Contacts of the strand formed by residues 199 - 207 (chain A) in PDB entry 6RIP


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 ASP 199 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  PRO*     3.7     2.4    -      -       -      -
     31A  LEU*     2.9    40.4    +      -       +      +
     32A  GLU      5.8     1.1    -      -       -      +
     33A  ARG*     4.8    11.2    -      -       -      +
     34A  GLY      4.9     3.1    +      -       -      -
     36A  GLY*     5.4     6.2    -      -       -      -
    187A  VAL*     4.7    15.3    -      -       +      +
    188A  GLU*     3.6    16.2    -      -       -      +
    189A  ALA*     3.4    14.1    +      -       -      +
    190A  ALA*     4.1     0.2    -      -       -      -
    197A  ASP*     3.4    31.0    -      -       -      +
    198A  LEU*     1.3    75.8    -      -       -      +
    200A  LYS*     1.3    65.5    +      -       -      +
    201A  LEU      3.8     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 200 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  THR*     3.7    33.2    -      -       +      +
     28A  LEU      3.9     9.9    -      -       -      +
     29A  GLU      4.9     0.4    -      -       -      -
     30A  PRO*     5.4     0.7    -      -       -      -
    186A  ASN      4.0     0.5    -      -       -      +
    187A  VAL*     3.5     4.5    -      -       -      -
    188A  GLU*     2.9    57.1    +      -       +      +
    190A  ALA*     3.5    25.4    -      -       +      +
    191A  ARG*     5.3     6.2    -      -       -      +
    199A  ASP*     1.3    73.0    -      -       -      +
    201A  LEU*     1.3    62.6    +      -       -      +
    202A  VAL*     3.9    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  THR*     3.6     0.9    -      -       -      -
     28A  LEU*     3.2    60.6    +      -       +      +
     31A  LEU*     4.6    12.1    -      -       +      +
     36A  GLY*     4.1    13.2    -      -       -      +
     39A  LEU*     4.6     9.4    -      -       +      -
     40A  GLY*     4.3    20.2    -      -       -      +
     43A  LEU*     5.3     0.9    -      -       +      -
    185A  TYR*     4.4    15.0    -      -       +      -
    186A  ASN      3.6    11.2    -      -       -      +
    187A  VAL*     3.6    21.3    -      -       +      -
    199A  ASP      3.8     1.8    +      -       -      -
    200A  LYS*     1.3    73.2    -      -       -      +
    202A  VAL*     1.3    78.2    +      -       -      +
    203A  ILE*     4.3    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 202 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  LYS*     4.5    22.0    -      -       +      +
     26A  VAL      3.6     9.2    -      -       -      +
     27A  THR*     4.1    11.9    -      -       +      +
    185A  TYR*     3.2     4.0    -      -       -      +
    186A  ASN*     2.9    47.7    +      -       +      +
    188A  GLU*     4.8     9.0    -      -       +      +
    200A  LYS*     3.9    23.3    -      -       +      +
    201A  LEU*     1.3    82.4    -      -       -      +
    203A  ILE*     1.3    69.5    +      -       -      +
    204A  GLU*     4.2     0.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 203 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  LYS*     3.4     6.2    -      -       -      +
     26A  VAL*     3.0    47.9    +      -       +      +
     28A  LEU*     5.1     4.7    -      -       +      +
     40A  GLY*     5.6     2.7    -      -       -      +
     43A  LEU*     4.0    24.9    -      -       +      -
     44A  ARG      6.0     0.2    -      -       -      +
     47A  LEU*     5.2     2.5    -      -       +      -
    183A  ILE*     4.3    13.2    -      -       +      -
    184A  ALA      3.5     8.3    -      -       -      +
    185A  TYR*     3.9    17.3    -      -       +      -
    201A  LEU*     4.3    15.9    -      -       +      -
    202A  VAL*     1.3    77.0    -      -       -      +
    204A  GLU*     1.3    71.1    +      -       -      +
    205A  MET*     4.2    13.8    +      -       +      +
    217A  ILE*     4.0    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 204 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  HIS*     2.9    39.6    +      -       +      -
     24A  ALA      3.8     6.3    -      -       -      +
     25A  LYS*     4.1    18.4    -      -       +      +
    182A  ARG*     4.0    23.4    +      -       -      +
    183A  ILE*     3.5     4.3    -      -       -      +
    184A  ALA*     2.9    43.0    +      -       +      +
    202A  VAL*     4.2     1.4    +      -       +      -
    203A  ILE*     1.3    73.3    -      -       -      +
    205A  MET*     1.3    63.0    +      -       -      +
   1090C  ASN*     5.2     4.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 205 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  HIS*     3.0    20.8    -      -       -      +
     24A  ALA      3.3    20.0    +      -       -      +
     25A  LYS*     6.0     0.7    -      -       -      -
     26A  VAL*     5.0     9.0    -      -       +      -
     47A  LEU*     4.2    21.3    -      -       +      -
    180A  VAL*     4.8     9.6    -      -       +      -
    182A  ARG      3.6     4.5    -      -       -      -
    183A  ILE*     3.5    15.9    -      -       +      -
    203A  ILE*     4.1    11.1    +      -       +      +
    204A  GLU*     1.3    76.5    -      -       -      +
    206A  GLU*     1.3    59.7    +      -       -      +
    207A  THR*     4.1    15.7    -      -       -      +
    211A  ILE*     5.7     0.9    -      -       -      -
    213A  PRO*     4.2    36.3    -      -       +      +
    216A  ALA*     4.4    12.8    -      -       +      -
    217A  ILE*     4.3    15.3    -      -       +      -
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Residues in contact with GLU 206 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  THR*     3.7    15.8    +      -       -      -
     23A  HIS*     3.0    31.3    +      -       -      +
    180A  VAL*     5.0     0.6    -      -       -      +
    181A  GLU*     3.1    38.9    +      -       +      +
    182A  ARG*     3.0    59.6    +      -       +      +
    183A  ILE*     4.5     0.8    -      -       -      +
    205A  MET*     1.3    74.3    -      -       -      +
    207A  THR*     1.3    59.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 207 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  THR*     3.4    41.4    +      -       -      +
     23A  HIS*     4.1     1.0    -      -       -      +
    179A  PRO      3.9    10.8    -      -       -      +
    180A  VAL*     4.5     7.4    -      -       +      +
    181A  GLU*     5.2     0.7    -      -       -      -
    205A  MET*     3.9    22.8    -      -       -      +
    206A  GLU*     1.3    76.7    -      -       -      +
    208A  ASN*     1.3    69.6    +      -       -      +
    209A  GLY*     3.1    27.3    +      -       -      +
    211A  ILE*     3.9    29.4    +      -       +      +
    213A  PRO*     5.6     2.1    -      -       -      +
----------------------------------------------------------
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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