3    62.1    +      -       -      +
     98A  ASN*     5.7     0.4    -      -       -      -
    125A  SER*     5.1     0.3    +      -       -      -
    146A  LEU      4.0     0.3    -      -       -      -
    147A  SER*     3.5    21.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  GLY      3.0     5.0    +      -       -      -
     33A  ILE*     2.7    43.5    +      -       +      +
     35A  PHE*     3.6    21.5    -      -       +      -
     96A  TYR*     1.3    75.4    -      -       -      +
     98A  ASN*     1.3    64.0    +      -       -      +
     99A  ILE*     3.5    37.2    -      -       +      -
    144A  VAL*     3.8    13.7    -      -       +      -
    145A  SER      3.6     7.2    -      -       -      +
    146A  LEU*     4.5     2.2    -      -       +      +
    176A  ALA*     3.9    26.5    -      -       +      +
    179A  TRP*     4.0    24.5    -      -       +      -
    180A  VAL*     4.1     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  PHE      3.5     5.8    -      -       -      +
     31A  LEU*     3.1    17.3    -      -       +      +
     32A  GLY*     2.7    28.8    +      -       -      -
     63A  TYR*     4.2    15.3    -      -       -      -
     64A  PRO*     3.7     9.9    -      -       -      +
     97A  LEU*     1.3    74.3    -      -       -      +
     99A  ILE*     1.3    64.6    +      -       -      +
    100A  TRP*     3.9    20.5    -      -       +      -
    125A  SER*     3.3    33.3    +      -       -      -
    144A  VAL*     3.0     9.0    -      -       -      +
    145A  SER*     2.9    35.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  ALA*     3.5     1.6    -      -       -      +
     30A  PHE*     2.8    47.4    +      -       +      +
     31A  LEU*     5.0     0.2    -      -       -      +
     33A  ILE*     3.3    32.1    -      -       +      -
     97A  LEU*     3.5    17.9    -      -       +      -
     98A  ASN*     1.3    79.0    -      -       -      +
    100A  TRP*     1.3    64.4    +      -       -      +
    101A  VAL*     3.6    23.6    -      -       +      -
    142A  VAL*     3.7    21.5    -      -       +      -
    143A  LEU      3.3     5.2    -      -       -      +
    144A  VAL*     4.4     6.3    -      -       +      -
    179A  TRP*     4.1     8.1    -      -       +      -
    184A  ILE*     4.2    11.2    -      -       +      -
    187A  PHE*     3.7    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  VAL*     5.1     5.3    -      -       +      +
     27A  ILE*     4.5     7.2    -      -       +      -
     28A  SER      3.5     3.6    -      -       -      +
     29A  ALA*     3.8    22.1    -      -       +      +
     31A  LEU*     3.9    15.3    -      -       +      +
     63A  TYR*     3.7    24.8    +      +       -      -
     98A  ASN*     3.9    23.8    -      -       +      -
     99A  ILE*     1.3    74.1    -      -       -      +
    101A  VAL*     1.3    60.7    +      -       -      +
    125A  SER      5.1     2.9    -      -       -      -
    130A  TYR      4.0     5.4    -      -       -      -
    131A  ASN*     3.9    13.2    +      -       -      +
    132A  GLY*     3.7    31.0    -      -       -      -
    133A  LYS*     3.6    23.5    -      -       +      +
    136A  ALA*     3.9    19.1    -      -       +      +
    141A  VAL      3.8     4.0    -      -       -      +
    142A  VAL*     3.7     5.4    -      -       -      +
    143A  LEU*     2.9    42.4    +      -       +      +
    145A  SER*     3.3    27.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  ILE*     3.4     5.1    -      -       -      +
     28A  SER*     2.8    32.3    +      -       -      +
     30A  PHE*     3.8    26.0    -      -       +      -
     99A  ILE*     3.6    25.1    -      -       +      -
    100A  TRP*     1.3    72.3    -      -       -      +
    102A  PRO*     1.3    87.6    -      -       +      +
    105A  ARG*     4.2    10.5    -      -       +      +
    106A  PRO*     3.8    10.1    -      -       +      -
    136A  ALA*     5.3     0.7    -      -       -      -
    142A  VAL*     4.5     5.6    -      -       +      -
    187A  PHE*     3.3    34.3    -      -       +      +
----------------------------------------------------------
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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