Contacts of the strand formed by residues 144 - 154 (chain F) in PDB entry 6RI7


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 144 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140F  ASN*     3.9     3.6    -      -       -      -
    141F  THR*     2.5    56.2    +      -       -      +
    142F  PRO      3.3     1.0    -      -       -      -
    143F  ALA*     1.3    74.3    -      -       -      +
    145F  GLU*     1.3    60.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 145 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138F  VAL*     5.9     3.9    -      -       +      +
    139F  VAL      2.9    15.5    -      -       -      +
    140F  ASN*     3.8     8.5    -      -       +      +
    144F  GLY*     1.3    75.9    -      -       -      -
    146F  ALA*     1.3    68.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 146 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138F  VAL*     3.1     6.7    -      -       -      +
    139F  VAL*     2.9    33.5    +      -       +      +
    141F  THR*     5.7     4.0    -      -       +      +
    144F  GLY      5.3     0.4    -      -       -      +
    145F  GLU*     1.3    80.6    -      -       -      +
    147F  SER*     1.3    63.4    +      -       -      +
    148F  TRP*     4.0    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 147 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95F  ASN*     4.2     9.9    -      -       -      +
     96F  ASP*     5.0     9.4    +      -       -      -
    136F  LEU*     5.4     4.0    -      -       -      -
    137F  ALA      2.9    14.6    -      -       -      -
    138F  VAL*     3.6    14.1    -      -       -      -
    146F  ALA*     1.3    78.9    -      -       -      +
    148F  TRP*     1.3    83.7    +      -       -      +
    149F  TYR*     5.7     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 148 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    670D  SER*     4.3    20.4    -      -       -      -
     93F  ILE*     3.3    41.3    -      -       +      +
     94F  GLU      3.0    27.6    -      -       -      +
     95F  ASN*     3.6    23.0    -      -       -      +
     99F  VAL*     4.8     6.2    +      -       -      +
    124F  MET*     3.6    34.1    -      -       +      -
    135F  ASP      3.7     0.2    -      -       -      +
    136F  LEU*     3.6     0.9    -      -       -      -
    137F  ALA*     2.9    41.4    +      -       +      +
    139F  VAL*     3.9    22.9    -      -       +      -
    141F  THR*     5.8     1.3    -      -       +      -
    146F  ALA*     4.0    21.5    -      -       +      -
    147F  SER*     1.3    93.4    -      -       -      +
    149F  TYR*     1.3    73.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 149 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93F  ILE*     3.2     7.4    -      -       -      -
     94F  GLU*     2.9    42.5    +      -       +      +
     96F  ASP*     5.4     8.3    +      -       -      -
    134F  GLY*     6.1     1.6    -      -       -      -
    135F  ASP      3.7    10.8    -      -       -      +
    136F  LEU*     3.3    37.2    -      -       +      +
    147F  SER*     5.7     4.3    -      -       -      -
    148F  TRP*     1.3    83.1    -      -       -      +
    150F  VAL*     1.3    70.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 150 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85F  VAL*     5.7     2.9    -      -       +      -
     91F  VAL*     5.0     4.3    -      -       +      -
     92F  GLU      3.9     5.8    -      -       -      +
     93F  ILE*     4.5     4.0    -      -       +      -
    128F  LEU*     4.8    15.9    -      -       +      -
    131F  LYS*     4.7    11.9    -      -       +      -
    132F  GLU      3.2    24.7    -      -       -      +
    133F  VAL*     3.0    25.7    +      -       -      +
    134F  GLY*     4.8     1.2    -      -       -      -
    135F  ASP*     3.6    18.6    +      -       +      +
    137F  ALA*     5.5     4.0    -      -       +      -
    149F  TYR*     1.3    80.4    -      -       -      +
    151F  ASN*     1.3    65.8    +      -       -      +
    152F  ALA      4.0     4.7    -      -       -      +
    153F  ILE*     3.5    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 151 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92F  GLU*     2.9    30.6    +      -       +      +
     94F  GLU*     2.5    44.3    +      -       +      +
    133F  VAL*     4.4     4.7    -      -       -      -
    149F  TYR      4.7     0.2    -      -       -      +
    150F  VAL*     1.3    77.9    -      -       -      +
    152F  ALA*     1.3    63.4    +      -       -      +
    153F  ILE*     5.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 152 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90F  TRP      4.0     3.1    -      -       -      +
     91F  VAL*     3.3    24.5    -      -       -      +
     92F  GLU*     3.4    34.6    +      -       +      +
    150F  VAL*     4.0     2.2    -      -       -      +
    151F  ASN*     1.3    81.9    -      -       -      +
    153F  ILE*     1.3    73.2    +      -       -      +
    154F  GLU*     5.4     8.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 153 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82F  GLU*     4.5    17.3    -      -       +      +
     83F  GLY*     4.8     6.7    -      -       -      +
     84F  LYS      4.7     1.8    -      -       -      +
     85F  VAL*     3.7    29.4    -      -       +      -
     89F  ALA*     4.6     4.9    -      -       +      -
     90F  TRP      3.4     3.6    -      -       -      -
     91F  VAL*     4.9     1.3    -      -       +      -
    132F  GLU      4.4     2.0    -      -       -      -
    133F  VAL*     3.7    32.1    -      -       +      +
    150F  VAL*     3.5    24.2    -      -       +      -
    152F  ALA*     1.3    83.8    -      -       -      +
    154F  GLU*     1.3    70.9    +      -       -      +
    155F  TYR*     4.3    28.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 154 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82F  GLU*     5.5     2.5    -      -       -      -
     89F  ALA*     3.6     0.3    -      -       -      -
     90F  TRP*     2.9    44.2    +      -       +      +
    102F  ARG*     3.5    25.1    +      -       -      -
    152F  ALA*     5.4     7.7    -      -       +      +
    153F  ILE*     1.3    84.7    -      -       -      +
    155F  TYR*     1.3    76.3    +      -       -      +
----------------------------------------------------------
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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