Contacts of the strand formed by residues 66 - 73 (chain M) in PDB entry 6E0P


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 66 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60M  LYS      3.6     1.0    -      -       -      +
     61M  GLN*     3.4     7.1    -      -       -      -
     62M  THR*     3.0    34.7    +      -       -      -
     63M  PRO*     5.0     0.8    -      -       -      -
     64M  ARG      3.6     2.0    -      -       -      +
     65M  GLN*     1.3    80.9    -      -       -      +
     67M  LEU*     1.3    62.1    +      -       -      -
     68M  GLU*     3.9     2.3    +      -       -      +
    245M  TYR*     5.1    11.9    -      -       -      -
    257M  GLY      5.4     2.5    -      -       -      -
    258M  SER*     5.3     7.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 67 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59M  VAL*     3.7    16.6    -      -       +      -
     60M  LYS      3.4     1.1    -      -       -      -
     61M  GLN*     3.7    35.4    -      -       +      +
     65M  GLN      3.8     2.3    +      -       -      +
     66M  GLY*     1.3    72.9    -      -       -      -
     68M  GLU*     1.3    65.3    +      -       -      +
    117M  TYR*     4.9     5.8    -      -       +      -
    132M  TRP*     5.1     1.3    -      -       +      -
    194M  TYR*     6.0     1.1    -      -       +      -
    196M  GLN*     4.7     2.7    -      -       -      +
    202M  PRO*     4.8    13.5    -      -       +      -
    245M  TYR*     3.7    47.6    -      -       +      -
    256M  PHE*     3.5    53.6    +      -       +      +
    257M  GLY      4.9     2.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 68 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59M  VAL*     3.4     6.4    -      -       -      -
     60M  LYS*     2.7    55.1    +      -       +      +
     62M  THR*     5.7     1.6    -      -       -      -
     65M  GLN*     2.9    43.3    -      -       -      +
     66M  GLY      4.7     2.2    -      -       -      +
     67M  LEU*     1.3    80.0    -      -       -      +
     69M  TRP*     1.3    64.5    +      -       -      +
     83M  ASN*     5.6     2.5    -      -       -      +
     85M  LYS*     3.7    30.9    +      -       -      -
     86M  PHE*     3.9    17.1    -      -       +      -
    256M  PHE*     4.2     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 69 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57M  GLN*     2.5    28.1    +      -       +      +
     58M  TRP      3.8     9.9    -      -       -      -
     59M  VAL*     4.6     7.6    -      -       +      +
     68M  GLU*     1.3    71.5    -      -       -      +
     70M  ILE*     1.3    62.7    +      -       -      +
     71M  GLY*     3.5    21.9    +      -       -      -
     72M  TYR*     3.5    33.4    -      +       -      -
     81M  LYS*     4.2    13.5    -      -       +      -
     82M  TYR      4.3     2.9    -      -       -      -
     83M  ASN*     3.0    49.8    +      -       +      +
     86M  PHE*     4.1     3.1    -      -       -      -
    129M  LEU*     5.6     3.4    -      -       +      -
    247M  LEU*     6.2     0.7    -      -       +      -
    252M  SER      3.3    24.9    -      -       -      -
    253M  PRO*     4.0     4.9    -      -       +      -
    254M  TYR*     3.3    57.9    +      +       +      +
    256M  PHE*     4.0    14.1    -      +       +      -
----------------------------------------------------------
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Residues in contact with ILE 70 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58M  TRP*     2.8    24.0    +      -       +      +
     59M  VAL      3.9     4.5    -      -       -      +
     60M  LYS*     3.7    32.5    -      -       +      +
     69M  TRP*     1.3    77.8    -      -       -      +
     71M  GLY*     1.3    56.4    +      -       -      +
     82M  TYR*     3.5     5.4    -      -       +      +
     83M  ASN*     2.7    34.5    +      -       -      +
     86M  PHE*     4.0    38.0    -      -       +      +
     90M  ALA*     4.0    11.0    -      -       +      -
     92M  LEU*     5.7     2.0    -      -       +      -
    103M  MET*     3.7    35.4    -      -       +      -
    116M  TYR*     3.8    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 71 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57M  GLN*     3.4     2.1    -      -       -      -
     58M  TRP*     2.8    29.8    +      -       -      +
     69M  TRP*     3.5    18.0    +      -       -      -
     70M  ILE*     1.3    83.5    -      -       -      +
     72M  TYR*     1.3    59.9    +      -       -      -
     81M  LYS      3.2    14.1    -      -       -      -
     82M  TYR*     4.3     1.8    -      -       -      -
     92M  LEU*     3.9    10.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 72 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55M  THR*     3.9    24.0    -      -       +      -
     56M  ILE      3.3    15.5    -      -       -      +
     57M  GLN*     3.3    30.3    -      -       -      +
     69M  TRP*     3.5    16.8    -      +       -      -
     71M  GLY*     1.3    73.2    -      -       -      -
     73M  ILE*     1.3    67.2    +      -       -      +
     74M  TYR*     4.6     4.9    -      -       +      -
     79M  GLY      4.4    10.1    -      -       -      -
     80M  THR*     3.3     5.1    +      -       -      -
     81M  LYS*     3.1    74.1    +      -       +      +
     92M  LEU*     3.5    12.8    -      -       -      +
    254M  TYR*     4.7    10.3    -      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 73 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55M  THR*     3.4     2.8    -      -       -      -
     56M  ILE*     3.1    31.5    +      -       +      +
     72M  TYR*     1.3    75.9    -      -       -      +
     74M  TYR*     1.3    65.1    -      -       -      +
     75M  PRO*     3.4     4.2    -      -       +      +
     78M  ALA*     4.2    18.4    -      -       +      +
     79M  GLY      3.4     4.9    -      -       -      +
     80M  THR*     3.7    16.8    -      -       +      -
     92M  LEU*     3.6    29.7    -      -       +      +
     93M  THR*     3.7    19.5    -      -       -      -
     94M  SER*     3.7    14.4    -      -       -      +
    101M  VAL*     3.7    39.5    -      -       +      -
----------------------------------------------------------
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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