Contacts of the strand formed by residues 175 - 183 (chain A) in PDB entry 6DWY


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 175 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  ALA      4.4     0.4    -      -       -      -
    170A  VAL*     3.6    43.1    -      -       +      +
    173A  ASP      3.2     3.5    +      -       -      +
    174A  GLY*     1.3    76.4    -      -       -      +
    176A  SER*     1.3    62.6    +      -       -      +
    196A  LEU*     4.7     6.7    -      -       +      -
    197A  HIS      4.0     2.0    -      -       -      -
    198A  TYR*     4.4     6.5    -      -       +      -
    243A  ILE*     4.0    17.4    -      -       +      -
    244A  LYS*     3.2    29.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 176 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175A  ALA*     1.3    76.3    +      -       -      +
    177A  ALA*     1.3    58.8    +      -       -      +
    196A  LEU*     3.2     5.9    -      -       -      +
    197A  HIS*     2.4    55.6    +      -       -      -
    244A  LYS*     3.4     9.2    -      -       -      +
    560A  SER      4.4     0.7    +      -       -      -
    563A  SER*     3.5    21.1    +      -       -      -
    564A  ILE*     3.2    34.8    -      -       -      +
    565A  PRO*     4.0     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 177 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176A  SER*     1.3    74.3    -      -       -      +
    178A  THR*     1.3    65.0    +      -       -      +
    179A  ILE      4.3     0.4    -      -       -      -
    194A  VAL*     4.6     7.9    -      -       +      -
    195A  THR      3.2     9.9    -      -       -      +
    196A  LEU*     3.7    13.9    -      -       +      -
    232A  PHE*     5.1     2.0    -      -       +      -
    243A  ILE*     4.0     6.5    -      -       +      +
    244A  LYS      2.9     6.7    +      -       -      -
    245A  PHE*     3.5    33.9    -      -       +      -
    246A  VAL*     3.0    30.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 178 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177A  ALA*     1.3    75.3    -      -       -      +
    179A  ILE*     1.3    63.7    +      -       -      +
    194A  VAL*     3.3     1.9    -      -       -      -
    195A  THR*     2.7    50.7    +      -       -      -
    197A  HIS*     3.7    16.8    +      -       -      -
    246A  VAL*     3.2    22.8    -      -       -      +
    565A  PRO*     3.9     4.5    -      -       -      +
    567A  SER      3.6     6.0    +      -       -      +
    568A  SER*     3.6    31.9    -      -       -      -
    570A  ALA*     4.8     0.7    -      -       +      -
    571A  SER*     3.6    21.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 179 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178A  THR*     1.3    80.7    -      -       -      +
    180A  ASP*     1.3    63.6    +      -       -      +
    192A  LEU*     4.3     4.9    -      -       +      -
    193A  GLY      3.2     9.2    -      -       -      +
    194A  VAL*     3.5    30.3    -      -       +      -
    224A  ILE*     4.8    14.4    -      -       +      -
    228A  LEU*     4.0    17.5    -      -       +      -
    245A  PHE*     4.1    13.9    -      -       +      -
    246A  VAL      3.7     4.0    +      -       -      +
    247A  THR*     3.1    22.5    +      -       -      +
    253A  VAL*     3.9    18.6    -      -       +      -
    256A  SER*     6.0     0.2    -      -       -      -
    257A  LEU*     3.7    38.8    -      -       +      -
    568A  SER*     4.8     1.2    +      -       -      -
    571A  SER*     3.9     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 180 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179A  ILE*     1.3    78.6    -      -       -      +
    181A  LEU*     1.3    72.2    +      -       -      +
    192A  LEU*     3.3     7.6    -      -       -      +
    193A  GLY      3.0    28.2    +      -       -      -
    247A  THR*     4.0     2.6    +      -       -      -
    248A  ASP*     2.6    26.4    -      -       -      +
    253A  VAL*     4.7     6.7    -      -       -      +
    568A  SER*     4.7     5.9    +      -       -      -
    571A  SER*     3.4    18.4    +      -       -      +
    572A  GLU*     3.0    25.1    -      -       -      +
    575A  PHE*     3.7    11.6    -      -       +      -
    701A   CA      3.1    16.3    -      -       -      -
     17C    G      4.6     0.2    -      -       -      +
     18C    G      3.4     6.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 181 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180A  ASP*     1.3    89.2    +      -       -      +
    182A  TRP*     1.3    63.1    +      -       -      +
    190A  ASN*     6.5     0.2    -      -       +      -
    191A  PHE      3.4    16.4    -      -       -      +
    192A  LEU*     4.0    23.3    -      -       +      -
    214A  LEU*     5.0     7.4    -      -       +      -
    219A  SER*     5.1     8.3    -      -       -      +
    224A  ILE*     3.6    33.4    -      -       +      -
    252A  ASN*     4.2    15.7    -      -       +      +
    253A  VAL*     3.8    19.5    -      -       +      -
    575A  PHE*     4.1     3.6    -      -       -      -
    701A   CA      4.2     4.6    -      -       -      -
     17C    G      5.0     3.6    +      -       -      -
     18C    G      4.2    36.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 182 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180A  ASP      4.3     0.2    +      -       -      -
    181A  LEU*     1.3    75.3    -      -       -      +
    183A  THR*     1.3    77.6    +      -       -      +
    184A  ASP*     3.6    32.3    -      -       +      -
    185A  ASN*     4.8     4.5    -      -       +      -
    191A  PHE*     2.7    56.8    +      +       +      +
    211A  LEU*     4.6     3.8    -      -       +      -
    575A  PHE*     3.4    56.7    -      +       +      +
    578A  ALA*     3.6    29.2    -      -       +      -
    579A  GLY*     3.9    13.5    -      -       -      -
    582A  ILE*     4.7     3.4    -      -       +      -
     16C    T      3.5    23.7    +      -       -      -
     17C    G      3.3    25.6    +      -       -      -
     18C    G      3.4    12.5    -      +       -      +
----------------------------------------------------------
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Residues in contact with THR 183 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182A  TRP*     1.3    92.4    +      -       -      +
    184A  ASP*     1.3    60.3    +      -       -      +
    185A  ASN*     3.9     0.9    +      -       -      -
    188A  LYS*     3.3    33.0    +      -       +      -
    189A  ARG      2.8    25.7    +      -       -      -
    190A  ASN*     3.7     6.1    +      -       -      -
     17C    G      5.0     1.4    +      -       -      -
     18C    G      3.0    38.3    +      -       +      +
     19C    G      5.0    11.4    -      -       -      +
     20C    T      5.3     3.1    -      -       -      +
----------------------------------------------------------
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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