Contacts of the strand formed by residues 138 - 142 (chain M) in PDB entry 5X22


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 138 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21M  ILE*     3.9    16.4    -      -       -      +
     22M  GLN*     3.7    17.6    +      -       -      +
    136M  ILE      3.5     2.0    +      -       -      -
    137M  VAL*     1.3    79.7    -      -       -      +
    139M  GLN*     1.3    58.5    +      -       -      +
    140M  ILE      4.2     0.2    -      -       -      -
    333M  ILE*     3.6    23.6    -      -       -      -
    334M  ARG      3.4     9.9    -      -       -      -
    335M  THR*     3.9    13.7    -      -       -      +
    336M  VAL      4.6     0.2    +      -       -      -
    339M  LEU*     4.7     1.1    -      -       -      -
    407M  LYS      5.0     0.5    +      -       -      -
    409M  ARG      3.8    12.0    +      -       -      -
    410M  ILE*     3.5     4.2    -      -       -      -
    411M  SER*     2.9    23.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 139 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137M  VAL      3.7     0.2    +      -       -      -
    138M  SER*     1.3    73.5    -      -       -      +
    140M  ILE*     1.3    69.4    +      -       -      +
    141M  HIS*     5.2     2.5    -      -       +      -
    333M  ILE*     4.4     1.3    -      -       -      -
    334M  ARG*     2.9    74.0    +      -       -      +
    339M  LEU*     3.8     9.7    -      -       +      +
    391M  LEU*     3.6    23.5    -      -       +      +
    411M  SER      3.2    13.9    -      -       -      +
    412M  ALA      5.0     0.4    -      -       -      -
    413M  LEU      2.5    25.4    +      -       -      +
    414M  GLY      3.5     8.3    +      -       -      -
    415M  PRO      3.2    21.0    +      -       -      +
    416M  GLY      4.9     0.9    -      -       -      -
    417M  GLY*     3.6    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 140 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139M  GLN*     1.3    77.9    -      -       -      +
    141M  HIS*     1.3    68.1    +      -       -      +
    328M  LEU*     4.2     5.6    -      -       +      -
    331M  ARG*     3.6    57.6    +      -       +      +
    332M  ARG      3.3    12.8    -      -       -      +
    333M  ILE*     3.7    22.0    -      -       +      -
    410M  ILE*     3.7    16.8    -      -       +      +
    411M  SER      2.9    20.7    +      -       -      +
    412M  ALA*     3.8    19.0    -      -       +      +
    417M  GLY*     5.5     0.9    -      -       -      -
    418M  LEU*     5.7     1.6    -      -       -      +
    438M  ILE*     4.2    21.3    -      -       +      -
    451M  LEU      5.3     1.3    -      -       -      +
    453M  THR*     5.7     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 141 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139M  GLN*     4.8     4.5    -      -       +      +
    140M  ILE*     1.3    78.4    -      -       -      +
    142M  ARG*     1.3    71.4    +      -       -      +
    144M  PRO*     4.6     5.4    -      -       +      -
    165M  LEU*     4.8     0.4    -      -       +      -
    166M  PRO*     3.5    39.3    -      -       +      +
    331M  ARG*     3.3     7.5    -      -       -      -
    332M  ARG*     2.9    79.5    +      -       +      +
    334M  ARG*     3.5    25.2    -      -       +      +
    416M  GLY      4.9    11.5    +      -       -      +
    417M  GLY*     5.6     2.7    -      -       -      -
    418M  LEU*     6.3     1.3    -      -       -      -
     14R    G      4.5    11.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 142 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141M  HIS*     1.3    86.0    +      -       -      +
    143M  SER*     1.3    68.3    +      -       -      +
    144M  PRO*     3.5     6.2    -      -       -      +
    147M  TYR*     3.8    20.8    -      -       -      +
    149M  THR*     6.1     2.6    -      -       -      +
    161M  SER*     5.4     3.0    -      -       -      -
    163M  ILE*     3.4    29.5    -      -       +      +
    164M  PRO      5.5     0.3    -      -       -      +
    171M  TRP*     3.3    36.4    -      -       +      -
    325M  ILE*     3.6    44.6    +      -       -      +
    330M  ASN      3.6     5.6    -      -       -      +
    331M  ARG*     4.6     1.1    -      -       -      +
     14R    G      3.7    60.2    +      -       +      +
----------------------------------------------------------
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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