Contacts of the strand formed by residues 92 - 102 (chain S) in PDB entry 5GAG


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 TRP 92 (chain S).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1162A    G      4.1     5.6    -      -       -      +
   1163A    G      3.9    33.5    +      -       -      -
     22S  LEU      4.4     0.3    -      -       -      +
     23S  GLU*     3.7    19.8    -      -       -      +
     24S  LYS*     3.9    34.8    +      -       +      +
     66S  HIS*     5.2     6.7    -      -       +      -
     67S  GLY*     3.0    45.3    -      -       -      -
     68S  ARG*     3.5    32.8    -      -       +      +
     90S  ARG      4.5     6.5    -      -       -      -
     91S  GLN*     1.3    84.8    +      -       -      +
     93S  PHE*     1.3    60.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 93 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21S  ARG*     3.7    40.6    -      -       +      -
     22S  LEU      3.3    12.8    -      -       -      +
     24S  LYS*     4.5     3.2    -      -       -      +
     65S  ALA*     4.8     4.0    -      -       +      -
     66S  HIS*     4.0    12.9    +      -       -      +
     67S  GLY*     2.9    44.2    +      -       -      +
     68S  ARG      3.3    21.5    -      -       -      -
     69S  GLY*     3.4    25.4    -      -       -      -
     91S  GLN*     4.0     2.2    -      -       +      +
     92S  TRP*     1.3    77.3    -      -       -      +
     94S  THR*     1.3    68.4    +      -       -      +
     95S  ASP*     3.0    32.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 94 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22S  LEU*     2.9    36.6    +      -       -      +
     23S  GLU      3.9     4.0    +      -       -      -
     24S  LYS*     3.5     3.6    -      -       -      +
     25S  LEU*     3.2    42.5    +      -       +      -
     63S  VAL*     4.1    15.9    -      -       +      -
     65S  ALA      3.5     9.4    -      -       -      +
     66S  HIS*     3.0    36.7    +      -       +      -
     93S  PHE*     1.3    76.4    +      -       -      +
     95S  ASP*     1.3    68.6    +      -       -      +
     96S  VAL*     4.0     1.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 95 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19S  THR*     4.3     8.8    -      -       +      +
     20S  VAL      3.3    10.8    -      -       -      +
     21S  ARG*     3.2    38.3    +      -       -      +
     63S  VAL*     3.9     1.2    -      -       -      -
     64S  VAL*     3.1    39.1    +      -       +      +
     65S  ALA*     2.9    19.2    +      -       +      +
     93S  PHE*     3.0    26.8    -      -       +      -
     94S  THR*     1.3    73.9    -      -       -      +
     96S  VAL*     1.3    65.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 96 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18S  GLN      4.2     0.2    -      -       -      +
     19S  THR*     3.2     6.4    -      -       -      +
     20S  VAL*     2.9    52.2    +      -       +      +
     22S  LEU*     3.7    16.4    -      -       +      -
     25S  LEU*     4.6    10.5    -      -       +      -
     33S  VAL*     4.4    10.1    -      -       +      -
     35S  PHE*     4.9     2.9    -      -       +      -
     61S  ALA*     4.4     8.3    -      -       +      -
     62S  GLU      3.2    18.8    -      -       -      +
     63S  VAL*     3.8    20.4    -      -       +      -
     64S  VAL*     4.0     1.1    -      -       -      -
     94S  THR*     4.7     4.0    -      -       +      +
     95S  ASP*     1.3    80.4    -      -       -      +
     97S  LYS*     1.3    58.3    +      -       -      +
     98S  ILE*     3.9    12.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 97 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17S  GLY*     3.6    36.4    +      -       -      +
     18S  GLN      4.2     0.7    -      -       -      -
     19S  THR*     3.9    12.8    -      -       -      +
     62S  GLU*     3.0    36.2    +      -       +      +
     64S  VAL*     3.7    21.4    -      -       +      +
     96S  VAL*     1.3    72.1    -      -       -      +
     98S  ILE*     1.3    70.6    +      -       -      +
     99S  THR*     3.3    14.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 98 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5S  PHE*     5.3     7.2    -      -       +      -
     14S  VAL*     4.1    25.1    -      -       +      -
     15S  SER      3.7    17.3    -      -       -      +
     16S  GLU*     3.3     7.5    -      -       -      +
     17S  GLY*     2.7    31.2    +      -       -      -
     18S  GLN      3.3    16.6    +      -       -      +
     20S  VAL*     4.8     6.5    -      -       +      -
     35S  PHE*     5.3     1.3    -      -       +      -
     59S  ILE*     3.7    29.4    -      -       +      -
     60S  LYS      4.2     0.4    -      -       -      +
     61S  ALA*     3.6    22.4    -      -       +      -
     96S  VAL*     4.4    14.8    -      -       +      +
     97S  LYS*     1.3    75.5    -      -       -      +
     99S  THR*     1.3    60.6    +      -       -      +
    100S  GLY      4.0     7.9    -      -       -      +
    101S  ILE*     4.5     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 99 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16S  GLU*     4.1     9.1    -      -       -      +
     32S  THR*     5.6     1.4    -      -       -      +
     60S  LYS*     2.6    31.8    +      -       -      +
     61S  ALA*     3.7     3.6    -      -       -      -
     62S  GLU*     3.6    30.0    -      -       +      +
     97S  LYS*     3.3    23.3    +      -       +      +
     98S  ILE*     1.3    74.2    -      -       -      +
    100S  GLY*     1.3    57.0    +      -       -      +
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Residues in contact with GLY 100 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16S  GLU*     3.2    12.7    -      -       -      +
     58S  VAL      4.7     0.2    -      -       -      -
     59S  ILE*     3.3    10.1    -      -       -      +
     60S  LYS*     2.9    38.0    +      -       -      -
     98S  ILE*     3.6     2.8    -      -       -      +
     99S  THR*     1.3    79.5    -      -       -      +
    101S  ILE*     1.3    64.0    +      -       -      -
    102S  SER*     4.2     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 101 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1S  MET*     4.0    41.4    -      -       +      +
      2S  TYR      5.5     0.2    -      -       -      -
      3S  ALA*     3.8    35.0    -      -       +      +
     14S  VAL*     4.7     8.5    -      -       +      +
     15S  SER*     5.2     0.9    -      -       -      -
     16S  GLU*     3.0    28.0    +      -       +      +
     41S  ILE*     4.4    13.0    -      -       +      -
     58S  VAL      4.0     2.2    -      -       -      +
     59S  ILE*     3.8    28.0    -      -       +      -
     98S  ILE*     4.5     7.0    -      -       +      -
    100S  GLY*     1.3    73.2    -      -       -      -
    102S  SER*     1.3    69.5    +      -       -      +
    103S  ALA      3.8     2.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 102 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41S  ILE*     3.6     5.9    -      -       -      +
     56S  GLY      4.1     8.7    -      -       -      -
     57S  GLY*     3.0     7.3    -      -       -      -
     58S  VAL*     2.9    53.1    +      -       -      +
     60S  LYS*     5.8     4.5    -      -       -      +
    100S  GLY      5.5     0.5    -      -       -      -
    101S  ILE*     1.3    73.0    -      -       -      +
    103S  ALA*     1.3    59.4    +      -       -      +
----------------------------------------------------------
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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