Contacts of the strand formed by residues 21 - 28 (chain B) in PDB entry 1MJP


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 VAL 21 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  SER*     4.2     3.6    -      -       -      -
     28A  ILE      3.3    22.2    -      -       -      +
     29A  PRO*     3.8    14.1    -      -       +      -
     30A  LEU*     4.1     3.0    -      -       -      +
     12B  ALA*     3.3    31.6    -      -       +      -
     17B  LYS*     2.5    43.6    +      -       +      +
     18B  SER*     4.3    10.2    -      -       -      +
     19B  GLU      3.7     0.9    -      -       -      -
     20B  GLN*     1.3    74.9    -      -       -      +
     22B  LYS*     1.3    69.1    +      -       -      +
     23B  LYS*     5.2     2.5    -      -       +      -
      3C    A      4.1    17.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 22 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  ILE*     2.5    51.6    +      -       -      +
     30A  LEU*     3.6    21.5    -      -       +      +
     33A  LEU*     4.8    15.9    -      -       +      -
     21B  VAL*     1.3    77.2    -      -       -      +
     23B  LYS*     1.3    76.7    +      -       -      +
     24B  ILE*     4.6     6.3    -      -       +      -
      3D    A      4.3    17.7    +      -       -      +
      4D    C      2.8    28.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 23 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  THR*     3.7    20.1    -      -       +      +
     26A  VAL      3.3     5.2    -      -       -      +
     27A  SER*     3.3    27.6    -      -       -      +
     21B  VAL*     5.2     2.7    -      -       +      -
     22B  LYS*     1.3    92.3    +      -       -      +
     24B  ILE*     1.3    67.9    +      -       -      +
      2C    T      6.4     0.2    -      -       -      -
      3C    A      4.0    13.9    +      -       -      +
      4C    G      2.8    47.1    +      -       -      +
      5C    A      4.7     3.0    -      -       -      +
      3D    A      4.7     2.4    +      -       -      +
      6D    T      4.8     2.0    +      -       -      -
      7D    C      4.9     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 24 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  ILE      3.3     0.2    -      -       -      +
     25A  THR*     3.0     7.3    -      -       -      -
     26A  VAL*     2.7    59.0    +      -       +      -
     28A  ILE*     3.5    27.6    -      -       +      -
     33A  LEU*     4.6    17.9    -      -       +      -
     36A  LEU*     5.3     3.4    -      -       +      -
     53A  ASN*     5.5     6.3    -      -       +      +
     57A  LEU*     4.3    12.1    -      -       +      -
     22B  LYS*     4.3     8.3    -      -       +      +
     23B  LYS*     1.3    80.7    -      -       -      +
     25B  THR*     1.3    62.5    +      -       -      +
     26B  VAL*     3.5    14.1    -      -       +      +
      2D    G      5.8     1.1    -      -       -      -
      3D    A      3.7    17.3    -      -       -      +
      4D    C      6.4     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 25 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  LYS*     4.0    30.3    -      -       +      -
     24A  ILE      3.4     9.9    -      -       -      +
     25A  THR*     4.3     5.0    +      -       -      +
     54A  SER*     4.0     4.3    +      -       -      -
     24B  ILE*     1.3    74.0    -      -       -      +
     26B  VAL*     1.3    60.4    +      -       -      +
     27B  SER*     3.7     5.2    +      -       -      -
      6C    C      6.2     0.2    -      -       -      +
      7C    G      5.7     0.2    -      -       -      +
      1D    A      5.1     0.2    -      -       -      +
      2D    G      3.6    24.8    -      -       +      +
      3D    A      2.7    48.9    +      -       -      +
      4D    C      3.4    15.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 26 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  LYS*     3.4     1.7    -      -       -      -
     24A  ILE*     2.7    40.2    +      -       +      -
     26A  VAL*     3.1    43.7    -      -       +      -
     54A  SER*     3.4    13.0    -      -       -      +
     57A  LEU*     3.9    20.4    -      -       +      -
     58A  CYS*     4.8     4.0    -      -       -      -
     24B  ILE*     3.5    11.9    -      -       +      -
     25B  THR*     1.3    72.8    -      -       -      +
     27B  SER*     1.3    64.8    +      -       -      +
     28B  ILE*     3.5    23.6    -      -       +      +
     57B  LEU*     5.8     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 27 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  LYS*     5.5     0.7    -      -       -      -
     21A  VAL*     4.0    15.0    -      -       -      -
     22A  LYS      3.6     5.4    -      -       -      -
     23A  LYS*     3.5    30.0    -      -       -      +
     54A  SER*     3.0    27.8    +      -       -      -
     58A  CYS*     3.6     8.5    -      -       -      -
     25B  THR      4.1     2.9    +      -       -      -
     26B  VAL*     1.3    72.9    -      -       -      +
     28B  ILE*     1.3    59.8    +      -       -      +
      1D    A      3.6    30.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 28 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  VAL*     3.9     4.8    -      -       -      +
     22A  LYS*     2.6    57.4    +      -       -      +
     24A  ILE*     3.4    26.0    -      -       +      -
     58A  CYS*     3.7    10.5    -      -       -      -
     26B  VAL*     3.5    13.0    -      -       +      +
     27B  SER*     1.3    77.2    -      -       -      +
     29B  PRO*     1.3    77.7    -      -       +      +
     32B  VAL*     3.4    17.7    -      -       +      -
     33B  LEU*     3.2    40.6    -      -       +      +
     36B  LEU*     4.6    12.1    -      -       +      -
     57B  LEU*     6.2     0.4    -      -       +      -
----------------------------------------------------------
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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