Contacts of the strand formed by residues 140 - 145 (chain G) in PDB entry 5UQ9


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 SER 140 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127G  GLY      3.6     3.8    -      -       -      +
    129G  SER*     3.4    25.9    +      -       -      -
    138G  GLY      3.8     2.2    +      -       -      -
    139G  PRO*     1.3    73.3    -      -       -      +
    141G  LEU*     1.3    63.6    +      -       -      +
    142G  MET*     4.6     2.6    -      -       -      +
    161G  ALA*     5.1     0.2    -      -       -      -
    170G  CYS      3.9     5.5    +      -       -      -
    361G  MET*     2.1    39.9    +      -       -      +
    364G  GLY      3.8    19.8    +      -       -      -
    365G  GLY*     4.1     2.4    -      -       -      -
    366G  CYS*     3.5    25.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 141 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18G  LEU*     5.7     4.0    -      -       +      -
    126G  SER*     4.0     8.3    -      -       -      +
    127G  GLY      3.2     3.1    -      -       -      -
    128G  VAL*     3.6    24.0    -      -       +      -
    139G  PRO*     3.3    33.2    +      -       +      +
    140G  SER*     1.3    76.7    +      -       -      +
    142G  MET*     1.3    65.0    +      -       -      +
    143G  PRO*     3.5     6.0    -      -       +      +
    157G  PHE*     3.5    48.5    -      -       +      +
    160G  ILE*     5.0     6.3    -      -       +      -
    161G  ALA*     3.8    15.5    -      -       +      -
    170G  CYS      4.1     4.4    +      -       -      -
    171G  CYS*     3.5    21.6    -      -       -      +
    361G  MET*     3.4    18.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 142 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125G  GLY      3.5     4.2    -      -       -      +
    126G  SER*     3.2     6.8    +      -       -      -
    127G  GLY*     2.8    30.5    +      -       -      +
    129G  SER*     4.9     2.5    -      -       -      -
    140G  SER*     4.6     2.0    -      -       -      +
    141G  LEU*     1.3    78.9    -      -       -      +
    143G  PRO*     1.3    65.5    -      -       -      +
    144G  GLY      3.5     0.2    +      -       -      -
    174G  VAL*     3.8     5.6    -      -       +      -
    180G  GLY*     3.7    14.6    -      -       -      +
    183G  VAL*     4.1    11.2    -      -       +      -
    184G  LYS*     3.7    41.7    -      -       +      -
    187G  HIS*     3.8    14.1    -      -       +      -
    361G  MET*     3.5    22.4    -      -       +      +
    362G  TRP*     3.7    24.9    -      -       +      -
    366G  CYS*     3.8    23.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 143 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124G  VAL*     4.3     7.2    -      -       +      -
    126G  SER*     3.4    18.6    -      -       -      +
    141G  LEU      3.5     7.2    -      -       -      +
    142G  MET*     1.3    87.8    -      -       -      +
    144G  GLY*     1.3    59.3    +      -       -      +
    150G  TRP*     3.9    22.4    -      -       +      -
    153G  ILE*     4.3     2.7    -      -       +      -
    157G  PHE*     4.3    11.0    -      -       +      -
    171G  CYS*     4.0    11.7    -      -       -      -
    172G  ASP      3.3    23.3    -      -       -      +
    173G  TRP*     3.3    23.5    -      -       +      -
    174G  VAL*     3.1    19.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 144 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124G  VAL*     3.5     2.3    -      -       -      +
    125G  GLY*     2.7    45.9    +      -       -      +
    142G  MET      3.5     0.2    +      -       -      -
    143G  PRO*     1.3    74.6    -      -       -      +
    145G  GLY*     1.3    55.9    +      -       -      -
    173G  TRP*     3.6    10.6    -      -       -      -
    174G  VAL*     4.7     0.9    -      -       -      -
    175G  GLY      3.3    13.9    -      -       -      -
    178G  GLY*     4.4     7.8    +      -       -      -
    180G  GLY*     4.2    11.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 145 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109G  THR*     5.8     0.7    -      -       -      -
    113G  CYS*     3.2    17.7    -      -       -      -
    123G  PHE*     3.6     9.4    -      -       -      -
    124G  VAL*     4.5     0.4    -      -       -      -
    125G  GLY      4.7     0.4    -      -       -      -
    144G  GLY*     1.3    75.5    -      -       -      -
    146G  ASN*     1.3    61.3    +      -       -      +
    173G  TRP*     3.3     2.4    -      -       -      -
    175G  GLY      3.2    10.3    +      -       -      -
    176G  ASP*     3.9     5.2    -      -       -      +
    177G  GLU*     3.0    29.4    +      -       -      +
    178G  GLY*     3.5     8.9    -      -       -      +
----------------------------------------------------------
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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