Contacts of the strand formed by residues 221 - 225 (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 ARG 221 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  THR*     4.1     6.0    +      -       +      +
    194A  VAL      3.7     1.3    +      -       -      +
    195A  THR*     3.2    21.9    -      -       +      +
    196A  ILE*     3.1    26.7    +      -       -      +
    219A  PHE*     4.2     3.9    -      -       -      -
    220A  ARG*     1.3   111.1    -      -       +      +
    222A  ALA*     1.3    61.6    +      -       -      +
    317A  THR*     3.6     7.9    -      -       -      +
    318A  GLN*     2.9    47.9    +      -       -      +
    476A  PHE*     3.0    30.5    -      -       +      -
    477A  ALA*     2.7    30.3    +      -       -      +
    478A  LYS      3.9    10.1    +      -       -      -
    479A  THR      3.2    18.6    +      -       -      -
    480A  GLY*     3.2    13.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 222 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  THR*     4.4     0.9    -      -       -      -
    196A  ILE*     3.5     8.5    -      -       +      +
    206A  VAL*     3.5    24.9    -      -       +      -
    210A  ILE*     3.8    28.5    -      -       +      -
    219A  PHE*     4.9     0.9    -      -       +      -
    221A  ARG*     1.3    77.9    -      -       -      +
    223A  ILE*     1.3    63.2    +      -       -      +
    224A  LEU*     4.1     2.0    -      -       +      -
    317A  THR*     5.0     1.0    -      -       +      +
    318A  GLN      3.6     4.2    +      -       -      -
    319A  ILE*     3.2    11.0    -      -       +      +
    320A  LEU      2.9    23.9    +      -       -      -
    476A  PHE*     3.8     3.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 223 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  MET*     4.2    12.6    -      -       +      -
    195A  THR*     4.2    15.2    -      -       +      +
    196A  ILE      3.2     7.4    +      -       -      +
    197A  PHE*     3.2    21.6    -      -       +      -
    198A  GLY      3.1    22.9    +      -       -      -
    206A  VAL*     4.0     3.3    -      -       -      +
    222A  ALA*     1.3    75.2    -      -       -      +
    224A  LEU*     1.3    64.8    +      -       -      +
    225A  GLN*     3.7    15.0    -      -       -      +
    320A  LEU*     3.0    26.7    -      -       +      +
    421A  TYR*     5.7     0.2    -      -       +      -
    473A  TRP*     3.5    56.1    -      -       +      +
    476A  PHE*     4.2     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 224 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198A  GLY      3.8     3.4    -      -       -      -
    203A  GLY*     3.1    27.6    -      -       -      +
    206A  VAL*     3.7    15.7    -      -       +      -
    207A  GLY*     3.9    18.8    -      -       -      +
    210A  ILE*     4.8     1.8    -      -       +      -
    222A  ALA*     4.1    16.4    -      -       +      +
    223A  ILE*     1.3    76.5    -      -       -      +
    225A  GLN*     1.3    61.2    +      -       -      +
    226A  SER      4.1     0.4    -      -       -      -
    227A  GLY      3.8    16.8    -      -       -      +
    228A  SER*     4.5     4.7    -      -       -      -
    319A  ILE*     4.3    12.3    -      -       +      -
    320A  LEU      3.0     7.4    +      -       -      -
    321A  LEU*     3.1    23.0    -      -       +      +
    322A  GLY      3.0    24.8    +      -       -      +
    404A  LEU*     4.8     0.7    -      -       +      +
    407A  PHE*     4.1    21.1    -      -       +      -
    421A  TYR*     4.7     0.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 225 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  TRP*     3.5    25.0    -      -       -      -
    197A  PHE*     5.2     0.7    -      -       -      -
    198A  GLY      2.9    19.3    +      -       -      +
    199A  GLU*     3.1    17.2    -      -       +      +
    200A  SER      2.9    30.7    +      -       -      -
    203A  GLY*     4.3     1.0    -      -       -      -
    223A  ILE*     3.7     9.9    -      -       +      +
    224A  LEU*     1.3    72.1    -      -       -      +
    226A  SER*     1.3    58.3    +      -       -      +
    227A  GLY*     3.6     0.6    -      -       -      -
    322A  GLY      3.8     0.2    -      -       -      -
    421A  TYR*     3.0    19.8    +      -       -      +
    443A  GLU*     3.5    22.5    -      -       -      +
    444A  ILE*     4.8     1.6    -      -       -      +
    447A  VAL*     4.3    14.4    -      -       -      +
    473A  TRP*     3.2    42.0    +      -       -      +
----------------------------------------------------------
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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