Contacts of the strand formed by residues 207 - 217 (chain A) in PDB entry 5IVK


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 207 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  LYS*     2.8    21.2    -      -       -      +
    127A  ARG      3.6     3.4    -      -       -      -
    129A  VAL*     3.6    19.7    -      -       -      -
    159A  VAL*     3.8     7.1    -      -       -      +
    202A  CYS*     2.9    18.7    +      -       -      -
    203A  ALA*     3.8     6.2    -      -       -      -
    205A  PHE      3.4     2.4    +      -       -      -
    206A  GLY*     1.3    77.9    -      -       -      +
    208A  ASN*     1.3    60.2    +      -       -      -
    209A  PRO*     3.6     8.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 208 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  LYS*     3.7    18.3    +      -       +      +
    127A  ARG      2.7    24.3    +      -       -      +
    129A  VAL*     3.7     2.2    -      -       -      +
    202A  CYS*     4.2     1.8    -      -       -      -
    207A  GLY*     1.3    72.1    -      -       -      -
    209A  PRO*     1.3    63.6    -      -       -      +
    210A  ASP*     3.1    21.5    +      -       -      +
    211A  ASN*     2.8    54.1    +      -       +      +
    212A  ILE*     4.0     3.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 209 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  LYS*     5.3     2.7    -      -       +      -
    199A  LYS*     3.6    41.5    +      -       +      +
    202A  CYS*     3.7    16.8    -      -       -      -
    203A  ALA*     4.6    15.7    -      -       +      +
    207A  GLY      3.6     9.9    -      -       -      +
    208A  ASN*     1.3    86.5    -      -       -      +
    210A  ASP*     1.3    69.1    +      -       -      +
    211A  ASN      3.3     1.3    -      -       -      -
    212A  ILE*     3.9     6.7    -      -       +      +
    238A  HIS*     3.3    14.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 210 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199A  LYS*     4.1    10.0    +      -       -      -
    208A  ASN*     3.0    15.9    +      -       -      +
    209A  PRO*     1.3    91.2    -      -       -      +
    211A  ASN*     1.3    59.7    +      -       -      +
    238A  HIS*     3.2    26.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 211 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  PRO*     3.6    12.1    -      -       +      +
    129A  VAL      3.0    24.1    +      -       -      +
    208A  ASN*     2.8    32.8    +      -       +      +
    210A  ASP*     1.3    80.3    -      -       -      +
    212A  ILE*     1.3    57.4    +      -       -      +
    213A  THR*     5.3     0.2    +      -       -      -
    238A  HIS*     3.6     3.1    -      -       -      +
    239A  ARG*     3.0    34.2    +      -       -      +
    508A  ALA*     3.3     9.7    +      -       -      +
    509A  THR*     3.1    28.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 212 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  VAL*     3.3    13.9    -      -       +      +
    131A  VAL*     3.8    26.9    -      -       +      -
    195A  LEU*     5.4     2.7    -      -       +      +
    198A  ILE*     4.1    11.9    -      -       +      -
    199A  LYS*     4.0    24.5    -      -       +      +
    202A  CYS*     4.5     1.6    -      -       -      -
    208A  ASN      4.0     6.5    -      -       -      +
    209A  PRO*     3.9    21.3    -      -       +      +
    211A  ASN*     1.3    77.2    -      -       -      +
    213A  THR*     1.3    64.6    +      -       -      +
    214A  VAL*     4.5     2.2    -      -       +      -
    236A  LEU      3.6    17.5    -      -       -      +
    237A  PHE*     3.5    19.7    -      -       +      +
    238A  HIS*     2.8    36.9    +      -       -      +
    239A  ARG*     3.3     5.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 213 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  VAL      2.7    13.7    +      -       -      +
    130A  LEU*     3.4    10.3    -      -       +      -
    131A  VAL*     2.8    28.9    +      -       -      +
    211A  ASN      5.3     0.3    +      -       -      -
    212A  ILE*     1.3    72.0    -      -       -      +
    214A  VAL*     1.3    73.0    +      -       -      +
    215A  PHE*     4.8     3.4    -      -       +      -
    239A  ARG*     3.3    33.8    -      -       +      +
    241A  ILE*     4.2    23.3    -      -       +      -
    508A  ALA*     3.3    33.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 214 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131A  VAL*     3.5    11.7    -      -       +      +
    133A  ILE*     3.7    23.1    -      -       +      -
    195A  LEU*     4.1    20.2    -      -       +      -
    212A  ILE*     4.5     1.8    -      -       +      -
    213A  THR*     1.3    76.8    -      -       -      +
    215A  PHE*     1.3    64.2    +      -       -      +
    224A  THR*     3.4    25.6    -      -       +      +
    227A  MET*     5.1     0.4    -      -       +      -
    237A  PHE*     3.4    49.4    -      -       +      -
    239A  ARG      3.1     5.5    +      -       -      -
    240A  GLY*     3.3     5.5    -      -       -      -
    241A  ILE      3.1    21.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 215 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  LEU*     3.9    24.7    -      -       +      -
    131A  VAL      2.9    24.9    +      -       -      +
    132A  TYR*     3.3    47.0    -      +       +      -
    133A  ILE*     2.9    24.6    +      -       -      +
    153A  PHE*     4.0    26.9    -      +       -      -
    160A  LEU*     4.1     5.8    -      -       +      -
    213A  THR*     4.7     2.7    -      -       +      -
    214A  VAL*     1.3    77.4    -      -       -      +
    216A  GLY*     1.3    57.6    +      -       -      +
    224A  THR*     3.3     7.9    +      -       -      -
    241A  ILE*     3.4    31.2    -      -       +      +
    243A  MET*     3.9     9.4    -      -       -      -
    478A  PHE*     5.0     2.7    -      +       -      -
    479A  PHE*     4.2     6.7    -      +       -      -
    504A  TRP*     3.6    31.0    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLY 216 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  TYR*     3.5     9.2    -      -       -      -
    133A  ILE      3.2    17.7    -      -       -      -
    215A  PHE*     1.3    79.1    -      -       -      +
    217A  GLU*     1.3    60.0    +      -       -      -
    220A  GLY      3.5     8.1    -      -       -      -
    221A  ALA*     3.3    11.1    -      -       -      +
    224A  THR*     3.4     3.2    +      -       -      -
    241A  ILE      3.5     2.1    +      -       -      +
    243A  MET*     3.1    27.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 217 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  TYR*     3.3    19.6    +      -       -      +
    135A  GLY*     3.4     9.5    +      -       -      -
    148A  TYR*     5.4     0.3    +      -       -      -
    216A  GLY*     1.3    74.0    -      -       -      -
    218A  SER*     1.3    70.9    +      -       -      +
    219A  ALA      3.2     0.5    +      -       -      -
    220A  GLY*     2.9    15.4    +      -       -      -
    221A  ALA      3.5     0.8    -      -       -      +
    243A  MET*     3.1    15.5    -      -       +      +
    244A  SER*     4.7     1.7    -      -       -      -
    457A  TYR*     4.3     9.4    +      -       -      -
    471A  HIS*     3.3    24.4    -      -       -      -
    472A  THR*     3.4    22.7    +      -       -      +
    474A  GLU*     3.2    24.0    -      -       -      +
    475A  LEU*     3.7    27.3    -      -       +      +
    601A  DPF      4.3     0.9    -      -       -      +
----------------------------------------------------------
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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