Contacts of the strand formed by residues 209 - 221 (chain A) in PDB entry 1QFG


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 GLU 209 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201A  ALA      3.5    13.2    -      -       -      +
    202A  ASN*     3.9    16.7    +      -       -      +
    203A  ALA      3.8     1.1    -      -       -      +
    207A  GLY      3.9     6.7    +      -       -      +
    208A  SER*     1.3    78.0    -      -       -      +
    210A  GLU*     1.3    67.5    +      -       -      +
    211A  GLN*     4.1    13.4    +      -       +      +
    240A  GLU*     3.5    35.2    -      -       +      +
    242A  GLY*     3.3    23.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 210 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  LYS*     5.0     9.7    +      -       -      +
     83A  ALA      5.0     5.9    -      -       -      +
     85A  ASN*     4.8    17.3    +      -       -      +
    199A  ARG*     3.4    31.0    +      -       -      +
    200A  SER*     3.2     4.6    -      -       -      -
    201A  ALA*     2.9    33.7    +      -       -      +
    202A  ASN      5.1     1.6    -      -       -      -
    203A  ALA*     3.9    25.2    -      -       +      +
    209A  GLU*     1.3    78.4    -      -       -      +
    211A  GLN*     1.3    68.1    +      -       -      +
    240A  GLU*     3.2     6.1    -      -       -      +
    241A  THR      3.5    24.1    -      -       -      +
    242A  GLY*     4.1     3.0    -      -       -      -
    243A  TYR      5.3     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 211 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199A  ARG*     3.5     7.9    -      -       -      +
    200A  SER*     4.3    13.0    -      -       -      +
    209A  GLU*     4.1    16.6    +      -       +      -
    210A  GLU*     1.3    81.7    -      -       -      +
    212A  ARG*     1.3    63.9    +      -       -      +
    213A  TYR*     4.2    16.6    +      -       +      +
    238A  GLU*     3.5    18.9    -      -       -      +
    239A  PRO*     3.5    32.9    -      -       +      +
    240A  GLU*     2.7    42.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 212 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  LYS      5.4     2.4    +      -       -      -
     65A  SER*     6.1     1.8    -      -       -      -
     85A  ASN*     4.7    18.5    +      -       -      +
    120A  VAL*     3.6    22.0    -      -       -      +
    121A  ILE      4.7     1.2    -      -       -      -
    122A  ASP*     2.8    55.2    +      -       -      +
    123A  PRO*     4.9     2.8    -      -       -      +
    197A  LEU*     3.7    12.0    -      -       +      +
    198A  ALA*     3.4     5.9    -      -       -      -
    199A  ARG*     2.9    52.9    +      -       +      +
    211A  GLN*     1.3    76.3    -      -       -      +
    213A  TYR*     1.3    70.8    +      -       -      +
    214A  ALA*     4.2     1.6    -      -       +      -
    236A  GLN*     3.8    23.7    +      -       +      +
    237A  ASN      3.6     3.1    -      -       -      -
    238A  GLU*     2.9    32.9    +      -       +      +
    277A  ARG*     4.2     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 213 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197A  LEU      3.5     2.2    -      -       -      +
    198A  ALA*     3.7    27.6    -      -       +      -
    199A  ARG      4.2    10.9    +      -       -      -
    200A  SER*     5.2     2.8    -      -       -      -
    211A  GLN*     4.2    17.5    +      -       +      +
    212A  ARG*     1.3    82.4    -      -       -      +
    214A  ALA*     1.3    62.3    +      -       -      +
    235A  PHE      3.9     0.4    -      -       -      +
    236A  GLN*     3.1     6.6    -      -       -      +
    237A  ASN*     2.8    65.5    +      -       +      +
    239A  PRO*     4.3    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 214 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  ASP*     5.3     0.2    -      -       +      -
    125A  MET*     4.6     7.7    -      -       -      +
    195A  THR      4.0     0.2    -      -       -      +
    196A  GLY*     3.0     4.2    -      -       -      -
    197A  LEU*     2.6    56.9    +      -       +      +
    212A  ARG*     4.2     3.1    -      -       +      -
    213A  TYR*     1.3    78.2    -      -       -      +
    215A  ILE*     1.3    61.2    +      -       -      +
    234A  TYR*     4.2    12.1    -      -       +      +
    235A  PHE      3.4     7.9    -      -       -      +
    236A  GLN*     3.9    20.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 215 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  MET*     4.6     1.6    -      -       -      -
    178A  PHE*     3.6    28.0    -      -       +      -
    194A  LEU*     4.0    24.0    -      -       +      -
    195A  THR      3.1    16.8    -      -       -      +
    196A  GLY*     3.7     3.8    -      -       -      -
    214A  ALA*     1.3    71.4    -      -       -      +
    216A  ALA*     1.3    59.6    +      -       -      +
    217A  PRO*     3.4     6.6    -      -       +      +
    234A  TYR*     4.8     0.9    -      -       -      -
    235A  PHE*     2.9    50.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 216 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  MET*     3.5    28.6    -      -       +      +
    193A  ARG      3.7     2.3    -      -       -      +
    194A  LEU*     3.6     3.3    -      -       -      -
    195A  THR*     2.7    33.7    +      -       -      +
    215A  ILE*     1.3    70.5    -      -       -      +
    217A  PRO*     1.3    65.8    -      -       -      +
    218A  ALA*     3.7     1.8    +      -       +      +
    233A  SER      3.3    15.7    -      -       -      +
    234A  TYR*     3.8     9.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 217 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  ARG      3.6     0.7    -      -       -      +
    194A  LEU*     3.5    27.4    -      -       +      -
    215A  ILE*     3.4    13.9    -      -       +      +
    216A  ALA*     1.3    90.9    -      -       -      +
    218A  ALA*     1.3    58.0    +      -       -      +
    231A  PHE*     4.0     5.4    -      -       +      -
    232A  LEU      4.0     0.2    -      -       -      -
    233A  SER*     2.5    50.9    +      -       -      +
    235A  PHE*     4.0    16.2    -      -       +      -
   1014A  MYR      4.4    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 218 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154A  LYS      4.4     7.9    -      -       -      +
    156A  PRO*     3.9    21.5    -      -       +      -
    192A  TYR*     3.3     5.4    -      -       -      +
    193A  ARG*     2.8    40.3    +      -       +      +
    216A  ALA*     3.7     2.2    +      -       +      +
    217A  PRO*     1.3    72.8    -      -       -      +
    219A  PHE*     1.3    62.2    +      -       -      +
    231A  PHE*     3.1    13.2    -      -       -      +
    232A  LEU*     4.3    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 219 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  PRO*     4.2     0.4    -      -       -      -
    184A  LEU*     5.1    10.5    -      -       +      -
    190A  TYR*     4.1    33.9    -      +       +      -
    191A  SER      3.3    19.1    -      -       -      -
    192A  TYR*     4.1    12.8    -      -       +      -
    218A  ALA*     1.3    75.5    -      -       -      +
    220A  THR*     1.3    70.7    +      -       -      +
    221A  TRP*     4.7     7.9    -      -       +      -
    229A  PHE*     3.7     5.4    -      +       -      +
    230A  THR*     3.3     1.9    -      -       -      -
    231A  PHE*     2.6    55.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 220 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  ARG*     4.9     1.2    -      -       -      +
    156A  PRO*     3.4    22.6    +      -       -      +
    188A  GLY      5.9     0.7    -      -       -      +
    189A  VAL      3.4     4.0    -      -       -      +
    190A  TYR*     3.6     1.9    -      -       -      -
    191A  SER*     2.7    48.5    +      -       -      +
    219A  PHE*     1.3    77.7    -      -       -      +
    221A  TRP*     1.3    73.5    +      -       -      +
    222A  ARG*     3.8    28.9    +      -       +      +
    228A  ASN*     4.0     9.9    +      -       -      +
    229A  PHE      3.5     2.5    -      -       -      -
    230A  THR*     2.9    22.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 221 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189A  VAL*     3.2    19.4    -      -       +      +
    190A  TYR*     3.2    38.5    +      +       -      -
    219A  PHE*     4.7     8.7    -      +       +      -
    220A  THR*     1.3    78.3    -      -       -      +
    222A  ARG*     1.3    56.1    +      -       -      +
    223A  PRO*     3.5    32.3    -      -       +      +
    227A  THR*     5.6     3.4    -      -       +      -
    228A  ASN*     3.7     0.2    -      -       -      -
    229A  PHE*     2.9    59.2    +      +       +      +
    286A  PHE*     6.2     2.0    -      +       -      -
----------------------------------------------------------
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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