Contacts of the strand formed by residues 29 - 35 (chain E) in PDB entry 2MF0


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 GLN 29 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25E  VAL*     3.6     2.3    -      -       -      +
     26E  SER*     2.8    48.1    +      -       -      +
     27E  GLY      4.3     0.5    -      -       -      +
     28E  GLN*     1.3    81.5    -      -       +      +
     30E  VAL*     1.3    61.8    +      -       -      +
      5F  THR*     3.0    47.1    +      -       +      +
      6F  ARG*     3.0    14.2    +      -       -      +
      7F  LYS*     3.7    27.4    -      -       +      +
     38G    A      5.0     2.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 30 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22E  ILE*     3.2    32.3    -      -       +      -
     24E  GLY      3.6     4.7    -      -       -      +
     25E  VAL*     4.7     2.5    -      -       +      -
     28E  GLN      3.7     8.5    -      -       -      +
     29E  GLN*     1.3    82.3    +      -       -      +
     31E  ARG*     1.3    57.8    +      -       -      +
     32E  ILE*     3.4    22.8    -      -       +      +
      5F  THR*     3.4     2.4    -      -       -      -
      6F  ARG      2.8    40.2    +      -       -      +
     22F  ILE*     4.1    16.4    -      -       +      -
     25F  VAL*     3.8    22.9    -      -       +      -
     30F  VAL*     4.0    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 31 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22E  ILE*     3.5     4.3    -      -       -      +
     23E  LEU*     2.8    49.6    +      -       +      +
     24E  GLY*     2.8    20.6    +      -       -      +
     26E  SER*     5.5     2.8    +      -       -      +
     30E  VAL*     1.3    70.5    -      -       -      +
     32E  ILE*     1.3    54.2    +      -       -      +
      3F  ILE*     3.4    27.4    -      -       +      +
      4F  LEU      3.4     5.8    -      -       -      +
      5F  THR*     4.0    19.3    +      -       +      +
     18G    A      3.1    24.0    +      -       -      -
     42G    C      3.5    11.5    +      -       -      -
     43G    A      2.8    52.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 32 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20E  ILE*     4.0    23.1    -      -       +      -
     21E  THR      3.5    15.9    -      -       -      +
     22E  ILE*     4.5     4.9    -      -       +      +
     23E  LEU*     4.0     4.3    -      -       -      -
     30E  VAL*     3.4    31.2    -      -       +      +
     31E  ARG*     1.3    79.6    -      -       -      +
     33E  GLY*     1.3    60.2    +      -       -      +
     34E  ILE*     4.1     7.9    +      -       +      +
      2F  LEU      4.0     0.2    -      -       -      +
      3F  ILE*     3.4     1.4    -      -       -      -
      4F  LEU*     2.9    40.2    +      -       +      +
      6F  ARG*     4.3    17.0    -      -       +      -
     12F  ILE*     4.8    10.3    -      -       +      -
     20F  ILE*     5.9     7.9    -      -       +      -
     22F  ILE*     5.0    10.8    -      -       +      -
     32F  ILE*     5.7    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 33 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19E  THR      4.8     0.2    -      -       -      -
     20E  ILE*     3.4     7.2    -      -       -      +
     21E  THR*     2.8    39.9    +      -       -      +
     23E  LEU*     3.5    10.2    -      -       -      +
     32E  ILE*     1.3    73.9    -      -       -      +
     34E  ILE*     1.3    62.9    +      -       -      +
     35E  ASN      4.3     0.4    -      -       -      -
      1F  MET*     3.9    19.3    -      -       -      -
      2F  LEU      3.3     7.6    -      -       -      -
      3F  ILE*     4.2     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 34 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18E  ILE*     4.9     3.4    -      -       +      -
     19E  THR      3.8     2.5    -      -       -      +
     20E  ILE*     3.8    21.8    -      -       +      -
     32E  ILE*     4.5     9.9    -      -       +      +
     33E  GLY*     1.3    77.9    -      -       -      +
     35E  ASN*     1.3    65.4    +      -       -      +
     36E  ALA*     4.0     4.8    +      -       +      +
     42E  VAL*     3.9    32.6    -      -       +      +
      1F  MET*     3.4     3.3    -      -       -      +
      2F  LEU*     2.8    42.9    +      -       +      +
      4F  LEU*     4.2    22.7    -      -       +      -
     12F  ILE*     4.0    25.6    -      -       +      -
     14F  ILE*     3.9    16.4    -      -       +      -
     20F  ILE*     6.4     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 35 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17E  ASP      3.6     2.8    -      -       -      +
     18E  ILE*     3.4     5.4    -      -       -      -
     19E  THR*     2.8    51.8    +      -       -      +
     33E  GLY      5.7     0.2    -      -       -      -
     34E  ILE*     1.3    73.3    -      -       -      +
     36E  ALA*     1.3    63.5    +      -       -      +
      1F  MET*     4.0    29.5    +      -       +      +
     58G    U      5.9     4.8    -      -       -      -
----------------------------------------------------------
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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