Contacts of the strand formed by residues 103 - 109 (chain M) in PDB entry 7K63


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 103 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56M  GLN*     3.5    26.7    -      -       +      -
     57M  GLN      3.3    23.6    -      -       -      +
     58M  LYS*     3.6    10.3    -      -       +      +
     59M  PRO*     4.9     4.5    -      -       -      -
    101M  ASP      3.2     4.2    +      -       -      +
    102M  THR*     1.3    75.7    +      -       -      +
    104M  THR*     1.3    62.9    +      -       -      +
    105M  TYR*     3.6     7.1    -      -       +      -
    122M  LYS*     4.7     5.8    -      -       -      +
    123M  LEU*     2.9    30.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 104 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55M  TYR      3.8     0.3    -      -       -      +
     56M  GLN*     3.6     1.0    -      -       -      -
     57M  GLN*     2.7    46.8    +      -       -      +
     59M  PRO*     5.9     1.2    -      -       -      +
    103M  ALA*     1.3    72.8    -      -       -      +
    105M  TYR*     1.3    62.2    +      -       -      +
    106M  TYR*     3.5    36.0    +      -       +      +
    120M  GLY*     3.8    16.6    -      -       -      +
    121M  THR      3.4    13.5    -      -       -      +
    122M  LYS*     3.9    18.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 105 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25M  GLN*     2.9    24.8    +      -       -      +
     40M  ILE*     3.9    26.0    -      -       +      -
     54M  TRP*     4.7     2.0    -      -       +      -
     55M  TYR      3.1    15.9    -      -       -      +
     56M  GLN*     3.1    25.4    +      -       +      -
     66M  LEU*     3.6    22.4    -      -       +      -
     81M  PHE*     3.8     8.3    -      +       -      -
     92M  LEU*     3.7    18.6    -      -       +      -
     94M  ILE*     3.7    16.8    -      -       +      +
    101M  ASP*     2.6    25.4    +      -       -      -
    103M  ALA      3.6    20.0    -      -       -      -
    104M  THR*     1.3    72.4    -      -       -      +
    106M  TYR*     1.3    61.2    +      -       -      +
    120M  GLY*     3.3     0.9    -      -       -      -
    121M  THR      3.0    24.9    +      -       -      +
    123M  LEU*     3.7    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 106 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25M  GLN*     3.6     2.2    -      -       -      -
     54M  TRP*     3.4     5.0    -      -       -      -
     55M  TYR*     2.8    46.3    +      -       +      -
     57M  GLN*     3.1    33.3    +      -       +      -
     63M  PRO*     5.5     0.2    -      -       +      -
    104M  THR*     3.5    36.3    +      -       +      +
    105M  TYR*     1.3    73.4    -      -       -      +
    107M  CYS*     1.3    68.2    +      -       -      +
    117M  PHE*     4.2     6.3    -      -       +      -
    118M  GLY      3.6    13.7    -      -       -      -
    119M  SER      3.7     9.1    +      -       -      -
    120M  GLY*     3.5    22.2    -      -       -      -
    188M  GLN*     3.7     9.4    +      -       -      -
    193M  GLY*     5.2     4.9    -      -       -      -
    194M  LEU*     3.5    37.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 107 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23M  MET*     3.5    12.8    -      -       +      -
     25M  GLN*     3.5    15.6    +      -       -      -
     42M  CYS*     3.4    30.7    -      -       -      -
     52M  LEU*     4.1     6.3    -      -       +      -
     53M  SER      3.2     8.3    -      -       -      +
     54M  TRP*     3.9    20.6    -      -       +      -
    106M  TYR*     1.3    73.7    -      -       -      +
    108M  LEU*     1.3    62.7    +      -       -      +
    109M  GLN      4.3     0.2    -      -       -      -
    117M  PHE*     3.2     7.3    -      -       -      -
    118M  GLY*     2.9    44.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 108 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23M  MET*     4.2     2.0    -      -       -      -
     51M  TYR      3.7     0.9    -      -       -      +
     52M  LEU*     3.4     3.6    -      -       -      +
     53M  SER*     2.7    29.6    +      -       -      +
     55M  TYR*     3.3    41.3    -      -       +      +
    107M  CYS*     1.3    76.8    -      -       -      +
    109M  GLN*     1.3    78.3    +      -       -      +
    110M  HIS*     3.8    11.2    +      -       +      +
    115M  TYR*     3.8    18.6    -      -       +      -
    116M  THR      3.5    10.5    -      -       -      +
    117M  PHE*     3.6    33.0    -      -       +      -
    196M  TRP*     6.2     0.2    -      -       +      -
    255M  THR*     4.2     6.1    -      -       -      +
    256M  LEU*     3.9    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 109 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21M  ILE*     3.9    29.0    -      -       +      +
     23M  MET*     3.5    36.7    -      -       +      +
     48M  ILE*     3.7    19.5    -      -       +      +
     51M  TYR      3.4     5.4    -      -       -      -
    108M  LEU*     1.3    76.0    -      -       -      +
    110M  HIS*     1.3    62.2    +      -       -      +
    111M  GLY      3.1    16.1    +      -       -      -
    112M  GLU      3.6     8.4    +      -       -      -
    114M  PRO      2.6    30.5    +      -       -      -
    115M  TYR*     3.4     4.9    -      -       -      -
    116M  THR*     3.1    40.8    +      -       -      +
----------------------------------------------------------
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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