Contacts of the strand formed by residues 206 - 216 (chain s) in PDB entry 3J7Y


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 VAL 206 (chain s).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205s  PRO*     1.3    81.2    -      -       -      +
    207s  HIS*     1.3    64.1    +      -       -      +
    233s  ILE      3.8     1.4    -      -       -      +
    234s  ASP*     3.4     1.7    -      -       -      -
    235s  ASP*     2.8    50.2    +      -       +      +
    237s  PRO*     3.8    14.4    -      -       +      -
    240s  GLN*     3.5    30.7    -      -       -      +
    283s  PHE      3.5     9.2    -      -       -      +
    284s  VAL      4.5     2.7    -      -       -      -
    298s  GLN*     3.9     4.3    -      -       -      +
    331s  SER      4.5     3.6    -      -       -      +
    334s  ALA*     4.3    11.2    -      -       +      -
    335s  TRP*     4.1    37.2    -      -       +      +
    338s  ALA*     5.4     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 207 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1675  THR*     3.3    40.6    +      -       +      +
    205s  PRO*     3.6    21.6    -      -       +      +
    206s  VAL*     1.3    82.5    +      -       -      +
    208s  PHE*     1.3    63.0    +      -       -      +
    233s  ILE      3.4     3.4    -      -       -      -
    234s  ASP*     2.7    36.5    +      -       +      +
    235s  ASP      4.6     2.0    -      -       -      -
    281s  HIS*     3.2    32.7    +      +       +      +
    283s  PHE*     2.8    47.6    +      +       +      +
    338s  ALA*     4.4     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 208 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207s  HIS*     1.3    74.2    -      -       -      +
    209s  TYR*     1.3    74.0    +      -       -      +
    210s  TRP*     3.7    37.7    -      +       +      -
    232s  GLN*     3.4     5.5    -      -       -      +
    233s  ILE*     2.8    36.2    +      -       -      -
    281s  HIS      3.3     5.6    +      -       -      -
    282s  ILE*     4.0    12.8    -      -       +      +
    333s  PHE*     3.9    18.6    -      +       -      -
    334s  ALA*     3.4    36.3    -      -       +      +
    337s  GLY*     3.5    24.5    -      -       -      -
    338s  ALA*     3.7    13.0    -      -       -      -
    341s  MET*     3.8    18.8    -      -       +      -
    377s  LEU*     4.0    14.8    -      -       +      -
    379s  LEU*     5.6     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 209 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83s  LEU*     4.3    16.8    +      -       +      -
     84s  THR*     5.1     0.6    +      -       -      -
     86s  MET      4.5     3.6    +      -       -      -
     88s  PHE*     5.5     0.9    -      -       -      -
     90s  LYS*     4.0    19.3    -      -       +      -
    208s  PHE*     1.3    88.7    -      -       -      +
    210s  TRP*     1.3    59.2    +      -       -      +
    211s  VAL*     4.5    13.9    -      -       +      +
    230s  ARG*     3.5    46.3    +      -       +      +
    231s  TYR      3.3    20.0    -      -       -      -
    232s  GLN*     4.6     3.6    -      -       +      -
    280s  ASN*     3.2    38.8    +      -       +      -
    281s  HIS      3.9    13.6    +      -       -      +
    282s  ILE*     3.9    26.1    -      -       +      +
    341s  MET*     4.9     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 210 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93s  VAL*     4.0     8.5    -      -       +      -
    109s  PHE*     3.1    40.2    +      -       +      -
    110s  THR*     4.6     1.1    -      -       -      -
    208s  PHE*     3.7    28.5    -      +       +      -
    209s  TYR*     1.3    74.8    -      -       -      +
    211s  VAL*     1.3    79.5    +      -       -      +
    212s  ARG*     3.8     2.6    -      -       +      +
    230s  ARG*     3.7     1.6    -      -       -      +
    231s  TYR*     2.8    72.2    +      +       +      +
    233s  ILE*     3.4    51.1    -      -       +      -
    333s  PHE*     3.5    27.4    -      +       -      -
    379s  LEU*     4.3    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 211 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209s  TYR*     4.5    14.6    -      -       +      +
    210s  TRP*     1.3    80.8    -      -       -      +
    212s  ARG*     1.3    63.1    +      -       -      +
    213s  GLY      4.5     3.4    -      -       -      +
    228s  ASP*     3.7    38.8    -      -       +      +
    229s  LEU      3.7    14.1    -      -       -      +
    230s  ARG*     4.3    14.8    -      -       +      +
    379s  LEU*     3.4     8.0    -      -       -      +
    380s  THR*     3.4    40.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 212 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108s  TYR*     2.9    56.0    +      -       +      +
    109s  PHE*     3.3    26.9    -      -       -      +
    111s  LYS*     3.6    33.0    -      -       -      +
    210s  TRP*     3.8     9.5    -      -       +      +
    211s  VAL*     1.3    73.4    -      -       -      +
    213s  GLY*     1.3    62.4    +      -       -      +
    229s  LEU*     3.4    15.9    +      -       -      +
    231s  TYR*     3.6    20.8    +      -       +      -
    261s  ILE*     5.4     4.9    -      -       -      +
    379s  LEU*     3.5    28.0    +      -       -      -
    381s  THR*     6.2     1.4    -      -       -      +
    384s  ASP*     2.7    27.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 213 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108s  TYR*     5.9     3.8    -      -       -      -
    211s  VAL*     4.1     2.8    +      -       -      +
    212s  ARG*     1.3    77.0    -      -       -      +
    214s  GLU*     1.3    64.6    +      -       -      -
    228s  ASP*     3.5     8.7    -      -       -      +
    229s  LEU*     3.1    28.4    +      -       -      +
    379s  LEU      4.1     6.1    +      -       -      -
    380s  THR*     4.8     1.0    -      -       -      +
    381s  THR*     3.6    19.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 214 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213s  GLY*     1.3    75.5    -      -       -      +
    215s  GLU*     1.3    62.3    +      -       -      +
    226s  ILE*     3.5    36.1    -      -       +      +
    227s  ASP      3.7     4.0    -      -       -      -
    228s  ASP*     4.4     5.8    -      -       +      +
    229s  LEU*     3.2    11.6    -      -       -      +
    381s  THR*     2.7    38.3    +      -       +      +
    382s  GLN*     5.7     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 215 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91s  TYR*     3.9     8.0    +      -       -      -
    214s  GLU*     1.3    79.9    -      -       -      +
    216s  ILE*     1.3    76.2    +      -       -      +
    217s  ILE*     4.8     5.4    -      -       +      +
    218s  PRO*     5.2     5.6    -      -       +      -
    225s  ARG      3.4     0.2    -      -       -      +
    226s  ILE*     4.7     1.1    -      -       -      -
    227s  ASP*     2.8    52.3    +      -       +      +
    229s  LEU*     3.7    23.5    -      -       +      +
    267s  LYS*     3.1    35.4    -      -       -      +
    268s  PRO*     5.5     1.4    -      -       -      +
    275s  LYS*     3.8    20.5    +      -       -      -
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Residues in contact with ILE 216 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215s  GLU*     1.3    79.4    -      -       -      +
    217s  ILE*     1.3    67.4    +      -       -      +
    218s  PRO*     3.3     6.3    -      -       +      +
    224s  GLY*     4.7    16.2    -      -       -      +
    225s  ARG      3.5     9.2    -      -       -      +
    226s  ILE*     5.1    13.5    -      -       +      -
----------------------------------------------------------
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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