Contacts of the strand formed by residues 37 - 49 (chain H) in PDB entry 1PPB


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 PRO 37 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35H  ARG*     3.3    32.3    -      -       -      +
     36H  SER*     1.4    81.6    -      -       +      +
     38H  GLN*     1.3    73.0    +      -       -      +
     39H  GLU*     3.1    34.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 38 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34H  PHE*     3.8    20.6    -      -       +      -
     35H  ARG      3.5     6.5    -      -       -      +
     36H  LYS*     3.3    21.9    +      -       -      +
     37H  PRO*     1.3    76.9    -      -       -      +
     39H  GLU*     1.3    61.4    +      -       -      +
     65H  LEU*     6.2     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 39 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34H  PHE*     3.5    12.3    -      -       -      -
     35H  ARG*     2.8    66.8    +      -       +      -
     37H  PRO*     3.1    24.8    +      -       -      +
     38H  GLN*     1.3    77.1    -      -       -      +
     40H  LEU*     1.3    69.8    +      -       -      +
     41H  LEU*     3.6     6.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 40 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32H  MET*     3.5    42.8    -      -       +      -
     34H  PHE*     3.7    12.8    -      -       +      -
     39H  GLU*     1.3    80.7    -      -       -      +
     41H  LEU*     1.3    59.3    +      -       -      +
     42H  CYS      3.8    22.7    -      -       -      +
     73H  ARG*     3.7    28.9    -      -       +      +
    141H  TRP*     3.8    26.7    -      -       +      +
    142H  GLY*     5.8     0.2    -      -       -      -
    193H  GLY*     4.2    14.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 41 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1H  0G6      5.0     0.3    +      -       -      -
     33H  LEU*     2.9    41.2    +      -       +      +
     35H  ARG*     3.4    37.5    -      -       +      -
     39H  GLU*     3.6     6.7    +      -       -      +
     40H  LEU*     1.3    75.4    -      -       -      +
     42H  CYS*     1.3    67.5    +      -       -      +
     58H  CYS*     3.5    26.9    -      -       +      +
     59H  LEU*     4.7     0.4    -      -       +      -
     60H  PHE*     4.0    21.3    -      -       +      +
     64H  LEU*     3.8    26.0    -      -       +      -
    193H  GLY*     4.2    13.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 42 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1H  0G6      4.4     6.5    -      -       -      -
     32H  MET*     3.9     1.4    -      -       -      -
     33H  LEU*     2.9    34.7    +      -       +      +
     40H  LEU*     3.8    12.3    -      -       -      +
     41H  LEU*     1.3    86.4    -      -       +      +
     43H  GLY*     1.3    65.0    +      -       -      +
     58H  CYS*     2.0    55.9    -      -       +      -
     60H  LYS*     5.7     1.8    -      -       -      -
    141H  TRP*     5.4     0.3    -      -       -      -
    193H  GLY      3.7    12.1    -      -       -      -
    195H  SER*     3.0    16.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 43 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30H  GLN*     4.1    13.7    -      -       -      -
     31H  VAL      3.4    10.3    -      -       -      -
     32H  MET*     4.8     0.2    -      -       -      -
     33H  LEU*     4.5     2.5    -      -       -      +
     42H  CYS*     1.3    77.6    -      -       -      +
     44H  ALA*     1.3    61.2    +      -       -      +
     54H  THR*     3.0    19.1    +      -       -      -
    140H  GLY*     6.2     0.4    -      -       -      -
    141H  TRP*     5.4     2.9    -      -       -      -
    193H  GLY      4.0     4.8    +      -       -      -
    194H  ASP*     4.5     2.2    +      -       -      -
    195H  SER      2.9    10.4    +      -       -      +
    196H  GLY*     3.3    11.6    -      -       -      -
    197H  GLY*     4.2     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 44 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30H  GLN*     3.8     2.1    -      -       -      -
     31H  VAL*     2.9    35.1    +      -       +      +
     33H  LEU*     4.9     8.7    -      -       +      -
     43H  GLY*     1.3    73.9    -      -       -      +
     45H  SER*     1.3    62.3    +      -       -      +
     52H  VAL*     3.5    24.0    -      -       +      -
     53H  LEU      3.4     8.1    -      -       -      +
     54H  THR*     4.1     7.0    -      -       -      -
    106H  MET*     5.6     0.2    -      -       -      -
    196H  GLY      3.3    14.8    +      -       -      -
    197H  GLY      4.3     0.2    -      -       -      +
    198H  PRO*     3.8    11.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 45 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29H  TRP*     3.3     9.4    -      -       -      -
     31H  VAL*     4.0     5.2    -      -       -      -
     44H  ALA*     1.3    77.4    -      -       -      +
     46H  LEU*     1.3    60.9    +      -       -      +
     47H  ILE*     3.6     2.3    +      -       -      +
     52H  VAL*     3.2     5.9    -      -       -      -
     53H  LEU*     2.9    41.1    +      -       -      +
    121H  VAL*     4.5     9.9    -      -       -      -
    196H  GLY      5.0     0.2    +      -       -      -
    198H  PRO*     4.2    17.5    -      -       -      -
    209H  GLN*     2.8    31.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 46 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29H  TRP*     2.8    27.0    +      -       -      +
     31H  VAL*     3.7     5.5    -      -       +      +
     45H  SER*     1.3    69.5    -      -       -      +
     47H  ILE*     1.3    61.1    +      -       -      +
     48H  SER      3.4    25.6    -      -       -      +
     49H  ASP*     4.9     1.8    -      -       -      -
     51H  TRP      3.8     7.6    -      -       -      +
     52H  VAL*     4.0    15.9    -      -       +      -
     68H  ILE*     4.3    24.7    -      -       +      -
    108H  LEU*     4.9     5.8    -      -       +      -
    112H  VAL*     5.2     3.1    -      -       +      -
    114H  PHE*     3.8    24.2    -      -       +      -
    118H  ILE*     3.9    17.0    -      -       +      -
    119H  HIS      4.3     0.2    -      -       -      -
    120H  PRO*     4.0    13.5    -      -       +      -
    121H  VAL*     3.0    28.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 47 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45H  SER*     3.6    20.4    +      -       -      +
     46H  LEU*     1.3    76.9    -      -       -      +
     48H  SER*     1.3    65.4    +      -       -      +
     51H  TRP*     3.1    24.4    +      -       +      +
     53H  LEU*     4.1    19.5    -      -       +      -
    105H  LEU*     4.0    22.0    -      -       +      -
    120H  PRO*     3.7     6.4    -      -       -      +
    121H  VAL*     4.1    23.1    -      -       +      +
    123H  LEU*     4.0    26.2    -      -       +      -
    209H  GLN*     4.3     0.4    -      -       -      +
    238H  ILE*     4.5     1.3    -      -       +      -
    242H  ILE*     3.7    27.8    -      -       +      +
      1L  GLU*     3.2    19.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 48 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46H  LEU*     3.4    11.9    -      -       -      +
     47H  ILE*     1.3    80.6    -      -       -      +
     49H  ASP*     1.3    61.5    +      -       -      +
     50H  ARG      3.0     7.6    +      -       -      -
     51H  TRP*     3.4    26.2    -      -       -      +
    114H  PHE*     4.2     5.6    -      -       -      -
    120H  PRO*     3.6     5.8    -      -       -      +
    242H  ILE*     5.8     2.0    -      -       -      -
      1L  SER*     2.6    60.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 49 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46H  LEU*     4.9     1.8    -      -       -      -
     48H  SER*     1.3    69.3    -      -       -      +
     50H  ARG*     1.3    91.7    +      -       -      +
    108H  LEU*     3.9     8.9    -      -       -      +
    111H  PRO*     3.3    23.1    -      -       -      +
    112H  VAL*     3.2    40.8    +      -       -      +
    114H  PHE*     3.6    23.0    -      -       +      -
      1L  SER*     2.8    36.1    -      -       +      +
----------------------------------------------------------
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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