Contacts of the strand formed by residues 80 - 86 (chain L) in PDB entry 4R2G


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 ASP 80 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30L  ASN*     4.5     9.6    -      -       -      +
     31L  SER*     2.9    37.9    +      -       -      -
     32L  ASN*     5.4     0.7    +      -       -      -
     77L  GLU      5.2     2.2    -      -       -      +
     78L  ASP      3.1    10.6    +      -       -      +
     79L  SER*     1.3    75.6    -      -       -      +
     81L  THR*     1.3    80.5    +      -       -      +
     82L  TYR*     3.9    18.2    -      -       +      +
     94L  GLN*     3.7     5.1    -      -       -      +
     95L  LEU*     3.0    29.7    +      -       -      +
     96L  LEU*     5.5     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 81 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30L  ASN      3.3     2.1    -      -       -      -
     31L  SER*     3.0    31.9    +      -       -      -
     80L  ASP*     1.3    86.7    +      -       -      +
     82L  TYR*     1.3    67.4    +      -       -      +
     83L  ILE*     4.4     3.6    -      -       +      +
     92L  GLU*     4.0    30.5    -      -       +      +
     93L  VAL      3.7    11.2    -      -       -      +
     94L  GLN*     3.5    22.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 82 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14L  LEU*     3.7    19.3    -      -       +      -
     28L  TRP*     3.8    22.0    -      -       +      -
     29L  LYS      3.4    13.9    -      -       -      +
     30L  ASN*     3.9    14.4    -      -       +      -
     36L  ILE*     3.7    15.5    -      -       +      -
     51L  LEU*     3.6    32.8    -      -       +      +
     69L  LEU*     4.8     5.2    -      -       +      -
     71L  ILE*     4.5     3.1    -      -       +      +
     78L  ASP*     2.6    37.0    +      -       -      +
     80L  ASP*     3.9    23.9    -      -       +      +
     81L  THR*     1.3    71.3    -      -       -      +
     83L  ILE*     1.3    64.2    +      -       -      +
     92L  GLU*     3.5     2.8    -      -       -      +
     93L  VAL*     2.9    38.5    +      -       -      +
     95L  LEU*     4.0    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 83 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27L  HIS      3.2     4.5    -      -       -      +
     28L  TRP*     3.2     4.5    -      -       -      -
     29L  LYS*     2.9    36.1    +      -       +      +
     30L  ASN      3.1    31.0    -      -       -      +
     31L  SER*     4.8     2.7    -      -       -      -
     33L  GLN*     3.5    17.3    -      -       -      +
     81L  THR*     4.4     4.5    -      -       +      +
     82L  TYR*     1.3    79.7    -      -       -      +
     84L  CYS*     1.3    62.1    +      -       -      +
     85L  GLU*     3.9     5.4    -      -       +      +
     90L  LYS*     4.3    24.7    -      -       +      -
     91L  GLU      3.3    17.7    -      -       -      +
     92L  GLU*     3.8    28.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 84 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16L  CYS*     2.0    50.4    -      -       +      -
     26L  PHE*     4.9     7.2    -      -       -      -
     27L  HIS      3.4     4.9    -      -       -      -
     28L  TRP*     3.6    35.6    -      -       +      -
     67L  PHE      4.5     0.4    -      -       -      -
     83L  ILE*     1.3    75.0    -      -       -      +
     85L  GLU*     1.3    58.6    +      -       -      +
     86L  VAL*     3.5     9.4    +      -       -      +
     89L  GLN*     3.5     9.2    -      -       -      +
     91L  GLU*     3.0    26.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 85 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279A  ASP*     4.3    13.4    -      -       -      +
    281A  ALA*     4.6     5.5    -      -       -      +
    282A  LYS*     6.0     1.0    -      -       -      -
    516A  NAG      4.7     5.0    -      -       -      +
     25L  GLN      4.2     1.2    -      -       -      +
     26L  PHE*     3.4     3.6    -      -       -      -
     27L  HIS*     2.9    51.8    +      -       +      +
     29L  LYS*     3.1    34.6    +      -       +      +
     83L  ILE*     3.9     5.4    -      -       +      +
     84L  CYS*     1.3    69.8    -      -       -      +
     86L  VAL*     1.3    58.8    +      -       -      +
     88L  ASP      5.3     0.4    -      -       -      -
     89L  GLN      3.2     6.5    -      -       -      -
     90L  LYS*     3.4    40.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 86 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16L  CYS*     3.8    28.0    -      -       -      -
     17L  THR      3.9    15.0    -      -       -      +
     18L  ALA*     3.8    24.4    -      -       +      +
     24L  ILE*     4.3    10.1    -      -       +      -
     25L  GLN      4.1    14.6    -      -       -      +
     26L  PHE*     4.0    10.5    -      -       +      -
     67L  PHE*     3.9    15.9    -      -       +      -
     84L  CYS      4.2     3.1    -      -       -      +
     85L  GLU*     1.3    73.3    -      -       -      +
     87L  GLU*     1.3    73.1    +      -       +      +
     88L  ASP      3.2     1.6    -      -       -      +
     89L  GLN*     3.2    22.5    +      -       +      +
----------------------------------------------------------
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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