Contacts of the strand formed by residues 175 - 183 (chain L) in PDB entry 1G9N


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 TYR 175 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179H  HIS*     5.2     0.2    -      -       -      -
    105L  ARG*     4.2     9.3    +      -       -      -
    107L  GLU*     2.5    49.6    +      -       -      +
    140L  ASN*     3.2     2.3    -      -       -      -
    141L  PHE*     2.8    48.7    +      -       +      +
    142L  TYR*     4.2     4.5    -      +       -      -
    143L  PRO      4.1     1.1    -      -       -      -
    144L  ARG*     3.4    50.5    -      -       +      -
    165L  VAL*     3.8    11.7    -      -       +      -
    166L  THR*     3.0    24.2    -      -       -      -
    167L  GLU*     3.9     1.3    -      -       -      -
    168L  GLN*     3.0    42.1    -      -       +      +
    174L  THR*     1.3    74.1    -      -       -      +
    176L  SER*     1.3    70.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 176 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179H  HIS*     2.7    37.5    +      -       -      -
    181H  PHE*     2.8    36.4    -      -       -      -
    138L  LEU      3.0    13.2    -      -       -      -
    139L  ASN*     3.8     1.3    -      -       -      -
    140L  ASN      3.4     5.9    +      -       -      -
    141L  PHE*     3.3     0.7    -      -       -      -
    165L  VAL*     3.5     3.4    -      -       -      +
    166L  THR*     3.2    26.5    +      -       -      -
    175L  TYR*     1.3    80.7    +      -       -      +
    177L  LEU*     1.3    60.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 177 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181H  PHE*     3.0    14.9    -      -       -      -
    138L  LEU*     3.2    42.3    +      -       +      -
    141L  PHE*     3.0    17.9    -      -       +      -
    146L  ALA*     3.3    22.9    -      -       +      +
    148L  VAL*     3.4    20.2    -      -       +      -
    163L  GLU*     3.2    47.1    -      -       +      +
    164L  SER      3.8     2.0    -      -       -      +
    165L  VAL*     3.7    25.4    -      -       +      +
    176L  SER*     1.3    73.1    -      -       -      +
    178L  SER*     1.3    74.4    +      -       -      +
    179L  SER      4.4     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 178 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181H  PHE*     3.3    38.4    -      -       -      +
    194H  SER*     4.5     6.1    +      -       -      -
    135L  VAL*     4.3     9.5    -      -       -      +
    136L  CYS      4.4     4.9    -      -       -      -
    137L  LEU*     4.8     2.0    -      -       -      +
    162L  GLN      3.2     6.1    -      -       -      +
    163L  GLU*     3.1    23.0    -      -       -      -
    164L  SER*     3.8     9.2    +      -       -      -
    177L  LEU*     1.3    85.4    -      -       -      +
    179L  SER*     1.3    59.4    +      -       -      +
    180L  THR*     4.2     9.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 179 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135L  VAL*     3.7     0.2    -      -       -      -
    136L  CYS*     2.9    37.4    +      -       -      -
    148L  VAL*     4.1    24.2    +      -       -      +
    150L  TRP*     3.0    33.4    +      -       -      -
    161L  SER*     4.5     4.9    -      -       -      -
    162L  GLN      3.9     3.4    -      -       -      -
    163L  GLU*     3.8    22.8    +      -       -      +
    177L  LEU*     4.4     1.4    -      -       -      +
    178L  SER*     1.3    74.8    -      -       -      +
    180L  THR*     1.3    61.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 180 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156H  LEU*     4.9     6.5    -      -       +      +
    194H  SER*     4.9     1.6    +      -       -      -
    133L  SER*     4.3    14.8    -      -       -      -
    134L  VAL      3.3    11.0    -      -       -      +
    135L  VAL*     3.8    21.1    -      -       +      +
    161L  SER*     2.9    22.3    -      -       -      -
    162L  GLN*     3.1    19.0    +      -       -      +
    178L  SER*     4.2     7.4    +      -       -      -
    179L  SER*     1.3    78.5    +      -       -      +
    181L  LEU*     1.3    60.9    +      -       -      +
    182L  THR*     3.5    20.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 181 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132L  ALA      3.8     0.7    -      -       -      +
    134L  VAL*     3.2    36.0    +      -       +      +
    150L  TRP*     3.6    54.8    -      -       +      +
    152L  VAL*     4.1    20.9    -      -       +      -
    157L  GLN      5.4     3.1    -      -       -      +
    159L  GLY      5.9     2.2    -      -       -      +
    160L  ASN*     3.2    23.6    -      -       +      +
    161L  SER*     3.9     2.2    -      -       -      -
    180L  THR*     1.3    70.2    -      -       -      +
    182L  THR*     1.3    60.4    +      -       -      +
    183L  LEU*     3.6    38.4    +      -       +      +
    194L  TYR*     4.6     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 182 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158H  LYS*     4.3    19.4    +      -       -      +
    186H  GLN*     5.7     0.9    +      -       -      -
    131L  THR*     4.6     8.5    -      -       +      -
    132L  ALA      3.2    11.4    -      -       -      +
    133L  SER*     3.5    17.7    +      -       -      +
    160L  ASN*     3.2    33.2    +      -       -      +
    180L  THR*     3.5    17.5    +      -       -      +
    181L  LEU*     1.3    69.2    -      -       -      +
    183L  LEU*     1.3    68.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 183 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131L  THR*     3.6     3.7    -      -       -      -
    132L  ALA*     2.7    26.8    +      -       +      +
    152L  VAL*     4.7     4.7    -      -       +      -
    160L  ASN*     5.2     8.5    -      -       +      -
    181L  LEU*     3.6    31.0    +      -       +      -
    182L  THR*     1.3    79.3    -      -       -      +
    184L  SER*     1.3    70.5    +      -       -      +
    187L  ASP*     3.2    25.4    -      -       -      +
    188L  TYR*     4.3    18.6    -      -       +      +
    191L  HIS*     4.4     7.9    -      -       +      +
    194L  TYR*     3.6    36.3    -      -       +      +
----------------------------------------------------------
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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