Contacts of the strand formed by residues 28 - 36 (chain F) in PDB entry 4PJO


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 GLU 28 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72E  LYS*     4.1    16.6    +      -       -      -
     20F  MET*     3.2    33.3    -      -       +      +
     21F  VAL      3.1    13.7    -      -       -      +
     22F  LYS*     4.0    30.8    +      -       +      +
     26F  GLY      4.3     1.8    -      -       -      +
     27F  MET*     1.3    77.3    -      -       -      +
     29F  TYR*     1.3    69.6    +      -       -      +
     48F  GLU      3.9     0.2    -      -       -      +
     49F  GLU*     3.7     1.2    -      -       -      +
     50F  TYR*     2.9    41.9    +      -       +      +
     53F  GLY*     3.6    30.9    +      -       -      +
     71F  TYR*     4.8     2.3    +      -       -      -
     73F  ARG*     4.6     4.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 29 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45D  ASN*     4.6     3.6    +      -       -      -
    107D  ILE*     5.7     0.2    -      -       -      +
    108D  VAL*     4.1    21.9    -      -       +      +
     20F  MET*     3.4     3.3    -      -       -      -
     21F  VAL      2.8    34.0    +      -       -      +
     23F  LEU*     3.6    36.1    -      -       +      -
     27F  MET*     4.2    21.7    -      -       +      -
     28F  GLU*     1.3    75.2    -      -       -      +
     30F  LYS*     1.3    61.8    +      -       -      +
     44F  LEU*     3.7    15.3    -      -       +      +
     47F  THR*     3.8    17.0    -      -       +      -
     48F  GLU      3.4     5.8    -      -       -      -
     49F  GLU*     2.6    28.1    +      -       +      -
     59F  LEU*     3.3    35.2    -      -       +      -
     62F  VAL*     5.0     3.6    -      -       +      -
     64F  ILE*     4.3    13.2    -      -       +      -
     40K  GLY*     4.6     1.9    -      -       -      -
     41K  ILE*     4.2     7.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 30 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18F  PRO*     5.8     4.5    -      -       +      -
     19F  VAL      3.3     9.2    -      -       -      +
     20F  MET*     3.4    25.3    -      -       +      +
     29F  TYR*     1.3    73.2    -      -       -      +
     31F  GLY*     1.3    62.8    +      -       -      +
     44F  LEU*     4.3     0.4    -      -       -      -
     46F  ASN      3.6     1.9    -      -       -      +
     47F  THR*     3.1     6.0    -      -       -      -
     48F  GLU*     2.8    46.6    +      -       +      +
     50F  TYR*     3.2    41.5    +      -       +      -
     75F  VAL      4.0    20.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 31 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18F  PRO*     4.1     5.2    -      -       -      -
     19F  VAL*     2.9    36.1    +      -       -      +
     30F  LYS*     1.3    78.5    -      -       -      +
     32F  TYR*     1.3    62.1    +      -       -      -
     33F  LEU      3.1     5.2    +      -       -      -
     44F  LEU*     4.1     8.9    -      -       -      +
     45F  ALA      3.4    11.2    -      -       -      -
     46F  ASN      4.0     4.7    -      -       -      -
     47F  THR*     4.3     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 32 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16F  GLY      3.6    22.9    -      -       -      +
     17F  LYS      3.7     2.5    -      -       -      -
     18F  PRO*     3.5    33.2    -      -       +      +
     31F  GLY*     1.3    70.9    -      -       -      -
     33F  LEU*     1.3    67.7    +      -       -      +
     34F  VAL*     3.1     8.1    +      -       +      +
     44F  LEU*     3.6     0.8    -      -       -      -
     45F  ALA*     2.8    45.5    +      -       +      +
     46F  ASN*     4.0    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 33 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11F  LEU*     4.3     8.5    -      -       +      +
     14F  LEU*     3.9    32.3    -      -       +      +
     15F  THR*     4.0     8.3    -      -       +      -
     16F  GLY*     2.9    28.8    +      -       -      -
     17F  LYS      3.2     5.3    +      -       -      -
     19F  VAL*     3.6    14.6    -      -       +      -
     31F  GLY      3.1     6.9    +      -       -      -
     32F  TYR*     1.3    70.2    -      -       -      +
     34F  VAL*     1.3    59.0    +      -       -      +
     35F  SER      3.4    26.5    -      -       -      +
     36F  VAL*     3.6    18.8    -      -       +      -
     42F  MET*     4.4     7.2    -      -       +      -
     43F  GLN      3.6     9.4    -      -       -      +
     44F  LEU*     4.4    10.8    -      -       +      -
     72F  ILE*     3.7    27.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 34 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26D  THR      5.6     1.3    -      -       -      +
     15F  THR*     4.2    11.8    -      -       -      +
     16F  GLY      5.2     0.3    +      -       -      -
     32F  TYR*     3.2    17.9    -      -       +      +
     33F  LEU*     1.3    74.5    -      -       -      +
     35F  SER*     1.3    63.9    +      -       -      +
     43F  GLN*     3.0    43.8    +      -       +      +
     44F  LEU      4.1     2.0    -      -       -      -
     45F  ALA*     3.6    24.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 35 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26D  THR      4.0     7.6    -      -       -      -
     27D  GLY*     3.4    19.9    +      -       -      -
     28D  PRO*     3.3     8.0    -      -       -      +
     15F  THR*     5.0     3.8    -      -       -      -
     33F  LEU*     3.4     3.9    -      -       -      +
     34F  VAL*     1.3    80.5    -      -       -      +
     36F  VAL*     1.3    74.0    +      -       -      +
     42F  MET*     3.7     0.5    -      -       -      -
     43F  GLN*     2.6    55.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 36 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27D  GLY*     5.0     2.3    -      -       -      -
     28D  PRO*     3.7     6.8    -      -       -      +
      8F  LYS*     6.3     1.8    -      -       +      -
     11F  LEU*     4.3    26.7    -      -       +      -
     12F  ASN*     5.6     3.8    -      -       -      +
     15F  THR*     4.6     8.1    -      -       +      +
     33F  LEU*     3.6    28.3    -      -       +      -
     35F  SER*     1.3    87.4    -      -       -      +
     37F  ASP*     1.3    75.6    +      -       -      +
     40F  MET*     3.9    19.1    -      -       +      -
     41F  ASN      3.4    14.4    -      -       -      +
     42F  MET*     4.3     4.0    -      -       +      -
----------------------------------------------------------
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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