Contacts of the helix formed by residues 30 - 42 (chain U) in PDB entry 4GGF


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 30 (chain U).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68T  THR      2.7    29.0    +      -       -      -
     69T  ASN*     4.4     9.5    -      -       +      -
     70T  ALA*     4.8     0.2    -      -       -      +
     23U  LYS*     3.5    38.4    -      -       +      +
     24U  GLY*     3.7     7.4    -      -       -      -
     25U  ASN*     3.0    19.4    +      -       -      +
     28U  ALA*     3.6    18.2    -      -       +      -
     29U  VAL*     1.3    75.4    -      -       -      +
     31U  ARG*     1.3    62.6    +      -       -      +
     32U  ASP*     3.3    15.5    -      -       -      +
     33U  ASP*     3.0    25.7    +      -       -      +
     34U  LEU*     2.8    26.5    +      -       -      +
     55U  PHE*     3.9     0.9    -      -       -      -
     64U  GLY      3.6    20.4    -      -       -      +
     65U  ALA*     3.9     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 31 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30U  TYR*     1.3    76.2    -      -       -      +
     32U  ASP*     1.3    61.8    +      -       -      +
     34U  LEU*     3.3     3.6    +      -       -      +
     35U  LYS*     3.2    20.8    +      -       -      +
     51U  ALA*     5.4     3.3    -      -       +      +
     52U  ASP*     3.2    46.4    +      -       -      +
     55U  PHE*     3.5    58.5    -      -       +      +
     56U  LYS*     5.2     1.2    -      -       -      +
     64U  GLY      4.4     1.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 32 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23U  LYS*     2.9    35.9    +      -       -      -
     30U  TYR*     3.7    10.9    -      -       -      +
     31U  ARG*     1.3    73.2    -      -       -      +
     33U  ASP*     1.3    68.3    +      -       -      -
     35U  LYS*     3.4    11.9    +      -       +      +
     36U  LYS*     3.2    20.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 33 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19U  TYR*     3.9    25.5    -      -       +      +
     22U  ILE*     3.7    21.4    -      -       +      +
     23U  LYS*     2.7    29.4    +      -       -      +
     28U  ALA      4.2     1.2    -      -       -      +
     29U  VAL*     3.7    12.3    -      -       +      +
     30U  TYR*     3.0    40.8    +      -       -      +
     32U  ASP*     1.3    82.8    +      -       -      +
     34U  LEU*     1.3    56.8    +      -       -      +
     36U  LYS*     3.4     8.7    +      -       -      +
     37U  LEU*     2.9    27.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 34 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29U  VAL*     3.4    16.8    -      -       +      +
     30U  TYR      2.8    12.7    +      -       -      +
     31U  ARG      3.7     8.1    -      -       -      +
     32U  ASP      3.2     0.2    -      -       -      -
     33U  ASP*     1.3    75.1    -      -       -      +
     35U  LYS*     1.3    60.7    +      -       -      +
     37U  LEU*     3.1    17.7    +      -       +      +
     38U  LEU*     2.8    47.3    +      -       +      +
     51U  ALA      3.9     9.2    -      -       -      +
     54U  TRP*     4.1     5.8    -      -       +      -
     55U  PHE*     3.6    45.1    -      -       +      +
     58U  LEU*     4.3    18.8    -      -       +      -
     66U  VAL*     4.6     9.2    -      -       +      -
     71U  PHE*     5.8     0.9    -      -       +      -
     74U  LEU*     4.7     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 35 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31U  ARG      3.2    12.8    +      -       -      +
     32U  ASP*     3.4    14.6    +      -       +      +
     34U  LEU*     1.3    76.7    -      -       -      +
     36U  LYS*     1.3    56.4    +      -       -      +
     38U  LEU*     3.4     2.0    +      -       -      +
     39U  GLU*     2.7    69.3    +      -       +      +
     51U  ALA*     3.8    27.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 36 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19U  TYR*     3.7    15.3    -      -       +      -
     22U  ILE*     4.2    22.0    -      -       +      -
     32U  ASP      3.2    10.2    +      -       -      +
     33U  ASP*     3.5     9.9    -      -       -      +
     35U  LYS*     1.3    76.0    -      -       -      +
     37U  LEU*     1.3    65.2    +      -       -      +
     39U  GLU*     3.3     8.4    +      -       -      -
     40U  THR*     2.9    36.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 37 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15U  VAL*     5.2     0.9    -      -       +      +
     16U  TYR*     5.0     4.9    -      -       -      -
     19U  TYR*     3.6    43.5    -      -       +      -
     29U  VAL*     4.7    10.3    -      -       +      -
     33U  ASP      2.9    14.9    +      -       -      +
     34U  LEU*     3.1    20.2    +      -       +      +
     36U  LYS*     1.3    74.9    -      -       -      +
     38U  LEU*     1.3    62.6    +      -       +      +
     41U  GLU*     2.8    48.5    +      -       +      +
     42U  SER*     5.9     1.1    -      -       -      -
     71U  PHE*     3.9    29.4    -      -       +      -
     74U  LEU*     4.0    24.9    -      -       +      -
      8V  LEU*     4.9     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 38 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34U  LEU*     2.8    29.0    +      -       +      +
     35U  LYS*     3.8     3.8    -      -       -      +
     37U  LEU*     1.3    78.5    -      -       +      +
     39U  GLU*     1.3    62.2    +      -       +      +
     42U  SER*     2.8    42.2    +      -       -      +
     46U  ILE*     4.3     4.5    -      -       +      +
     47U  ARG*     3.4    14.5    -      -       +      +
     50U  GLY      5.0     0.2    -      -       -      -
     51U  ALA*     3.7    36.8    -      -       +      +
     54U  TRP*     3.9    34.3    -      -       +      -
     74U  LEU*     3.9    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 39 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35U  LYS*     2.7    60.4    +      -       +      +
     36U  LYS*     3.3     7.5    +      -       -      +
     38U  LEU*     1.3    78.0    -      -       +      +
     40U  THR*     1.3    61.0    +      -       -      +
     42U  SER      4.7     2.1    -      -       -      +
     47U  ARG*     3.8    30.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 40 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19U  TYR*     3.2    26.1    +      -       -      +
     36U  LYS*     2.9    26.1    +      -       -      +
     39U  GLU*     1.3    81.3    -      -       -      +
     41U  GLU*     1.3    65.0    +      -       -      +
     42U  SER      3.7     0.9    -      -       -      -
      6V  SER*     3.4    15.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 41 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15U  VAL*     3.7    19.7    -      -       +      +
     18U  LYS*     4.9     6.9    -      -       -      +
     19U  TYR*     2.5    39.1    +      -       +      +
     37U  LEU*     2.8    28.3    +      -       +      +
     40U  THR*     1.3    81.4    -      -       -      +
     42U  SER*     1.3    58.0    +      -       -      +
     78U  MET*     3.9     6.6    -      -       -      +
      6V  SER*     2.8    27.9    +      -       -      -
      7V  GLN*     3.7     7.6    +      -       -      +
      8V  LEU*     3.3    40.0    +      -       +      +
      9V  GLU*     3.6    10.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 42 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37U  LEU*     5.9     0.9    -      -       -      -
     38U  LEU*     2.8    34.6    +      -       -      +
     39U  GLU      4.7     2.4    -      -       -      +
     40U  THR      5.2     0.2    -      -       -      -
     41U  GLU*     1.3    80.8    -      -       -      +
     43U  PRO*     1.3    70.1    -      -       -      +
     46U  ILE*     3.6    23.6    -      -       -      +
     47U  ARG*     3.1    27.2    +      -       -      +
     78U  MET*     3.9    11.9    -      -       -      -
      9V  GLU*     4.2     3.1    -      -       -      -
----------------------------------------------------------
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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