Contacts of the strand formed by residues 199 - 204 (chain A) in PDB entry 1E1A


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 LYS 199 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  LYS*     6.1     1.2    -      -       -      +
    193A  ALA*     4.6     0.2    -      -       -      +
    194A  GLU*     3.1    28.7    +      -       -      +
    197A  THR*     3.2    34.8    -      -       -      +
    198A  LYS*     1.3    81.1    -      -       -      +
    200A  LEU*     1.3    70.7    +      -       -      +
    201A  TRP*     3.8    37.7    -      -       +      +
    216A  VAL*     4.3    22.2    -      -       +      +
    218A  GLY      3.6     6.1    -      -       -      +
    219A  HIS*     4.7     8.3    -      -       -      +
    220A  ILE*     4.2     2.6    -      -       -      +
    228A  ALA*     4.7     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 200 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191A  ILE*     4.3     3.8    -      -       +      -
    192A  VAL      3.5     2.5    -      -       -      -
    193A  ALA*     3.8    11.7    -      -       +      -
    199A  LYS*     1.3    79.7    -      -       -      +
    201A  TRP*     1.3    60.4    +      -       -      +
    216A  VAL*     3.7     4.3    -      -       -      +
    217A  TRP*     2.8    50.6    +      -       +      -
    218A  GLY*     3.0    21.0    +      -       -      +
    220A  ILE*     3.8     9.0    -      -       +      -
    228A  ALA*     3.8    13.9    -      -       +      -
    231A  MET*     3.7    26.2    -      -       +      -
    239A  LEU*     4.1     4.0    -      -       +      -
    241A  VAL*     4.1     9.2    -      -       +      -
    252A  PHE*     3.5    35.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171A  PHE*     3.5    30.7    -      +       +      -
    190A  LEU      3.6     0.3    -      -       -      +
    191A  ILE*     3.2     5.2    -      -       -      +
    192A  VAL*     2.7    46.1    +      -       +      +
    194A  GLU*     2.9    42.9    +      -       +      +
    199A  LYS*     3.8    29.8    -      -       +      +
    200A  LEU*     1.3    78.0    -      -       -      +
    202A  SER*     1.3    61.8    +      -       -      +
    203A  TYR*     4.8     6.1    -      -       +      -
    214A  LYS*     3.5    38.6    -      -       +      -
    215A  LYS*     3.3    22.0    -      -       -      -
    216A  VAL*     3.5    27.4    -      -       +      -
    217A  TRP*     4.1     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 202 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189A  GLN*     4.3     9.6    +      -       -      -
    190A  LEU      3.1     4.7    -      -       -      -
    191A  ILE*     3.7    12.3    -      -       -      -
    201A  TRP*     1.3    74.4    -      -       -      +
    203A  TYR*     1.3    64.8    +      -       -      +
    213A  ASN      3.4     1.5    +      -       -      +
    214A  LYS*     3.4     5.4    -      -       -      +
    215A  LYS*     2.8    64.5    +      -       -      +
    217A  TRP*     3.5    23.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 203 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  ILE*     4.6     2.2    -      -       +      +
    168A  ASP*     2.5    33.4    +      -       +      +
    171A  PHE*     3.0    27.6    -      +       -      -
    189A  GLN*     3.3     9.6    -      -       -      +
    190A  LEU*     3.0    47.4    +      -       +      -
    192A  VAL*     4.1    21.3    -      -       +      -
    201A  TRP*     4.8     3.6    -      -       +      -
    202A  SER*     1.3    79.2    -      -       -      +
    204A  ASP*     1.3    62.3    +      -       -      +
    211A  ILE*     3.7    45.1    -      -       +      -
    212A  GLU      3.5    12.1    -      -       -      +
    213A  ASN      3.8     2.9    -      -       -      -
    214A  LYS*     3.7    33.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 204 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188A  TYR*     3.5    11.8    -      -       -      +
    189A  GLN*     5.3     6.1    +      -       -      +
    203A  TYR*     1.3    73.5    -      -       -      +
    205A  ILE*     1.3    60.5    +      -       -      +
    206A  LYS*     3.5    28.9    +      -       -      +
    211A  ILE*     3.2     5.7    -      -       -      -
    212A  GLU      2.8    33.6    +      -       -      +
    213A  ASN*     3.0    32.5    +      -       -      +
----------------------------------------------------------
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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