Contacts of the strand formed by residues 198 - 207 (chain D) 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 D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164D  LEU*     4.3    19.7    -      -       +      -
    192D  ASN*     3.4    21.7    -      -       +      +
    194D  ARG*     3.5    26.9    -      -       -      +
    197D  GLU*     1.3    76.0    -      -       -      +
    199D  ASN*     1.3    62.3    +      -       -      +
    200D  VAL*     3.9     2.8    +      -       +      +
    222D  TRP      3.5     2.6    -      -       -      +
    223D  VAL*     3.6     1.6    -      -       -      +
    224D  ILE*     2.9    36.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 199 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194D  ARG*     4.8     2.2    -      -       -      +
    197D  GLU*     3.9    23.5    +      -       -      +
    198D  ALA*     1.3    74.1    -      -       -      +
    200D  VAL*     1.3    64.9    +      -       -      +
    222D  TRP      3.5     3.5    -      -       -      +
    223D  VAL*     3.3    28.7    -      -       -      +
    255D  ASP*     3.5     7.1    +      -       -      +
    256D  ILE*     2.9    44.5    +      -       +      +
    257D  VAL*     4.6    19.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 200 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161D  LEU*     4.6     0.7    -      -       +      -
    164D  LEU*     3.2    31.6    -      -       +      -
    190D  LEU*     4.6     9.2    -      -       +      -
    198D  ALA*     4.7     3.4    -      -       +      +
    199D  ASN*     1.3    82.5    -      -       -      +
    201D  GLU*     1.3    60.5    +      -       -      +
    202D  PHE*     5.2     2.0    -      -       +      -
    220D  GLU      3.9     0.3    -      -       -      +
    221D  LYS*     3.5     2.3    -      -       -      -
    222D  TRP*     2.8    57.9    +      -       +      +
    224D  ILE*     4.1    16.6    -      -       +      -
    253D  VAL*     3.9    16.6    -      -       +      -
    254D  VAL      3.1    11.7    -      -       -      +
    255D  ASP*     4.3     7.6    -      -       +      -
    256D  ILE*     3.5     9.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 201 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92C  ALA*     5.3     2.8    -      -       -      +
    121C  PRO*     3.9     4.7    -      -       -      +
    123C  TYR*     2.6    48.1    +      -       +      +
    124C  MET*     3.5     9.5    -      -       -      +
    200D  VAL*     1.3    74.5    -      -       -      +
    202D  PHE*     1.3    64.8    +      -       -      +
    203D  TRP*     3.7    21.4    -      -       +      -
    219D  ARG*     3.8    30.1    +      -       +      +
    220D  GLU      3.2    15.0    -      -       -      +
    221D  LYS*     4.0    15.2    +      -       +      +
    252D  GLN      4.1     0.2    -      -       -      +
    253D  VAL*     3.4     4.0    -      -       -      +
    254D  VAL*     2.8    35.3    +      -       +      +
    256D  ILE*     3.8     4.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 202 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168D  ILE*     4.5     3.8    -      -       +      -
    188D  VAL*     4.0    24.9    -      -       +      -
    190D  LEU*     4.3    18.4    -      -       +      -
    200D  VAL*     5.2     3.1    -      -       +      -
    201D  GLU*     1.3    76.6    -      -       -      +
    203D  TRP*     1.3    76.3    +      -       -      +
    204D  MET*     3.8    37.2    -      -       +      -
    217D  ASN*     3.7    27.8    -      -       -      -
    218D  ALA      3.4     2.3    -      -       -      +
    219D  ARG*     3.5     0.5    -      -       -      -
    220D  GLU*     2.8    45.7    +      -       +      +
    222D  TRP*     5.3     2.9    -      +       +      -
    230D  TYR*     4.2    24.5    -      +       -      -
    232D  LYS*     4.6     1.3    -      -       -      -
    251D  ALA*     4.5     8.5    -      -       +      -
    252D  GLN      3.4    14.1    -      -       -      +
    253D  VAL*     3.8    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 203 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86C  ILE*     5.1     1.3    -      -       +      -
     87C  TYR      2.7    27.6    +      -       -      -
     88C  PHE*     3.5    28.7    -      +       +      -
     89C  PRO*     3.9     4.0    -      -       +      -
    124C  MET*     3.5    22.7    -      -       +      -
    201D  GLU*     3.7    25.8    -      -       +      -
    202D  PHE*     1.3    93.7    -      -       -      +
    204D  MET*     1.3    74.1    +      -       -      +
    205D  THR*     4.7     1.3    -      -       +      -
    217D  ASN*     3.4    15.0    -      -       -      +
    218D  ALA      4.0     1.8    -      -       -      +
    219D  ARG*     3.6    26.0    -      -       +      -
    250D  ASN      5.5     0.2    -      -       -      -
    252D  GLN*     2.8    67.3    +      -       +      +
    254D  VAL*     3.3    31.2    -      -       +      -
    261D  ARG*     4.5     2.7    -      -       -      -
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Residues in contact with MET 204 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89C  PRO*     4.0     1.6    -      -       -      +
    168D  ILE*     4.3    15.5    -      -       +      -
    186D  PHE*     4.5    13.5    -      -       +      -
    188D  VAL*     4.2    13.2    -      -       -      -
    202D  PHE*     3.8    22.4    -      -       +      -
    203D  TRP*     1.3    82.9    -      -       -      +
    205D  THR*     1.3    70.6    +      -       -      +
    216D  VAL*     2.9    21.2    +      -       +      -
    217D  ASN*     2.9    45.3    +      -       +      +
    234D  ARG*     4.5     7.6    -      -       -      -
    249D  ILE*     4.0    26.0    -      -       +      -
    250D  ASN      3.2     5.4    -      -       -      +
    251D  ALA*     3.7    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 205 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79C  SER*     5.7     0.4    -      -       -      +
     87C  TYR*     3.8    30.0    -      -       -      +
     88C  PHE*     4.0     3.6    -      -       -      -
     89C  PRO*     4.0    25.4    -      -       +      -
    203D  TRP*     4.7     0.8    -      -       +      -
    204D  MET*     1.3    79.9    -      -       -      +
    206D  ALA*     1.3    57.2    +      -       -      +
    207D  VAL*     3.9     9.5    -      -       -      +
    213D  ILE*     3.9    22.0    -      -       +      -
    214D  ILE      3.2    11.7    -      -       -      +
    215D  PRO*     4.7     1.8    -      -       +      -
    216D  VAL*     3.7     6.9    -      -       -      +
    248D  THR      3.7     0.2    -      -       -      +
    249D  ILE*     3.6     3.5    -      -       -      +
    250D  ASN*     2.7    43.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 206 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205D  THR*     1.3    73.0    -      -       -      +
    207D  VAL*     1.3    63.4    +      -       -      +
    208D  GLY      3.6     2.4    +      -       -      -
    212D  LEU      3.7     0.3    -      -       -      +
    213D  ILE*     3.7     0.5    -      -       -      -
    214D  ILE*     2.7    44.9    +      -       +      +
    216D  VAL*     3.7    12.1    -      -       +      -
    236D  ILE*     4.0    10.8    -      -       +      -
    247D  TYR*     4.5    12.0    -      -       +      -
    248D  THR      3.5     4.7    -      -       -      -
    249D  ILE*     3.5    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 207 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87C  TYR*     3.8    37.7    -      -       +      -
   1272C  O4B      4.2    14.1    -      -       -      +
    205D  THR*     3.9    13.5    -      -       -      +
    206D  ALA*     1.3    72.1    -      -       -      +
    208D  GLY*     1.3    61.9    +      -       -      +
    212D  LEU      3.5    10.1    -      -       -      +
    213D  ILE*     4.5     4.3    -      -       +      +
    246D  GLU      3.8     1.2    -      -       -      +
    247D  TYR*     3.5     1.0    -      -       -      -
    248D  THR*     2.7    50.6    +      -       -      +
    250D  ASN*     4.9     2.2    -      -       +      -
   1272D  O4B      4.0    33.7    -      -       -      +
----------------------------------------------------------
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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