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


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 TYR 41 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  TYR*     3.8    15.9    -      +       -      -
      7B  ALA*     3.1     3.1    -      -       -      -
      8B  ARG*     2.9    55.1    +      -       -      +
     39B  GLU*     3.8     5.8    +      -       +      -
     40B  THR*     1.3    75.5    -      -       -      +
     42B  ALA*     1.3    62.4    +      -       -      +
     43B  GLU*     2.7    42.7    +      -       +      +
     65B  ALA*     3.5     7.3    -      -       +      +
     66B  TYR      3.4    14.8    -      -       -      -
     67B  SER*     4.0    12.6    -      -       -      -
     82B  ARG*     2.8    19.4    +      -       -      -
     74C  TRP*     3.9    23.1    -      +       -      -
      1E  BGC      4.0    17.7    -      -       -      -
      2E  GLC      3.5    24.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 42 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  PHE*     6.1     0.2    -      -       +      -
     62A  THR*     6.2     0.2    -      -       +      -
     81A  PHE*     3.4    35.6    -      -       +      -
     84A  ALA*     5.3     0.4    -      -       +      -
      6B  TYR      3.2     9.6    -      -       -      +
      7B  ALA*     3.8    11.2    -      -       +      -
     40B  THR*     5.4     0.2    -      -       +      -
     41B  TYR*     1.3    79.1    -      -       -      +
     43B  GLU*     1.3    63.1    +      -       -      +
     44B  LEU*     4.1     9.9    -      -       +      -
     64B  VAL      3.9     0.9    -      -       -      +
     65B  ALA*     3.3     2.6    -      -       -      +
     66B  TYR*     2.8    40.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 43 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  GLY*     3.1    24.9    -      -       -      -
      6B  TYR*     2.7    21.7    +      -       +      +
     41B  TYR*     2.7    38.1    +      -       +      +
     42B  ALA*     1.3    72.5    -      -       -      +
     44B  LEU*     1.3    66.9    +      -       -      +
     45B  LYS*     3.9     3.9    -      -       +      +
     63B  ASN*     3.2    34.1    +      -       -      +
     64B  VAL      3.6     4.5    -      -       -      -
     65B  ALA*     4.0     4.9    -      -       +      -
     82B  ARG*     3.4     4.0    +      -       -      -
    106B  PHE*     3.5     3.9    -      -       -      -
    427B  TRP*     3.6     0.2    -      -       -      -
      1E  BGC      2.9    20.6    +      -       -      -
      2E  GLC      2.9    23.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 44 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  LEU*     4.9    15.3    -      -       +      -
     60A  PHE*     5.2     0.2    -      -       +      -
     62A  THR*     4.4    29.6    -      -       +      +
     64A  VAL*     4.5    13.9    -      -       +      -
     81A  PHE*     4.8     2.9    -      -       +      -
      3B  PHE*     4.5     9.9    -      -       +      -
      4B  HIS      4.0     1.8    -      -       -      -
     42B  ALA*     4.6    11.4    -      -       +      -
     43B  GLU*     1.3    79.9    -      -       -      +
     45B  LYS*     1.3    62.7    +      -       -      +
     46B  LEU*     4.1     5.1    +      -       +      +
     62B  THR*     4.8     0.9    +      -       -      -
     63B  ASN*     3.7     1.1    +      -       -      -
     64B  VAL*     3.0    35.6    +      -       +      +
     66B  TYR*     4.3    25.6    -      -       +      +
    427B  TRP*     4.0    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 45 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  ASP      3.4     0.7    -      -       -      +
      3B  PHE*     3.4    10.4    -      -       -      -
      4B  HIS*     2.7    64.0    +      -       +      +
      5B  GLY*     4.4     8.3    -      -       -      -
     43B  GLU*     5.0     2.9    -      -       +      +
     44B  LEU*     1.3    73.5    -      -       -      +
     46B  LEU*     1.3    61.5    +      -       -      +
     47B  GLY      4.1     0.4    -      -       -      -
     61B  ASP*     2.7    34.2    +      -       -      +
     62B  THR      3.2    19.8    +      -       -      +
     63B  ASN*     3.8    22.7    -      -       -      +
     83B  GLU*     2.8    24.8    +      -       -      +
    106B  PHE*     6.1     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 46 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  VAL*     5.7     1.8    -      -       +      -
     46A  LEU*     4.2    21.1    -      -       +      -
      1B  VAL*     3.9    20.4    -      -       +      -
      2B  ASP      3.3     3.6    -      -       -      +
      3B  PHE*     3.9    21.8    -      -       +      -
     44B  LEU*     4.1     4.6    +      -       +      +
     45B  LYS*     1.3    80.3    -      -       -      +
     47B  GLY*     1.3    59.4    +      -       -      +
     60B  PHE*     5.0     0.3    -      -       -      -
     61B  ASP*     4.3     0.7    -      -       -      -
     62B  THR*     2.7    41.6    +      -       -      +
      3C  PHE*     3.9    33.2    -      -       +      -
     44C  LEU*     4.8    13.0    -      -       +      -
     46C  LEU*     4.2    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 47 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  VAL*     3.6     5.1    -      -       -      +
      2B  ASP      2.8    32.1    +      -       -      -
      4B  HIS*     6.0     0.4    -      -       -      -
     45B  LYS      4.1     0.4    -      -       -      -
     46B  LEU*     1.3    73.9    -      -       -      +
     48B  GLN*     1.3    65.4    +      -       -      +
     59B  TYR*     3.6    14.1    -      -       -      -
     60B  PHE*     3.1    14.4    -      -       -      -
     61B  ASP*     3.9     8.6    +      -       -      -
      3C  PHE*     4.6     3.4    -      -       -      -
----------------------------------------------------------
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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