Contacts of the strand formed by residues 610 - 615 (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 ARG 610 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70K  GLY*     5.8     1.6    -      -       -      +
    133K  GLU*     3.6    14.1    +      -       -      -
    134K  GLU      5.9     0.4    +      -       -      -
    605M  LYS*     3.2    47.7    -      -       -      +
    606M  VAL      3.8     0.2    -      -       -      -
    607M  ASP*     2.8    77.2    +      -       +      +
    608M  GLY      3.6     1.8    -      -       -      -
    609M  ASN*     1.3    84.1    -      -       +      +
    611M  ILE*     1.3    63.3    +      -       -      +
    612M  VAL*     3.7    14.5    -      -       -      +
    622M  GLU*     3.4    28.7    +      -       +      +
    623M  TYR      3.5    11.4    -      -       -      +
    624M  PRO*     4.3     5.4    -      -       +      -
    625M  LEU*     4.2     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 611 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    595M  LEU*     5.8     0.7    -      -       +      -
    603M  VAL*     4.6     2.2    -      -       +      -
    605M  LYS      3.4    11.9    -      -       -      +
    606M  VAL*     4.7     4.0    -      -       -      -
    607M  ASP      4.6     0.2    -      -       -      +
    610M  ARG*     1.3    80.9    -      -       -      +
    612M  VAL*     1.3    64.0    +      -       -      +
    613M  VAL*     4.0    19.7    -      -       +      -
    623M  TYR*     2.9    46.9    +      -       +      +
    625M  LEU*     4.2    11.4    -      -       +      -
    641M  PRO*     3.7    29.4    -      -       +      -
    643M  VAL*     4.0    21.3    -      -       +      -
    655M  LEU*     3.8    32.8    -      -       +      +
    656M  ALA*     4.3     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 612 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    603M  VAL*     3.8     0.9    -      -       -      +
    604M  ALA*     2.8    30.8    +      -       +      -
    605M  LYS*     2.9    39.3    +      -       +      +
    610M  ARG*     3.7    18.6    -      -       -      +
    611M  ILE*     1.3    71.3    -      -       -      +
    613M  VAL*     1.3    66.2    +      -       -      +
    620M  LEU*     3.6    34.8    -      -       +      -
    621M  VAL      3.5    10.1    -      -       -      +
    622M  GLU*     3.7    28.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 613 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    602M  GLU      3.5    17.5    -      -       -      +
    603M  VAL*     4.7     6.5    -      -       +      -
    604M  ALA*     4.6     0.2    -      -       -      -
    611M  ILE*     4.0    18.6    -      -       +      -
    612M  VAL*     1.3    80.5    -      -       -      +
    614M  ARG*     1.3    67.2    +      -       -      +
    615M  TYR*     3.8    35.1    +      -       +      +
    619M  ARG      3.8     1.2    -      -       -      +
    620M  LEU*     3.7     5.1    -      -       -      -
    621M  VAL*     2.9    37.3    +      -       -      +
    623M  TYR*     4.2     7.0    -      -       +      -
    649M  VAL*     4.4    11.4    -      -       +      -
    655M  LEU*     4.1    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 614 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    601M  GLY*     3.4     0.2    -      -       -      -
    602M  GLU*     2.9    41.8    +      -       +      +
    604M  ALA*     4.3     7.9    -      -       +      +
    613M  VAL*     1.3    71.9    -      -       -      +
    615M  TYR*     1.3    72.5    +      -       -      +
    618M  GLY*     2.9    33.4    +      -       -      +
    619M  ARG      3.7     4.0    -      -       -      -
    620M  LEU*     3.6    33.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 615 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    597M  ALA*     3.9     5.7    -      -       +      -
    598M  GLU*     3.1    20.9    +      -       +      -
    599M  GLU*     3.1    47.1    -      -       +      -
    600M  ASP      3.3    11.9    -      -       -      +
    601M  GLY*     4.5     2.0    -      -       -      -
    613M  VAL*     3.8    25.7    -      -       +      +
    614M  ARG*     1.3    79.9    -      -       -      +
    616M  GLU*     1.3    65.8    +      -       -      +
    617M  ASP*     3.1    16.2    -      -       +      +
    618M  GLY*     3.1    13.8    +      -       -      -
    619M  ARG*     3.4    20.5    +      -       +      +
    621M  VAL*     3.6    36.1    -      -       +      -
    623M  TYR*     2.5    35.5    +      -       -      -
    649M  VAL*     5.4     0.2    -      -       +      -
----------------------------------------------------------
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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