Contacts of the strand formed by residues 170 - 174 (chain B) in PDB entry 3AG2


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 LEU 170 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365A  ILE*     4.1     1.1    -      -       -      -
    366A  VAL*     4.6     1.6    -      -       -      +
    163B  TRP*     3.8    21.8    -      -       +      -
    164B  ALA*     3.2     4.1    -      -       -      +
    165B  VAL*     2.9    40.7    +      -       +      +
    166B  PRO*     4.4     1.6    -      -       -      +
    168B  LEU*     3.8    27.8    -      -       +      +
    169B  GLY*     1.3    81.9    -      -       -      +
    171B  LYS*     1.3    63.9    +      -       -      +
    182B  THR*     3.9    21.1    -      -       +      +
    183B  THR      3.5    22.0    -      -       -      +
    184B  LEU*     3.6    39.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 171 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294A  THR*     3.7    18.7    -      -       +      +
    365A  ILE*     2.8    52.7    +      -       -      +
    366A  VAL*     3.1    19.8    +      -       -      +
    368A  HIS*     2.7    45.3    +      -       +      +
    369A  ASP      5.3     0.2    -      -       -      -
    370A  THR*     4.0     6.3    -      -       -      +
    162B  SER*     3.4    17.9    -      -       -      +
    163B  TRP      3.3     6.3    -      -       -      -
    164B  ALA*     3.9    12.3    -      -       +      -
    166B  PRO*     6.3     1.7    -      -       -      +
    170B  LEU*     1.3    75.9    -      -       -      +
    172B  THR*     1.3    63.3    +      -       -      +
    182B  THR*     5.8     0.2    +      -       -      -
    197B  SER*     3.6    28.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 172 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294A  THR      3.9     3.8    -      -       -      +
    296A  GLY*     6.0     1.1    -      -       -      -
    154B  VAL*     3.7    26.1    -      -       +      +
    162B  SER*     3.5     2.9    -      -       -      -
    163B  TRP*     2.9    30.2    +      -       -      -
    170B  LEU*     6.5     0.2    -      -       -      -
    171B  LYS*     1.3    75.8    +      -       -      +
    173B  ASP*     1.3    66.2    +      -       -      +
    180B  ASN*     3.4    37.0    -      -       +      +
    181B  GLN      4.7     3.8    +      -       -      +
    182B  THR*     3.5    27.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 173 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  TYR*     6.1     0.5    -      -       -      -
    232A  GLN*     5.1     3.6    +      -       -      +
    294A  THR*     2.9    38.6    +      -       -      +
    295A  VAL*     3.4    23.5    -      -       -      +
    368A  HIS*     4.8     5.0    +      -       -      -
    154B  VAL*     3.8     3.2    -      -       -      +
    160B  LEU*     6.1     1.6    -      -       +      +
    161B  HIS      3.7     3.6    -      -       -      +
    162B  SER*     2.8    31.5    +      -       -      -
    171B  LYS*     4.7     0.2    -      -       -      +
    172B  THR*     1.3    80.6    -      -       -      +
    174B  ALA*     1.4    59.8    +      -       -      +
    175B  ILE*     3.9    21.0    +      -       +      +
    180B  ASN*     3.0    23.1    +      -       -      +
    197B  SER      4.9     1.0    -      -       -      +
    198B  GLU*     4.7    12.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 174 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  GLY      4.6     0.2    -      -       -      +
    106B  TRP*     4.0     8.3    -      -       +      -
    154B  VAL*     3.6    17.3    -      -       +      -
    155B  SER*     3.3    23.8    -      -       -      +
    156B  SER*     3.4     8.3    -      -       -      -
    160B  LEU*     3.3     8.1    -      -       -      -
    161B  HIS*     2.8    50.9    +      -       +      +
    162B  SER      4.3     0.2    -      -       -      +
    172B  THR      3.6     0.4    +      -       -      -
    173B  ASP*     1.4    69.2    -      -       -      +
    175B  ILE*     1.3    61.0    +      -       -      +
----------------------------------------------------------
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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