Contacts of the strand formed by residues 198 - 207 (chain H) in PDB entry 4BEI


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 198 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164H  LEU*     4.3    19.5    -      -       +      -
    192H  ASN*     3.4    22.2    -      -       +      +
    194H  ARG*     3.5    26.9    -      -       -      +
    197H  GLU*     1.3    74.0    -      -       -      +
    199H  ASN*     1.3    62.9    +      -       -      +
    200H  VAL*     3.9     2.7    +      -       +      +
    222H  TRP      3.5     2.4    -      -       -      +
    223H  VAL*     3.6     1.6    -      -       -      +
    224H  ILE*     2.9    36.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 199 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194H  ARG*     4.8     2.2    -      -       -      +
    197H  GLU*     3.9    22.3    +      -       -      +
    198H  ALA*     1.3    73.5    -      -       -      +
    200H  VAL*     1.3    65.5    +      -       -      +
    222H  TRP      3.5     2.9    -      -       -      +
    223H  VAL*     3.3    29.0    -      -       -      +
    255H  ASP*     3.5     6.4    +      -       -      +
    256H  ILE*     2.9    43.9    +      -       +      +
    257H  VAL*     4.7    19.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 200 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164H  LEU*     3.2    31.2    -      -       +      -
    190H  LEU*     4.6     9.0    -      -       +      -
    198H  ALA*     4.7     3.8    -      -       +      +
    199H  ASN*     1.3    82.8    -      -       -      +
    201H  GLU*     1.3    61.0    +      -       -      +
    202H  PHE*     5.2     2.0    -      -       +      -
    220H  GLU      3.9     0.2    -      -       -      +
    221H  LYS*     3.5     1.7    -      -       -      -
    222H  TRP*     2.8    57.3    +      -       +      +
    224H  ILE*     4.1    16.8    -      -       +      -
    253H  VAL*     3.9    17.3    -      -       +      -
    254H  VAL      3.1    11.7    -      -       -      +
    255H  ASP*     4.3     8.1    -      -       +      -
    256H  ILE*     3.5     8.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 201 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92G  ALA*     5.2     2.8    -      -       -      +
    121G  PRO*     3.9     4.6    -      -       -      +
    123G  TYR*     2.6    48.7    +      -       +      +
    124G  MET*     3.5     9.4    -      -       -      +
    200H  VAL*     1.3    74.3    -      -       -      +
    202H  PHE*     1.3    64.9    +      -       -      +
    203H  TRP*     3.7    22.0    -      -       +      -
    219H  ARG*     3.8    29.9    +      -       +      +
    220H  GLU      3.2    13.7    -      -       -      +
    221H  LYS*     4.0    14.6    +      -       +      +
    253H  VAL*     3.4     4.5    -      -       -      +
    254H  VAL*     2.8    34.5    +      -       +      +
    256H  ILE*     3.8     3.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 202 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168H  ILE*     4.5     4.5    -      -       +      -
    188H  VAL*     4.0    24.0    -      -       +      -
    190H  LEU*     4.3    18.8    -      -       +      -
    200H  VAL*     5.2     3.1    -      -       +      -
    201H  GLU*     1.3    77.6    -      -       -      +
    203H  TRP*     1.3    71.0    +      -       -      +
    204H  MET*     3.8    38.1    -      -       +      -
    217H  ASN*     3.7    28.3    -      -       -      -
    218H  ALA      3.4     2.4    -      -       -      +
    219H  ARG*     3.5     0.5    -      -       -      -
    220H  GLU*     2.8    45.5    +      -       +      +
    222H  TRP*     5.2     3.1    -      +       +      -
    230H  TYR*     4.2    24.7    -      +       -      -
    232H  LYS*     4.6     1.1    -      -       -      -
    251H  ALA*     4.5     8.1    -      -       +      -
    252H  GLN      3.4    11.7    -      -       -      +
    253H  VAL*     3.8    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 203 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86G  ILE*     5.1     1.8    -      -       +      -
     87G  TYR      2.7    27.2    +      -       -      -
     88G  PHE*     3.5    28.7    -      +       +      -
     89G  PRO*     3.9     4.5    -      -       +      -
    124G  MET*     3.5    22.0    -      -       +      -
    201H  GLU*     3.7    24.9    -      -       +      -
    202H  PHE*     1.3    87.0    -      -       -      +
    204H  MET*     1.3    72.9    -      -       -      +
    205H  THR*     4.7     0.4    -      -       +      -
    217H  ASN      3.5    14.6    -      -       -      +
    218H  ALA      4.0     1.1    -      -       -      +
    219H  ARG*     3.6    27.4    -      -       +      -
    250H  ASN*     5.5     0.4    -      -       -      -
    252H  GLN*     2.8    69.5    +      -       +      +
    254H  VAL*     3.3    32.1    -      -       +      -
    261H  ARG*     4.5     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 204 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89G  PRO*     4.0     1.2    -      -       -      +
    168H  ILE*     4.3    15.5    -      -       +      -
    186H  PHE*     4.5    13.5    -      -       +      -
    188H  VAL*     4.2    13.7    -      -       -      -
    202H  PHE*     3.8    22.0    -      -       +      -
    203H  TRP*     1.3    83.5    -      -       -      +
    205H  THR*     1.3    68.5    +      -       -      +
    215H  PRO      4.0     0.3    -      -       -      -
    216H  VAL*     2.9    20.6    +      -       +      -
    217H  ASN*     2.9    44.4    +      -       +      +
    234H  ARG*     4.5     7.9    -      -       -      +
    249H  ILE*     4.0    25.4    -      -       +      -
    250H  ASN      3.2     5.8    -      -       -      +
    251H  ALA*     3.7    23.1    -      -       +      -
    266H  MET*     5.2     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 205 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79G  SER*     5.7     0.2    -      -       -      +
     87G  TYR*     3.8    29.1    -      -       -      +
     88G  PHE*     4.1     2.5    -      -       -      -
     89G  PRO*     4.0    25.4    -      -       +      -
    203H  TRP*     4.7     0.4    -      -       +      -
    204H  MET*     1.3    80.8    -      -       -      +
    206H  ALA*     1.3    58.8    +      -       -      +
    207H  VAL*     3.9     9.7    -      -       -      +
    213H  ILE*     3.9    21.8    -      -       +      -
    214H  ILE      3.2    11.7    -      -       -      +
    215H  PRO*     4.7     1.6    -      -       +      -
    216H  VAL*     3.7     6.5    -      -       -      +
    248H  THR      3.7     0.3    -      -       -      +
    249H  ILE*     3.6     3.3    -      -       -      +
    250H  ASN*     2.8    43.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 206 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205H  THR*     1.3    72.1    -      -       -      +
    207H  VAL*     1.3    64.5    +      -       -      +
    208H  GLY      3.6     2.4    +      -       -      -
    212H  LEU      3.7     0.5    -      -       -      +
    213H  ILE*     3.7     0.6    -      -       -      -
    214H  ILE*     2.7    45.0    +      -       +      +
    216H  VAL*     3.7    11.4    -      -       +      -
    236H  ILE*     4.0    11.4    -      -       +      -
    247H  TYR*     4.5    11.8    -      -       +      -
    248H  THR      3.5     4.7    -      -       -      -
    249H  ILE*     3.5    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 207 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87G  TYR*     3.8    34.3    -      -       +      -
   1272G  O4B      4.0    21.5    -      -       -      +
    205H  THR*     3.9    14.8    -      -       -      +
    206H  ALA*     1.3    71.1    -      -       -      +
    208H  GLY*     1.3    62.5    +      -       -      +
    212H  LEU      3.5     9.0    -      -       -      +
    213H  ILE*     4.5     6.1    -      -       +      +
    246H  GLU      3.8     1.6    -      -       -      +
    247H  TYR*     3.5     0.8    -      -       -      -
    248H  THR*     2.7    43.5    +      -       -      +
    250H  ASN*     4.9     3.8    -      -       +      -
   1272H  O4B      3.8    31.9    -      -       -      +
----------------------------------------------------------
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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