Contacts of the strand formed by residues 245 - 255 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209A  PRO*     3.9     5.2    -      -       -      -
    243A  PRO      3.6     1.2    +      -       -      -
    244A  ALA*     1.3    75.4    -      -       -      +
    246A  GLU*     1.3    62.1    +      -       -      -
    247A  TYR*     3.7     6.2    -      -       -      -
    269A  VAL*     3.3     6.6    -      -       -      -
    270A  LYS      2.7    43.7    +      -       -      +
    210B  ASP*     4.6    12.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 246 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  LYS*     2.8    30.8    +      -       -      -
    207A  VAL      3.8     1.4    -      -       -      +
    208A  GLY*     3.4    19.4    -      -       -      -
    209A  PRO*     3.6     6.3    -      -       -      +
    245A  GLY*     1.3    71.2    -      -       -      -
    247A  TYR*     1.3    66.1    +      -       -      +
    248A  THR*     4.9     6.5    +      -       -      +
    267A  THR*     4.1    25.7    +      -       -      +
    268A  VAL      4.0     2.9    -      -       -      +
    269A  VAL*     4.4    11.4    -      -       +      +
   1272A  O4B      4.5    11.6    -      -       -      +
    210B  ASP*     3.8    14.9    +      -       -      +
    211B  GLY*     3.6    25.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 247 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206A  ALA*     4.5     7.4    -      -       +      -
    207A  VAL      3.5     1.3    -      -       -      -
    208A  GLY*     3.8    14.6    -      -       -      -
    209A  PRO*     3.5    17.9    -      -       +      -
    212A  LEU*     4.9     3.1    -      -       +      -
    214A  ILE*     3.7    27.4    -      -       +      -
    238A  PHE*     3.6    34.5    -      +       +      -
    242A  TYR*     3.6     9.3    -      -       +      +
    243A  PRO*     2.7    53.5    +      -       -      +
    245A  GLY      3.7    10.5    -      -       -      -
    246A  GLU*     1.3    74.9    -      -       -      +
    248A  THR*     1.3    61.3    +      -       -      +
    249A  ILE*     3.6     6.8    +      -       +      -
    267A  THR*     3.4     4.3    -      -       -      -
    268A  VAL*     2.7    46.3    +      -       -      +
    270A  LYS*     3.8    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 248 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  LYS*     4.5     0.7    -      -       -      +
    205A  THR      3.7     0.2    -      -       -      +
    207A  VAL*     2.7    41.0    +      -       -      +
    246A  GLU*     4.9     9.9    +      -       -      +
    247A  TYR*     1.3    71.0    -      -       -      +
    249A  ILE*     1.3    63.6    +      -       -      +
    250A  ASN*     3.3     5.6    +      -       +      +
    265A  SER*     4.3     8.1    -      -       -      -
    266A  MET      3.7     7.6    -      -       -      +
    267A  THR*     4.6     3.1    -      -       -      +
   1272A  O4B      3.5    77.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 249 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186A  PHE*     3.7    36.1    -      -       +      -
    204A  MET*     4.0    24.5    -      -       +      -
    205A  THR      3.6     5.6    -      -       -      +
    206A  ALA*     3.5    26.5    -      -       +      -
    216A  VAL*     4.9     6.3    -      -       +      -
    236A  ILE*     4.4     8.1    -      -       +      -
    238A  PHE*     4.0    22.2    -      -       +      -
    247A  TYR*     4.5     5.2    -      -       +      +
    248A  THR*     1.3    70.0    -      -       -      +
    250A  ASN*     1.3    60.3    -      -       -      +
    265A  SER*     3.2     5.0    -      -       -      -
    266A  MET*     2.6    52.7    +      -       +      +
    268A  VAL*     4.0    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 250 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203A  TRP*     5.5     0.2    -      -       -      -
    204A  MET*     3.2     4.9    -      -       -      +
    205A  THR*     2.7    54.4    +      -       -      +
    207A  VAL*     4.9     1.8    -      -       +      -
    248A  THR*     3.3     7.2    +      -       +      +
    249A  ILE*     1.3    76.6    -      -       -      +
    251A  ALA*     1.3    61.6    +      -       -      +
    252A  GLN*     2.9    37.4    +      -       -      +
    263A  GLU*     3.0    17.2    -      -       -      +
    264A  GLN      3.6     2.7    -      -       -      +
    265A  SER*     2.8    23.0    +      -       -      +
   1272A  O4B      3.6    16.3    -      -       -      +
     87B  TYR*     4.5    10.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 251 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  ILE*     6.4     0.2    -      -       -      -
    168A  ILE*     3.5    34.3    -      -       +      -
    202A  PHE*     4.5     2.0    -      -       +      -
    203A  TRP      3.4     4.7    -      -       -      +
    204A  MET*     3.7    26.0    -      -       +      -
    249A  ILE      4.3     0.2    -      -       -      -
    250A  ASN*     1.3    72.9    -      -       -      +
    252A  GLN*     1.3    65.2    +      -       -      +
    253A  VAL*     5.6     0.2    -      -       -      -
    263A  GLU*     3.3     4.0    -      -       -      +
    264A  GLN      2.8    40.3    +      -       -      +
    266A  MET*     5.3     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 252 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201A  GLU      4.1     0.4    -      -       -      +
    202A  PHE*     3.4     1.6    -      -       -      -
    203A  TRP*     2.8    71.5    +      -       +      +
    250A  ASN*     2.9    27.0    +      -       -      +
    251A  ALA*     1.3    78.9    -      -       -      +
    253A  VAL*     1.3    68.0    +      -       -      +
    261A  ARG*     3.2    37.3    -      -       +      +
    262A  VAL      3.4     8.1    -      -       -      +
    263A  GLU*     3.5    11.2    -      -       +      -
     85B  GLY      3.1    19.8    -      -       -      +
     86B  ILE*     4.1     1.2    -      -       -      +
     87B  TYR      3.8    12.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 253 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161A  LEU*     3.6    22.8    -      -       +      +
    164A  LEU*     4.7     1.1    -      -       +      -
    166A  ILE*     3.6    38.4    -      -       +      -
    168A  ILE*     5.4     1.1    -      -       +      -
    190A  LEU*     4.4     9.9    -      -       +      -
    200A  VAL*     3.9    21.8    -      -       +      -
    201A  GLU      3.4    10.1    -      -       -      +
    202A  PHE*     3.8    19.7    -      -       +      -
    252A  GLN*     1.3    80.7    -      -       -      +
    254A  VAL*     1.3    64.5    +      -       -      +
    261A  ARG*     3.4     2.2    -      -       -      -
    262A  VAL*     2.9    36.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 254 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161A  LEU*     4.0     3.4    -      -       -      -
    200A  VAL*     3.1     7.1    -      -       -      +
    201A  GLU*     2.8    38.1    +      -       +      +
    203A  TRP*     3.3    35.2    -      -       +      -
    253A  VAL*     1.3    75.6    -      -       -      +
    255A  ASP*     1.3    73.1    +      -       -      +
    256A  ILE*     3.4     0.5    +      -       -      +
    259A  GLY*     4.1    11.4    -      -       -      +
    260A  GLU      3.5    11.9    -      -       -      +
    261A  ARG*     3.9    19.1    -      -       +      -
    123B  TYR*     3.8    29.8    -      -       +      +
    124B  MET*     4.2     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 255 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161A  LEU*     3.6    17.8    -      -       +      +
    194A  ARG*     2.7    36.2    +      -       -      +
    199A  ASN      3.5    11.8    +      -       -      +
    200A  VAL*     4.3     3.1    -      -       +      -
    254A  VAL*     1.3    72.3    -      -       -      +
    256A  ILE*     1.3    56.2    +      -       -      +
    257A  VAL*     2.9    21.1    +      -       -      +
    258A  SER*     3.1    30.1    +      -       -      +
    259A  GLY*     2.8    34.1    +      -       -      -
    260A  GLU*     2.9    12.1    +      -       +      +
----------------------------------------------------------
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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