Contacts of the strand formed by residues 245 - 253 (chain A) in PDB entry 5MCO


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 TYR 245 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240A  ILE*     3.8    22.5    -      -       +      +
    241A  ASP      3.7     9.9    -      -       -      -
    242A  HIS*     3.2    52.8    +      -       -      +
    243A  SER      3.3     2.5    -      -       -      +
    244A  LEU*     1.3    79.4    -      -       -      +
    246A  THR*     1.3    69.7    +      -       -      +
    247A  GLY      3.5    22.2    -      -       -      -
    249A  LEU*     3.6    26.5    -      -       +      +
    403A  TYR*     3.2    33.9    -      +       +      -
    416A  ALA*     3.6    16.4    -      -       +      -
    417A  VAL      3.1    15.9    -      -       -      +
    419A  ALA*     3.8     3.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 246 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245A  TYR*     1.3    85.3    -      -       -      +
    247A  GLY*     1.3    68.6    +      -       -      +
    248A  SER      3.9     0.5    +      -       -      -
    416A  ALA*     4.1     0.2    -      -       -      +
    417A  VAL*     3.1    41.0    +      -       +      +
    418A  SER      5.4     0.4    -      -       -      -
    419A  ALA*     4.7    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 247 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245A  TYR*     3.5    16.3    -      -       -      -
    246A  THR*     1.3    79.3    +      -       -      +
    248A  SER*     1.3    60.0    +      -       -      -
    417A  VAL*     6.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 248 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245A  TYR*     4.9     0.2    -      -       -      -
    246A  THR      4.6     0.2    -      -       -      +
    247A  GLY*     1.3    73.9    -      -       -      -
    249A  LEU*     1.3    63.3    +      -       -      +
    250A  TRP*     3.9    27.5    +      -       -      -
    415A  PHE      3.5     3.5    -      -       -      +
    416A  ALA*     3.3    20.0    -      -       -      +
    431A  VAL*     4.7     4.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 249 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240A  ILE*     4.1    18.2    -      -       +      -
    245A  TYR*     3.6    34.2    -      -       +      +
    248A  SER*     1.3    76.1    -      -       -      +
    250A  TRP*     1.3    64.3    +      -       -      +
    251A  TYR*     3.9    32.9    -      -       +      +
    403A  TYR*     4.6     4.5    -      -       +      +
    405A  VAL*     3.6    23.8    -      -       +      -
    414A  GLY*     4.0    11.2    -      -       -      -
    415A  PHE      3.4    19.5    -      -       -      -
    416A  ALA*     3.9    12.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 250 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248A  SER*     3.9    23.0    -      -       -      -
    249A  LEU*     1.3    78.9    -      -       -      +
    251A  TYR*     1.3    62.8    +      -       -      +
    355A  GLN*     3.7    22.9    -      -       -      -
    357A  PHE*     3.4    45.9    -      +       +      -
    413A  ILE      3.7     0.9    -      -       -      +
    414A  GLY*     3.1     0.9    -      -       -      -
    415A  PHE      2.7    37.6    +      -       -      -
    431A  VAL*     3.6    32.4    +      -       +      -
    432A  GLU*     4.6     0.2    -      -       -      +
    433A  GLY      3.3    24.8    -      -       -      +
    434A  PRO*     3.3    32.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 251 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240A  ILE*     4.0    13.9    -      -       -      +
    249A  LEU*     3.9    43.0    -      -       +      +
    250A  TRP*     1.3    76.2    -      -       -      +
    252A  THR*     1.3    58.9    +      -       -      +
    349A  MET      3.8     0.3    -      -       -      +
    350A  GLY*     3.9     0.5    -      -       -      -
    351A  GLU*     3.5    47.0    +      -       +      +
    355A  GLN*     5.6     0.2    +      -       -      -
    357A  PHE*     3.3    14.6    -      -       -      -
    405A  VAL*     4.5     8.3    -      -       +      -
    407A  ASP*     4.4     7.9    +      -       +      -
    412A  ARG*     3.3    58.7    +      -       +      -
    413A  ILE      3.1     6.1    -      -       -      +
    414A  GLY*     3.3    30.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 252 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251A  TYR*     1.3    75.3    -      -       -      +
    253A  PRO*     1.3    69.0    +      -       -      +
    262A  VAL*     3.9    28.9    -      -       +      +
    263A  ILE      4.4     2.9    +      -       -      -
    348A  LEU*     3.7     9.8    -      -       +      +
    349A  MET*     2.6    30.3    +      -       -      +
    351A  GLU*     5.4     1.3    -      -       -      -
    357A  PHE*     3.8     9.1    -      -       -      -
    412A  ARG*     3.2     5.1    -      -       -      +
    413A  ILE*     2.8    45.8    +      -       +      +
    415A  PHE*     4.1    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 253 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251A  TYR      4.8     0.2    -      -       -      -
    252A  THR*     1.3    92.4    +      -       -      +
    254A  ILE*     1.3    68.0    +      -       -      +
    255A  ARG*     3.2     5.4    +      -       -      +
    261A  GLU      3.6     6.1    -      -       -      +
    262A  VAL*     4.0    13.0    -      -       -      +
    263A  ILE      4.9     0.7    +      -       -      -
    349A  MET*     3.3    38.9    -      -       +      +
    350A  GLY      3.4    19.3    -      -       -      +
    351A  GLU*     4.7     6.5    -      -       +      +
    411A  LYS      3.6     8.1    -      -       -      +
    412A  ARG*     4.3     2.7    -      -       +      -
----------------------------------------------------------
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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