Contacts of the strand formed by residues 187 - 196 (chain A) in PDB entry 3I7P


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 187 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183A  GLN*     4.6     3.8    -      -       -      -
    184A  ASP      2.8    21.2    +      -       -      +
    185A  PRO      2.8     7.7    +      -       -      -
    186A  GLN*     1.3    78.3    -      -       -      +
    188A  ARG*     1.3    64.0    +      -       -      -
    189A  HIS*     3.2    13.9    +      -       -      -
    214A  ALA*     5.4     8.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 188 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163A  HIS*     4.9     0.6    -      -       -      -
    165A  ILE*     3.4    27.3    -      -       -      +
    181A  VAL*     3.9    12.1    -      -       +      -
    182A  TYR      3.3    11.2    -      -       -      +
    183A  GLN*     2.7    45.9    +      -       +      +
    187A  GLY*     1.3    72.0    -      -       -      -
    189A  HIS*     1.3    74.4    +      -       -      +
    211A  ASN*     3.7     4.0    -      -       -      +
    212A  VAL*     3.1    23.2    +      -       +      +
    213A  GLU      3.3    26.5    -      -       -      +
    214A  ALA*     3.0    26.7    +      -       -      +
    215A  GLU*     4.4    12.2    +      -       -      -
    216A  ALA      3.1    24.3    +      -       -      -
    217A  SER*     6.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 189 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181A  VAL*     3.0     2.9    -      -       -      -
    182A  TYR*     2.8    54.7    +      -       +      +
    184A  ASP*     3.2    33.2    +      -       -      -
    186A  GLN*     4.1    19.5    +      -       +      +
    187A  GLY      3.2    25.9    +      -       -      -
    188A  ARG*     1.3    75.0    +      -       -      +
    190A  VAL*     1.3    59.8    +      -       -      +
    209A  GLN*     3.5    24.0    +      -       +      -
    210A  GLU      3.5    10.5    -      -       -      +
    211A  ASN*     2.8    28.8    +      -       -      -
    212A  VAL*     3.8     8.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 190 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179A  CYS*     3.8    27.8    -      -       -      -
    180A  PHE      3.5     8.3    -      -       -      +
    181A  VAL*     4.2     4.7    -      -       +      +
    189A  HIS*     1.3    74.1    -      -       -      +
    191A  LYS*     1.3    65.2    +      -       -      +
    207A  TRP*     5.3     9.6    -      -       -      +
    208A  LYS      4.2     1.9    -      -       -      +
    209A  GLN*     3.1    21.7    -      -       -      -
    210A  GLU*     3.3    29.6    +      -       +      +
    211A  ASN      4.3     0.2    -      -       -      +
    212A  VAL*     3.6    27.6    -      -       +      -
    231A  ILE*     4.5    12.1    -      -       +      -
    240A  HIS*     4.2    13.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 191 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160A  GLU*     5.9     0.4    -      -       -      +
    161A  GLU*     3.6    10.7    +      -       -      +
    179A  CYS*     3.4     2.8    -      -       -      -
    180A  PHE*     3.0    51.3    +      -       +      -
    182A  TYR*     3.5    16.8    -      -       +      +
    189A  HIS      4.1     0.2    -      -       -      -
    190A  VAL*     1.3    75.6    -      -       -      +
    192A  THR*     1.3    78.8    +      -       -      +
    193A  TYR*     2.8    40.6    +      -       -      +
    207A  TRP*     5.4     0.7    -      -       -      -
    209A  GLN*     3.2    40.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 192 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  LEU*     4.3    13.9    -      -       +      -
    178A  ILE      3.3    15.7    -      -       -      +
    179A  CYS*     4.3    11.2    -      -       +      -
    180A  PHE*     4.6     1.1    -      -       -      -
    190A  VAL*     5.9     0.2    -      -       +      -
    191A  LYS*     1.3    82.3    -      -       -      +
    193A  TYR*     1.3    82.2    +      -       -      +
    205A  GLY*     3.4    24.8    +      -       -      -
    206A  PRO*     4.1     4.5    -      -       +      -
    207A  TRP*     2.8    46.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  LEU*     5.0     4.5    -      -       +      -
    160A  GLU*     4.1    11.6    +      -       +      +
    161A  GLU*     2.8    25.6    +      -       -      -
    177A  THR*     3.0     8.3    -      -       -      +
    178A  ILE*     2.8    40.6    +      -       +      +
    180A  PHE*     3.6    27.8    -      +       -      -
    191A  LYS*     2.8    29.5    +      -       -      -
    192A  THR*     1.3    82.9    -      -       -      +
    194A  GLU*     1.3    70.2    +      -       -      +
    202A  PHE*     3.6    49.8    -      +       +      -
    203A  ASN      3.3    13.7    -      -       -      +
    204A  LYS*     4.9     2.9    -      -       -      -
    205A  GLY*     3.7     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174A  GLN*     5.6     1.4    -      -       -      +
    175A  ALA*     3.2    33.3    +      -       +      +
    176A  PRO      3.1     7.0    -      -       -      +
    177A  THR*     4.1    11.6    -      -       +      +
    193A  TYR*     1.3    83.1    -      -       -      +
    195A  VAL*     1.3    71.7    +      -       -      +
    196A  SER      4.1     0.2    -      -       -      -
    202A  PHE*     3.5     5.0    -      -       -      -
    203A  ASN*     2.5    41.8    +      -       +      +
    204A  LYS      3.2    20.6    -      -       -      +
    205A  GLY*     4.1     0.8    -      -       -      -
    206A  PRO*     5.1     7.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  MET*     3.4    29.2    -      -       +      -
    140A  PHE*     4.8     6.5    -      -       +      -
    142A  VAL*     4.6    14.1    -      -       +      -
    155A  PHE*     5.3     0.9    -      -       +      -
    157A  ILE*     4.6     8.7    -      -       +      -
    175A  ALA*     4.9     2.8    -      -       -      +
    176A  PRO*     2.6    36.3    +      -       +      +
    178A  ILE*     4.8    16.8    -      -       +      -
    193A  TYR      4.8     0.4    -      -       -      +
    194A  GLU*     1.3    85.2    -      -       -      +
    196A  SER*     1.3    70.4    +      -       -      +
    197A  LEU*     3.7    13.0    +      -       +      +
    201A  GLU      4.4     1.6    -      -       -      -
    202A  PHE*     3.5    26.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157A  ILE*     5.2     0.2    -      -       -      +
    194A  GLU      4.1     0.8    -      -       -      -
    195A  VAL*     1.3    72.9    -      -       -      +
    197A  LEU*     1.3    60.8    +      -       -      +
    198A  ARG*     3.8     9.8    +      -       -      +
    199A  GLU*     3.6    26.1    +      -       -      +
    200A  LYS*     3.5     3.5    +      -       -      -
    201A  GLU*     3.1    31.0    +      -       -      +
    203A  ASN*     3.4    30.5    -      -       -      +
----------------------------------------------------------
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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