Contacts of the strand formed by residues 149 - 154 (chain E) in PDB entry 4CQM


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 GLY 149 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98E  SER*     3.2    13.7    -      -       -      -
    142E  LEU*     4.1    13.7    -      -       -      -
    147E  CYS      3.9     0.6    -      -       -      -
    148E  ARG*     1.3    77.7    -      -       -      +
    150E  SER*     1.3    62.2    +      -       -      -
    191E  GLY      3.3     6.4    +      -       -      +
    192E  ILE*     3.5     8.6    -      -       -      +
    193E  ARG*     3.0    28.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 150 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98E  SER      2.9    10.4    +      -       -      -
     99E  VAL*     3.9     4.5    -      -       -      -
    100E  VAL      3.4    18.7    +      -       -      -
    142E  LEU*     5.1     0.6    -      -       -      +
    149E  GLY*     1.3    75.4    -      -       -      -
    151E  ILE*     1.3    63.2    +      -       -      +
    152E  ILE*     3.6    14.0    +      -       -      +
    192E  ILE*     4.8     0.2    -      -       -      +
    193E  ARG*     3.4    31.7    +      -       -      -
    195E  ASN*     5.1     1.6    +      -       -      -
    240E  LEU*     2.8    25.4    +      -       -      +
    241E  ALA*     4.2    12.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 151 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100E  VAL*     3.6    22.0    -      -       +      +
    135E  THR*     3.8    44.6    -      -       +      +
    138E  ALA*     4.7     2.9    -      -       +      -
    139E  ALA*     4.5     8.3    -      -       +      +
    142E  LEU*     5.0     6.5    -      -       +      -
    150E  SER*     1.3    71.3    +      -       -      +
    152E  ILE*     1.3    62.1    +      -       -      +
    153E  ASN*     3.9    19.0    +      -       -      +
    180E  THR*     4.8     0.3    -      -       -      +
    187E  LEU*     3.9     9.2    -      -       +      -
    192E  ILE*     3.9    20.4    -      -       +      -
    193E  ARG      2.6    12.6    +      -       -      +
    194E  CYS*     3.2    23.4    -      -       +      -
    195E  ASN*     3.0    26.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 152 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99E  VAL*     4.7     0.4    -      -       +      -
    100E  VAL      2.8    12.0    +      -       -      +
    101E  VAL*     3.2    15.6    -      -       +      +
    102E  SER      3.2    21.5    +      -       -      -
    150E  SER*     3.7    16.8    -      -       -      +
    151E  ILE*     1.3    76.1    -      -       -      +
    153E  ASN*     1.3    63.9    +      -       -      +
    154E  ILE*     4.6     2.2    -      -       +      -
    195E  ASN*     3.6     4.3    -      -       +      +
    197E  VAL*     3.9    16.8    -      -       +      -
    237E  VAL*     3.3    46.7    -      -       +      +
    240E  LEU*     3.7    29.4    -      -       +      -
    241E  ALA*     3.5    25.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 153 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102E  SER*     3.5    22.9    +      -       -      -
    131E  THR*     3.5    17.8    -      -       +      +
    135E  THR*     3.6    21.0    +      -       -      +
    151E  ILE*     3.9    13.3    -      -       -      +
    152E  ILE*     1.3    75.2    -      -       -      +
    154E  ILE*     1.3    63.8    +      -       -      +
    155E  SER      3.4     1.7    +      -       -      -
    176E  VAL*     3.9    13.4    -      -       +      +
    179E  LEU*     4.5     4.8    -      -       -      +
    180E  THR*     3.0    36.5    +      -       -      +
    195E  ASN      3.0     8.7    +      -       -      +
    196E  SER*     3.2     5.2    -      -       -      -
    197E  VAL      2.9    24.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 154 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23E  ILE*     4.7    14.6    -      -       +      -
    101E  VAL*     4.2     8.5    -      -       +      -
    102E  SER      3.3    24.3    +      -       -      +
    103E  CYS*     3.6    24.2    -      -       +      -
    152E  ILE*     4.6     1.3    -      -       +      -
    153E  ASN*     1.3    70.7    -      -       -      +
    155E  SER*     1.3    71.1    +      -       -      +
    173E  LYS*     3.4    17.2    +      -       -      +
    176E  VAL*     4.8     5.0    -      -       -      +
    197E  VAL*     3.7    24.7    -      -       +      +
    199E  PRO*     3.9    21.1    -      -       +      -
    233E  VAL*     4.5     5.8    -      -       +      -
    237E  VAL*     3.8    24.7    -      -       +      -
----------------------------------------------------------
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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