Contacts of the strand formed by residues 41 - 47 (chain A) in PDB entry 2MIB


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 ILE 41 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  HIS*     3.6    22.2    -      -       +      -
      8A  TYR      3.3     9.6    -      -       -      +
      9A  ARG*     3.5    32.3    -      -       +      +
     37A  ASN      6.0     1.1    -      -       -      +
     39A  GLN      3.7     4.7    +      -       -      +
     40A  VAL*     1.3    75.3    -      -       -      +
     42A  PHE*     1.3    70.8    +      -       -      +
     62A  LEU*     3.7     2.8    -      -       -      -
     63A  LYS*     2.8    56.4    +      -       +      +
    151A  VAL*     3.8    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  HIS*     3.3     5.5    -      -       -      -
      8A  TYR*     2.8    38.3    +      -       +      +
     10A  LEU*     3.7    40.4    -      -       +      -
     18A  LEU*     3.9    25.1    -      -       +      -
     26A  LEU*     4.2    14.8    -      -       +      -
     40A  VAL*     4.0    26.2    -      -       +      -
     41A  ILE*     1.3    78.4    -      -       -      +
     43A  SER*     1.3    62.3    +      -       -      +
     44A  MET*     4.0     0.9    -      -       +      -
     60A  LEU*     4.6    21.3    -      -       +      -
     61A  GLY      3.3     6.1    -      -       -      +
     62A  LEU*     3.5    28.0    -      -       +      -
     69A  LEU*     3.9    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  GLN*     4.0    27.2    +      -       -      -
      6A  LEU      3.4     5.8    -      -       -      -
      7A  HIS*     3.2    26.0    +      -       -      -
     42A  PHE*     1.3    71.0    -      -       -      +
     44A  MET*     1.3    61.0    +      -       -      +
     45A  SER*     4.1     0.5    +      -       -      -
     59A  ALA      3.4     5.4    -      -       -      +
     60A  LEU*     3.6     1.7    -      -       -      -
     61A  GLY*     2.8    35.1    +      -       -      -
     62A  LEU      3.9     1.6    +      -       -      -
     63A  LYS*     3.3    21.0    -      -       -      -
     68A  TYR*     5.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  ARG      4.1     0.2    -      -       -      +
      5A  GLN*     3.4     3.8    -      -       -      -
      6A  LEU*     2.9    48.6    +      -       +      +
      8A  TYR*     4.2    24.2    -      -       +      -
     10A  LEU*     6.2     1.1    -      -       +      -
     42A  PHE*     4.0     1.0    -      -       +      -
     43A  SER*     1.3    73.2    -      -       -      +
     45A  SER*     1.3    63.9    +      -       -      +
     58A  VAL*     3.7    29.8    -      -       +      -
     59A  ALA      3.4     4.5    -      -       -      -
     60A  LEU*     3.7    16.8    -      -       +      -
    103A  LYS*     3.8    22.9    -      -       +      -
    112A  PHE*     3.7    33.0    -      -       +      -
    148A  MET*     4.2     9.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  ILE*     3.6    22.6    -      -       -      +
      4A  ARG      3.6    19.7    -      -       -      -
      5A  GLN*     4.0    12.2    +      -       -      -
     43A  SER      5.1     0.7    +      -       -      -
     44A  MET*     1.3    75.2    -      -       -      +
     46A  PHE*     1.3    61.4    +      -       -      +
     47A  VAL*     5.1     0.5    -      -       -      +
     58A  VAL*     3.2     8.5    -      -       -      -
     59A  ALA*     2.9    42.3    +      -       -      +
     68A  TYR*     5.3     1.2    -      -       -      -
     91A  PRO*     4.3    10.0    -      -       -      +
     92A  LYS      5.4     0.5    +      -       -      -
     95A  MET*     5.6     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  ILE*     3.9    18.3    -      -       -      +
      4A  ARG      5.0     0.8    +      -       -      -
     45A  SER*     1.3    75.0    -      -       -      +
     47A  VAL*     1.3    75.5    +      -       -      +
     48A  GLN*     4.1    13.7    -      -       +      -
     50A  GLU*     2.9    42.6    -      -       -      -
     56A  ILE*     4.0    22.2    -      -       +      -
     57A  PRO*     3.8    18.8    -      -       +      -
     58A  VAL*     4.6     2.4    -      -       -      +
     92A  LYS      4.7     0.2    -      -       -      +
     93A  LYS*     4.0    18.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  SER*     4.2     0.9    -      -       -      +
     46A  PHE*     1.3    92.3    -      -       -      +
     48A  GLN*     1.3    62.0    +      -       -      +
     49A  GLY*     3.2    10.6    +      -       -      +
     50A  GLU*     3.7    10.9    -      -       -      +
     57A  PRO*     3.4    31.9    +      -       +      +
     58A  VAL      4.1     0.4    -      -       -      -
     59A  ALA*     3.8    22.4    -      -       +      +
     92A  LYS      5.0     0.2    -      -       -      +
     93A  LYS      3.4     6.3    -      -       -      +
     94A  LYS*     5.3     0.4    -      -       +      -
     95A  MET*     3.7    35.4    -      -       +      +
    100A  VAL*     3.8    24.0    -      -       +      -
----------------------------------------------------------
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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