Contacts of the strand formed by residues 135 - 145 (chain A) in PDB entry 5GGR


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 THR 135 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  SER*     4.4     0.7    +      -       -      -
    132A  SER*     2.2    54.9    +      -       -      +
    133A  GLY      4.4     3.8    -      -       -      +
    134A  GLY*     1.3    78.9    -      -       -      +
    136A  ALA*     1.3    54.1    +      -       -      +
    183A  THR*     3.9    14.2    -      -       +      -
    184A  VAL      2.9    28.1    +      -       -      -
    185A  PRO*     4.3     1.8    -      -       -      -
    186A  SER*     4.1     3.7    -      -       -      +
    114B  SER*     6.5     0.2    -      -       -      -
    116B  PHE*     4.8     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  PRO*     4.8     3.1    -      -       +      -
    127A  SER*     4.0    14.8    -      -       -      +
    132A  SER*     3.8     2.9    -      -       -      -
    135A  THR*     1.3    71.9    -      -       -      +
    137A  ALA*     1.3    59.6    +      -       -      +
    182A  VAL      3.9     0.2    -      -       -      +
    183A  THR*     3.5     1.3    -      -       -      -
    184A  VAL*     2.4    55.7    +      -       +      +
    186A  SER*     3.8     9.7    -      -       -      +
    189A  LEU*     3.6    37.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 137 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  PRO*     3.3    13.4    -      -       -      +
    127A  SER      3.8     5.4    +      -       -      +
    132A  SER*     4.3     3.4    +      -       -      -
    135A  THR      4.2     1.0    +      -       -      -
    136A  ALA*     1.3    72.5    -      -       -      +
    138A  LEU*     1.3    61.9    +      -       -      +
    182A  VAL      3.7     4.7    -      -       -      +
    183A  THR*     4.3    11.7    -      -       +      +
    116B  PHE*     3.8    32.6    -      -       +      -
    118B  PHE*     3.2    18.4    -      -       +      -
    135B  LEU*     3.9    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 138 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  LEU      3.9     9.6    -      -       -      +
    126A  PRO*     3.6    19.1    -      -       +      -
    136A  ALA      4.9     0.2    -      -       -      +
    137A  ALA*     1.3    73.7    -      -       -      +
    139A  GLY*     1.3    61.4    +      -       -      +
    154A  TRP*     3.4    30.2    -      -       +      -
    181A  VAL*     4.4     1.3    -      -       -      -
    182A  VAL*     3.0    40.2    +      -       +      +
    184A  VAL*     3.6    22.4    -      -       +      -
    189A  LEU*     3.8    14.1    -      -       +      -
    194A  TYR*     3.5    38.6    -      -       +      -
    211A  VAL*     3.9    15.0    -      -       +      +
    118B  PHE*     4.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 139 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  LEU*     2.9    40.9    +      -       -      +
    138A  LEU*     1.3    74.7    -      -       -      +
    140A  CYS*     1.3    70.5    +      -       -      -
    154A  TRP*     4.0     1.1    -      -       -      -
    180A  SER      3.2    10.3    -      -       -      -
    181A  VAL*     3.6    16.4    -      -       -      +
    211A  VAL*     4.0     2.6    -      -       -      +
    118B  PHE*     3.8     5.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 140 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  VAL*     4.6     6.1    -      -       +      -
    122A  PHE      3.5    11.0    -      -       -      +
    123A  PRO*     4.5     2.9    -      -       -      -
    124A  LEU*     4.1     2.9    -      -       -      +
    139A  GLY*     1.3    82.2    -      -       -      -
    141A  LEU*     1.3    62.0    +      -       -      +
    142A  VAL*     3.8     5.1    +      -       +      +
    154A  TRP*     3.4     6.1    -      -       +      -
    179A  SER*     3.4     2.2    -      -       -      -
    180A  SER*     2.5    43.8    +      -       -      +
    196A  CYS*     3.2    45.3    -      -       -      -
    209A  LYS*     4.7     4.7    -      -       -      -
    211A  VAL*     3.2    23.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 141 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  SER      3.5     1.7    -      -       -      +
    121A  VAL*     3.4     3.2    -      -       -      -
    122A  PHE*     2.7    50.6    +      -       +      +
    124A  LEU*     3.9    25.4    -      -       +      -
    140A  CYS*     1.3    71.3    -      -       -      +
    142A  VAL*     1.3    61.8    +      -       -      +
    143A  LYS*     3.1    34.8    +      -       +      +
    177A  SER*     5.6     2.7    -      -       -      -
    178A  LEU      3.4    12.1    -      -       -      +
    179A  SER*     3.4    23.8    -      -       -      +
    121B  SER*     5.9     0.2    -      -       -      -
    124B  GLN*     4.4     7.6    -      -       -      +
    131B  SER*     3.7    20.2    -      -       -      +
    133B  VAL*     4.5     8.5    -      -       +      -
    178B  THR*     5.1     6.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 142 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  PRO*     3.4    29.8    -      -       +      -
    120A  SER      3.4     4.0    -      -       -      +
    121A  VAL*     4.6     4.0    -      -       +      -
    140A  CYS*     4.3    10.1    -      -       +      +
    141A  LEU*     1.3    74.1    -      -       -      +
    143A  LYS*     1.3    59.0    +      -       -      +
    145A  TYR*     4.5     9.4    -      -       +      -
    150A  VAL*     4.6     9.6    -      -       +      -
    152A  VAL*     4.7     7.0    -      -       +      -
    177A  SER*     3.4     2.9    -      -       -      -
    178A  LEU*     2.9    59.2    +      -       +      +
    180A  SER*     5.4     1.3    -      -       -      +
    196A  CYS*     5.5     0.7    -      -       -      -
    198A  VAL*     3.8    35.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 143 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  PRO*     3.4     2.6    -      -       -      +
    120A  SER*     2.7    44.5    +      -       -      +
    122A  PHE*     3.7    19.3    -      -       +      -
    141A  LEU*     3.1    43.8    +      -       -      +
    142A  VAL*     1.3    75.0    -      -       -      +
    144A  ASP*     1.3    97.8    -      -       -      +
    145A  TYR*     3.5     2.5    -      -       -      -
    171A  GLN*     4.0     6.3    -      -       -      +
    176A  TYR      4.0     0.4    -      -       -      -
    177A  SER*     3.1    16.7    -      -       -      +
    124B  GLN*     3.4    21.3    -      -       -      +
    129B  THR*     5.8     4.3    -      -       +      -
    131B  SER*     3.2    11.7    +      -       -      +
    178B  THR*     5.5     1.0    -      -       -      +
    180B  THR*     5.2     8.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 144 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  LYS*     3.0    32.7    +      -       -      +
    118A  GLY      3.2     3.1    -      -       -      +
    120A  SER*     4.8     3.7    +      -       -      +
    143A  LYS*     1.3    94.2    -      -       -      +
    145A  TYR*     1.3    58.3    +      -       -      +
    171A  GLN*     3.0    17.5    -      -       -      +
    173A  SER*     3.6    16.6    +      -       -      -
    175A  LEU*     3.6    22.2    -      -       +      +
    176A  TYR      3.2     3.8    +      -       -      -
    177A  SER*     3.0    12.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  LYS      3.5     8.5    -      -       -      +
    119A  PRO*     3.4    34.3    -      -       +      -
    142A  VAL*     4.5     7.0    -      -       +      -
    143A  LYS      4.4     4.0    -      -       -      -
    144A  ASP*     1.3    80.9    -      -       -      +
    146A  PHE*     1.3    66.0    +      -       -      +
    147A  PRO      4.0    11.2    -      -       -      -
    148A  GLU*     3.5    15.4    -      -       +      +
    150A  VAL*     3.3    38.6    -      -       +      +
    168A  ALA*     3.2    24.9    -      -       -      +
    175A  LEU*     3.5     5.3    -      -       -      +
    176A  TYR*     2.9    60.4    +      -       +      -
    177A  SER*     3.8     8.7    -      -       -      -
    178A  LEU*     3.7     1.2    -      -       -      +
    200A  HIS*     3.8    19.3    -      +       -      -
----------------------------------------------------------
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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