Contacts of the strand formed by residues 467 - 475 (chain M) in PDB entry 5D4E


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 ILE 467 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140M  ILE*     5.4     0.2    -      -       +      -
    328M  LEU*     4.7    14.1    +      -       +      +
    331M  ARG      5.4     3.0    +      -       -      +
    333M  ILE*     3.6    37.0    -      -       +      -
    410M  ILE*     4.1     7.6    -      -       +      -
    437M  ARG*     3.0    49.1    +      -       +      -
    438M  ILE*     3.9    30.7    -      -       +      -
    455M  LEU*     3.9    10.5    -      -       +      -
    459M  ALA*     3.8    21.5    -      -       +      -
    460M  ARG      3.3     7.2    -      -       -      +
    461M  VAL*     4.3     6.1    -      -       +      +
    466M  PHE*     1.3    73.6    -      -       -      +
    468M  ARG*     1.3    63.5    +      -       -      +
    487M  THR*     4.1     5.9    -      -       -      -
    488M  ALA      4.7     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 468 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    437M  ARG*     4.6     2.2    -      -       -      -
    459M  ALA*     3.4     5.2    -      -       -      +
    460M  ARG*     2.5    40.2    +      -       +      +
    462M  ASP*     3.0    48.6    +      -       -      +
    466M  PHE      3.9     2.0    -      -       -      +
    467M  ILE*     1.3    78.4    -      -       -      +
    469M  THR*     1.3    60.3    +      -       -      +
    485M  TYR*     3.1    49.6    +      -       +      +
    486M  MET*     3.2    15.8    -      -       -      +
    487M  THR*     3.6    22.0    -      -       +      +
    490M  GLU*     5.6     5.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 469 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    435M  TYR      4.1     2.9    -      -       -      +
    436M  GLY*     3.3    26.4    +      -       -      -
    437M  ARG*     3.4    36.1    -      -       -      +
    468M  ARG*     1.3    73.6    -      -       -      +
    470M  PRO*     1.3    65.6    +      -       -      +
    471M  TYR*     3.5    25.9    -      -       +      +
    485M  TYR*     3.7     3.8    -      -       -      -
    486M  MET      3.1    21.8    +      -       -      +
    538M  GLN*     2.9    27.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 470 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13M  ILE*     3.9     3.6    -      -       +      -
    458M  TYR*     3.6    29.2    -      -       +      +
    469M  THR*     1.3    91.7    +      -       -      +
    471M  TYR*     1.3    68.7    +      -       -      +
    483M  VAL*     3.6    12.3    -      -       +      -
    484M  VAL      3.6     6.1    -      -       -      +
    485M  TYR*     3.4    35.9    -      -       +      +
    534M  VAL*     3.4    20.2    -      -       +      +
    538M  GLN*     3.0    31.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 471 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    435M  TYR*     4.0     7.6    -      +       -      -
    469M  THR*     3.5    36.9    -      -       +      +
    470M  PRO*     1.3    76.9    -      -       -      +
    472M  ARG*     1.3    64.6    +      -       -      +
    483M  VAL*     3.2     5.4    -      -       -      -
    484M  VAL*     2.9    30.9    +      -       -      +
    486M  MET*     3.6    35.9    -      -       +      -
    491M  GLU*     2.9    28.6    +      -       +      -
    496M  ILE*     3.5    41.7    -      -       +      -
    516M  ARG*     3.0    16.8    +      -       -      -
    531M  PHE*     4.1     7.6    -      -       +      -
    532M  MET      3.6     9.6    -      -       -      +
    533M  ASP*     3.6    16.2    -      -       -      -
    534M  VAL*     4.0     3.1    -      -       -      -
    538M  GLN*     4.4     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 472 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10M  ARG*     4.2    17.3    +      -       -      +
     12M  VAL*     3.3    40.5    -      -       +      +
    471M  TYR*     1.3    75.8    -      -       -      +
    473M  ARG*     1.3    65.0    +      -       -      +
    474M  VAL*     3.4     1.0    +      -       -      +
    479M  VAL*     3.4    32.0    +      -       +      +
    480M  THR      3.7    18.8    +      -       -      +
    481M  ASP*     4.3     1.4    +      -       -      +
    482M  GLU      3.4     3.1    -      -       -      +
    483M  VAL*     4.3    13.9    -      -       +      -
    499M  ALA*     5.3     1.2    +      -       -      +
    503M  LEU*     4.0    12.1    -      -       -      +
    506M  ASN*     5.5     1.0    +      -       -      -
    531M  PHE*     3.2     8.1    -      -       -      -
    532M  MET*     2.9    61.3    +      -       -      +
    533M  ASP      4.0    11.9    +      -       -      -
    534M  VAL*     4.5    15.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 473 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    471M  TYR      4.1     0.4    +      -       -      -
    472M  ARG*     1.3    71.3    -      -       -      +
    474M  VAL*     1.3    62.3    +      -       -      +
    475M  VAL*     3.8    24.7    -      -       +      -
    479M  VAL*     3.8     0.3    -      -       -      -
    480M  THR*     2.9    43.1    +      -       +      +
    482M  GLU*     2.9    55.5    +      -       -      +
    484M  VAL*     3.8    11.1    -      -       +      +
    494M  TYR*     5.6     4.2    +      -       -      -
    530M  GLU      4.6     2.9    -      -       -      -
    531M  PHE*     3.4    38.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 474 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    472M  ARG      3.6    10.8    -      -       -      +
    473M  ARG*     1.3    78.8    -      -       -      +
    475M  VAL*     1.3    64.2    +      -       -      +
    476M  GLY      4.1     0.5    +      -       -      -
    477M  GLY*     4.3     9.6    -      -       -      +
    478M  VAL      3.3    22.0    -      -       -      +
    479M  VAL*     3.9    18.6    -      -       +      -
    508M  ILE*     4.5     2.7    -      -       +      -
    529M  VAL*     3.1    44.1    -      -       +      +
    530M  GLU*     2.8    20.4    +      -       -      +
    531M  PHE      3.7    16.4    -      -       -      -
    532M  MET*     3.7    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 475 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    473M  ARG*     3.8    24.8    +      -       +      -
    474M  VAL*     1.3    75.3    -      -       -      +
    476M  GLY*     1.3    68.8    +      -       -      +
    477M  GLY      3.4     1.1    -      -       -      -
    478M  VAL*     2.9    28.9    +      -       +      +
    480M  THR*     5.2     8.3    -      -       +      -
----------------------------------------------------------
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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