Contacts of the strand formed by residues 245 - 255 (chain B) 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 GLY 245 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210A  ASP*     4.5    15.0    -      -       -      -
    209B  PRO*     3.9     7.2    -      -       -      -
    243B  PRO      3.6     0.8    +      -       -      -
    244B  ALA*     1.3    77.0    -      -       -      +
    246B  GLU*     1.3    61.4    +      -       -      -
    247B  TYR*     3.7     3.6    -      -       -      -
    269B  VAL*     3.3     7.1    -      -       -      -
    270B  LYS*     2.7    43.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 246 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210A  ASP*     3.8     8.7    -      -       -      +
    211A  GLY*     3.5    31.1    +      -       -      +
    144B  LYS*     2.7    29.3    +      -       -      -
    207B  VAL      3.8     1.2    -      -       -      +
    208B  GLY*     3.4    19.9    -      -       -      -
    209B  PRO*     3.6     6.0    -      -       -      +
    245B  GLY*     1.3    71.1    -      -       -      -
    247B  TYR*     1.3    66.7    +      -       -      +
    248B  THR*     4.1     5.7    +      -       -      +
    267B  THR*     4.1    22.7    +      -       -      +
    268B  VAL      4.0     3.1    -      -       -      +
    269B  VAL*     4.4    12.5    -      -       +      +
   1272B  O4B      3.9    18.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 247 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206B  ALA*     4.5     8.1    -      -       +      -
    207B  VAL      3.5     1.3    -      -       -      -
    208B  GLY*     3.8    13.7    -      -       -      -
    209B  PRO*     3.5    18.2    -      -       +      -
    212B  LEU*     4.9     3.1    -      -       +      -
    214B  ILE*     3.8    28.5    -      -       +      -
    238B  PHE*     3.7    31.4    -      +       +      -
    242B  TYR*     3.5     8.9    -      -       +      +
    243B  PRO*     2.7    53.0    +      -       -      +
    245B  GLY      3.7    10.5    -      -       -      -
    246B  GLU*     1.3    74.4    -      -       -      +
    248B  THR*     1.3    61.3    +      -       -      +
    249B  ILE*     3.6     7.2    +      -       +      -
    267B  THR*     3.4     3.8    -      -       -      -
    268B  VAL*     2.7    47.5    +      -       -      +
    270B  LYS*     3.8    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 248 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81B  LYS*     4.2     1.6    -      -       -      +
    205B  THR      3.7     0.2    -      -       -      +
    207B  VAL*     2.7    38.3    +      -       -      +
    246B  GLU*     5.0     5.0    +      -       -      +
    247B  TYR*     1.3    70.7    -      -       -      +
    249B  ILE*     1.3    65.9    +      -       -      +
    250B  ASN*     3.3     5.4    +      -       +      +
    265B  SER*     4.3     5.6    -      -       -      -
    266B  MET      3.7     7.9    -      -       -      +
    267B  THR*     4.6     4.8    -      -       -      +
   1272B  O4B      3.2    84.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 249 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186B  PHE*     3.7    37.5    -      -       +      -
    204B  MET*     4.0    24.0    -      -       +      -
    205B  THR      3.6     5.2    -      -       -      +
    206B  ALA*     3.5    25.6    -      -       +      -
    216B  VAL*     4.9     6.7    -      -       +      -
    236B  ILE*     4.4     8.5    -      -       +      -
    238B  PHE*     4.0    22.0    -      -       +      -
    247B  TYR*     4.5     5.2    -      -       +      -
    248B  THR*     1.3    70.5    -      -       -      +
    250B  ASN*     1.3    61.4    +      -       -      +
    265B  SER*     3.2     4.7    -      -       -      -
    266B  MET*     2.6    53.2    +      -       +      +
    268B  VAL*     4.0    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 250 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  TYR*     4.5    10.7    +      -       -      +
    203B  TRP*     4.1     0.4    -      -       -      +
    204B  MET*     3.2     4.6    -      -       -      +
    205B  THR*     2.7    55.7    +      -       -      +
    207B  VAL*     4.9     2.0    -      -       +      -
    248B  THR*     4.0     6.3    -      -       +      +
    249B  ILE*     1.3    75.1    -      -       -      +
    251B  ALA*     1.3    62.6    +      -       -      +
    252B  GLN*     2.9    37.6    +      -       -      +
    263B  GLU*     3.0    18.0    -      -       -      +
    264B  GLN      3.6     3.1    -      -       -      +
    265B  SER*     2.8    22.6    +      -       -      +
   1272B  O4B      4.0    15.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 251 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166B  ILE*     6.1     0.4    -      -       -      +
    168B  ILE*     3.5    34.9    -      -       +      +
    202B  PHE*     4.5     2.2    -      -       +      -
    203B  TRP      3.4     4.3    -      -       -      +
    204B  MET*     3.7    25.5    -      -       +      +
    250B  ASN*     1.3    72.7    -      -       -      +
    252B  GLN*     1.3    64.9    +      -       -      +
    253B  VAL*     5.6     0.4    -      -       -      -
    263B  GLU*     3.3     4.0    -      -       -      +
    264B  GLN      2.8    40.5    +      -       -      +
    266B  MET*     5.1     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 252 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  GLY      3.1    19.8    -      -       -      +
     86A  ILE*     4.1     9.3    -      -       -      +
     87A  TYR      3.7     4.8    +      -       -      +
    202B  PHE*     3.4     2.1    -      -       -      -
    203B  TRP*     2.8    68.8    +      -       +      +
    250B  ASN*     2.9    25.4    +      -       -      +
    251B  ALA*     1.3    80.3    -      -       -      +
    253B  VAL*     1.3    67.7    -      -       -      +
    261B  ARG*     3.2    36.1    -      -       +      +
    262B  VAL      3.4     7.6    -      -       -      +
    263B  GLU*     3.5    11.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 253 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161B  LEU*     3.6    21.9    -      -       +      +
    164B  LEU*     4.7     0.7    -      -       +      -
    166B  ILE*     3.6    38.1    -      -       +      -
    168B  ILE*     5.3     1.6    -      -       +      -
    190B  LEU*     4.4     9.0    -      -       +      -
    200B  VAL*     3.8    22.9    -      -       +      -
    201B  GLU      3.4    10.8    -      -       -      +
    202B  PHE*     3.8    20.2    -      -       +      -
    251B  ALA      5.6     0.2    -      -       -      -
    252B  GLN*     1.3    80.1    -      -       -      +
    254B  VAL*     1.3    63.3    +      -       -      +
    261B  ARG*     3.4     1.8    -      -       -      -
    262B  VAL*     2.9    36.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 254 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123A  TYR*     3.8    29.2    -      -       +      +
    124A  MET*     4.4     7.2    -      -       +      -
    161B  LEU*     4.0     3.6    -      -       -      -
    200B  VAL*     3.1     6.6    -      -       -      +
    201B  GLU*     2.8    39.8    +      -       +      +
    203B  TRP*     3.3    35.2    -      -       +      -
    253B  VAL*     1.3    76.1    -      -       -      +
    255B  ASP*     1.3    75.1    +      -       -      +
    256B  ILE*     3.4     0.7    +      -       -      +
    259B  GLY*     4.1    11.4    -      -       -      +
    260B  GLU      3.5    10.8    -      -       -      +
    261B  ARG*     3.9    18.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 255 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161B  LEU*     3.5    18.1    -      -       +      +
    194B  ARG*     2.7    37.3    +      -       -      +
    199B  ASN      3.5    11.8    +      -       -      +
    200B  VAL*     4.3     3.4    -      -       +      -
    254B  VAL*     1.3    71.6    -      -       -      +
    256B  ILE*     1.3    58.6    +      -       -      +
    257B  VAL*     2.9    21.5    +      -       -      +
    258B  SER*     3.1    30.8    +      -       -      +
    259B  GLY*     2.8    34.3    +      -       -      -
    260B  GLU      2.9    13.1    +      -       -      +
----------------------------------------------------------
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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