Contacts of the strand formed by residues 130 - 137 (chain A) in PDB entry 3QUM


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 ALA 130 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  PRO*     4.6     4.0    -      -       +      -
    124A  GLN*     3.5     2.6    -      -       -      +
    125A  LEU*     3.6    19.5    -      -       +      -
    129A  GLY*     1.3    76.0    -      -       -      +
    131A  SER*     1.3    54.1    +      -       -      +
    132A  VAL*     6.0     0.2    -      -       -      -
    181A  LEU*     2.5    46.5    +      -       -      +
    182A  THR      3.1    21.0    +      -       -      +
    183A  LYS*     4.4     2.2    -      -       -      -
    186A  TYR*     3.8    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  PRO*     3.8    14.0    -      -       -      +
    124A  GLN*     2.8    32.1    +      -       -      +
    130A  ALA*     1.3    71.6    -      -       -      +
    132A  VAL*     1.3    63.2    +      -       -      +
    133A  VAL*     4.0     1.3    +      -       -      -
    178A  THR*     5.2     3.4    -      -       -      -
    179A  LEU      2.7    18.6    -      -       -      -
    180A  THR*     3.4    22.7    -      -       -      -
    181A  LEU      4.3     0.2    -      -       -      -
    125B  LEU*     6.2     0.2    -      -       -      +
    142B  LEU*     4.4    16.9    -      -       -      +
    144B  LYS*     5.1     9.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  ILE*     4.7     9.2    -      -       +      -
    118A  PHE      3.3    13.7    -      -       -      +
    120A  PRO*     3.4    29.2    -      -       +      -
    131A  SER*     1.3    74.1    -      -       -      +
    133A  VAL*     1.3    68.0    +      -       -      +
    148A  TRP*     3.3    32.9    -      -       +      -
    178A  THR*     3.4     0.7    -      -       -      -
    179A  LEU*     2.5    49.2    +      -       +      +
    186A  TYR*     4.5    12.6    -      -       +      -
    192A  TYR*     5.1     4.3    -      -       +      -
    209A  PHE*     4.5    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  ILE      3.7     0.2    -      -       -      -
    118A  PHE*     2.7    41.2    +      -       +      +
    131A  SER      4.0     1.8    +      -       -      +
    132A  VAL*     1.3    75.7    -      -       -      +
    134A  CYS*     1.3    61.0    +      -       -      +
    135A  PHE*     4.3    26.0    -      -       +      -
    176A  SER*     4.5     7.2    -      -       -      +
    177A  SER      3.4     5.8    -      -       -      +
    178A  THR*     3.0    27.6    -      -       -      +
    125B  LEU*     3.7    29.6    -      -       +      +
    142B  LEU*     4.7    16.8    -      -       +      -
    179B  SER*     5.0    10.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  VAL*     4.0     7.4    -      -       -      -
    116A  SER      3.5     8.1    -      -       -      -
    117A  ILE*     3.5    16.6    -      -       +      -
    133A  VAL*     1.3    75.8    -      -       -      +
    135A  PHE*     1.3    64.5    +      -       -      +
    136A  LEU*     3.6    16.7    +      -       -      +
    148A  TRP*     3.9    12.3    -      -       +      -
    176A  SER*     3.9     1.7    +      -       -      -
    177A  SER*     2.8    36.6    +      -       -      +
    194A  CYS*     2.1    46.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 135 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  THR      3.2    12.1    -      -       -      +
    115A  VAL*     3.6     0.5    -      -       -      -
    116A  SER*     2.8    36.3    +      -       -      +
    118A  PHE*     4.1    28.0    -      +       -      -
    133A  VAL*     4.3    17.7    -      -       +      -
    134A  CYS*     1.3    72.3    -      -       -      +
    136A  LEU*     1.3    70.5    +      -       -      +
    137A  ASN*     3.8    10.1    -      -       -      +
    175A  MET      4.0     0.7    -      -       -      -
    176A  SER*     3.6    22.0    -      -       -      -
    125B  LEU*     5.0     2.5    -      -       +      -
    138B  THR*     4.4     5.8    -      -       +      -
    140B  GLY*     4.6     5.4    -      -       -      -
    167B  PHE*     3.5    34.5    -      +       -      -
    179B  SER*     4.7     5.4    -      -       -      -
    180B  SER*     3.0    29.8    -      -       -      -
    181B  SER*     3.4    22.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  PRO*     5.4     6.5    -      -       +      -
    114A  THR      3.6     3.8    -      -       -      +
    115A  VAL*     4.3    17.0    -      -       +      -
    134A  CYS*     3.6    25.8    -      -       -      +
    135A  PHE*     1.3    82.7    -      -       -      +
    137A  ASN*     1.3    59.6    +      -       -      +
    139A  PHE*     3.0    20.2    -      -       +      -
    144A  ILE*     3.9    23.3    -      -       +      -
    146A  VAL*     4.0    21.3    -      -       +      -
    175A  MET*     2.9    49.9    +      -       +      +
    177A  SER*     5.7     3.8    -      -       -      +
    194A  CYS*     4.5     3.4    -      -       -      -
    196A  ALA*     4.3    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 137 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  ALA      4.7     0.2    -      -       -      +
    113A  PRO      3.9     0.7    -      -       -      -
    114A  THR*     3.2    42.8    +      -       +      +
    135A  PHE*     3.8    12.9    -      -       -      +
    136A  LEU*     1.3    88.3    +      -       -      +
    138A  ASN*     1.3    83.5    +      -       -      +
    139A  PHE*     3.9     3.1    -      -       -      -
    174A  SER*     3.6    10.2    -      -       -      +
    175A  MET      4.1     3.1    +      -       -      +
    138B  THR*     6.3     0.4    -      -       -      +
    165B  HIS*     3.8    19.8    +      -       +      +
    167B  PHE*     4.5     1.9    -      -       -      -
    181B  SER*     3.3    26.7    +      -       -      -
    183B  THR*     5.8     1.4    +      -       -      -
----------------------------------------------------------
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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