Contacts of the strand formed by residues 220 - 226 (chain B) in PDB entry 2B4M


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 220 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  THR*     5.7     0.7    -      -       +      -
    102B  ILE      3.4    11.4    -      -       -      +
    103B  THR*     3.8     2.5    -      -       +      -
    107B  PHE*     5.2     0.4    -      -       +      -
    118B  LEU*     3.5    33.9    -      -       +      -
    171B  ILE*     5.2     1.3    -      -       +      -
    172B  ASN      3.2     2.6    +      -       -      -
    173B  LEU*     3.3    21.0    -      -       +      -
    174B  ALA*     2.7    33.4    +      -       -      +
    213B  ILE*     3.7     5.4    -      -       -      -
    218B  ALA      3.7     0.4    -      -       -      -
    219B  ASP*     1.3    82.3    -      -       +      +
    221B  SER*     1.3    58.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 221 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100B  HIS      4.0     0.2    -      -       -      +
    101B  THR*     3.7     2.9    -      -       -      +
    102B  ILE*     2.9    41.5    +      -       -      +
    173B  LEU*     5.6     1.1    -      -       -      -
    174B  ALA      3.0    21.6    +      -       -      -
    209B  MET*     3.4    28.7    -      -       -      +
    213B  ILE*     4.0    11.4    -      -       -      -
    220B  ALA*     1.3    74.4    -      -       -      +
    222B  LEU*     1.3    66.6    +      -       -      +
    223B  SER*     3.2    16.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 222 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99B  ILE*     3.6    18.2    -      -       -      +
    100B  HIS      3.8     9.9    -      -       -      -
    101B  THR*     3.7    35.0    -      -       +      +
    118B  LEU*     4.3    15.3    -      -       +      +
    121B  PHE*     4.0    18.2    -      -       +      -
    173B  LEU*     5.1     5.8    -      -       +      -
    174B  ALA      4.1     3.2    +      -       -      -
    181B  GLU*     3.6    10.2    -      -       -      +
    184B  SER*     3.7    25.1    +      -       -      +
    185B  THR*     3.7    36.4    +      -       +      +
    188B  ILE*     3.8    21.3    -      -       +      -
    221B  SER*     1.3    76.1    +      -       -      +
    223B  SER*     1.3    59.6    +      -       -      +
    224B  ALA      3.6     2.7    -      -       -      -
    247B  SER*     5.3     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 223 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175B  TYR*     3.7     5.9    -      -       -      +
    176B  VAL*     3.3    27.6    +      -       -      +
    181B  GLU*     3.2    27.5    -      -       -      +
    185B  THR*     4.5     0.5    +      -       -      -
    209B  MET*     3.8    15.4    -      -       -      +
    221B  SER*     3.2    16.2    +      -       -      -
    222B  LEU*     1.3    78.6    +      -       -      +
    224B  ALA*     1.3    61.0    +      -       -      +
    225B  TRP*     3.3     9.5    +      -       -      -
    230B  HIS*     3.2    20.8    -      -       -      -
    310B  PBE      6.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 224 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98B  GLU      3.7     0.3    -      -       -      +
     99B  ILE*     3.4     4.3    -      -       -      +
    100B  HIS*     2.7    48.8    +      -       +      +
    102B  ILE*     3.9    28.7    -      -       +      -
    209B  MET*     4.5     2.5    -      -       -      +
    210B  TRP*     3.9    19.1    -      -       +      -
    221B  SER*     4.6     1.2    +      -       -      -
    222B  LEU      3.6     1.6    -      -       -      -
    223B  SER*     1.3    74.8    -      -       -      +
    225B  TRP*     1.3    60.7    +      -       -      +
    226B  LEU*     3.9     5.8    -      -       +      -
    230B  HIS*     3.9     7.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 225 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  TRP*     4.1    11.9    -      +       +      -
     74B  PRO*     4.0    26.9    -      -       +      -
     97B  GLU*     3.6     6.3    -      -       +      +
     98B  GLU      3.4     4.5    -      -       -      -
     99B  ILE*     3.6    30.0    -      -       +      +
    180B  SER*     4.0    10.8    -      -       -      -
    181B  GLU*     3.1    25.9    +      -       -      -
    223B  SER      3.3    14.5    +      -       -      -
    224B  ALA*     1.3    74.8    -      -       -      +
    226B  LEU*     1.3    63.0    +      -       -      +
    229B  THR*     3.3    30.7    -      -       +      +
    230B  HIS*     3.1    35.2    +      -       +      +
    251B  VAL*     3.5    24.0    -      -       +      -
    252B  LYS      5.2     0.2    -      -       -      -
    253B  MET*     4.4     8.3    -      -       -      -
    310B  PBE      3.6    49.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 226 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97B  GLU*     3.1     5.4    -      -       -      -
     98B  GLU*     2.7    38.8    +      -       -      +
    100B  HIS*     3.8    34.5    -      -       +      +
    102B  ILE*     5.0     1.6    -      -       +      -
    210B  TRP*     4.2    11.9    -      -       +      -
    224B  ALA*     3.9    21.7    -      -       +      -
    225B  TRP*     1.3    83.5    -      -       -      +
    227B  PRO*     1.3    67.5    -      -       +      +
    230B  HIS*     3.7    24.9    -      -       +      +
    234B  ALA*     3.9    20.0    -      -       +      -
    241B  TYR*     4.4     8.5    -      -       -      +
    243B  ASP*     4.1     8.1    -      -       -      +
----------------------------------------------------------
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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