Contacts of the strand formed by residues 199 - 207 (chain G) in PDB entry 6ALG


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 199 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28G  LEU      4.3     0.2    -      -       -      +
     30G  PRO*     3.5     6.9    -      -       -      +
     31G  LEU*     2.8    56.9    +      -       +      +
     32G  GLU      3.7     2.3    -      -       -      +
     33G  ARG*     3.5    28.6    -      -       -      +
     34G  GLY      3.9     4.7    +      -       -      -
     36G  GLY*     4.7     6.8    +      -       -      -
    187G  VAL*     4.9    15.4    -      -       +      +
    188G  GLU*     3.3    10.4    +      -       -      +
    189G  ALA*     4.7     0.2    -      -       -      -
    190G  ALA*     4.7     4.0    -      -       -      -
    197G  ASP*     5.1     3.5    -      -       -      +
    198G  LEU*     1.3    84.5    -      -       -      +
    200G  LYS*     1.3    61.5    +      -       -      +
    201G  LEU      4.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 200 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27G  THR*     3.8    17.0    -      -       +      -
     28G  LEU      3.7     2.7    -      -       -      -
     29G  GLU*     3.5    42.0    -      -       +      +
    186G  ASN      3.3     7.8    -      -       -      +
    187G  VAL*     3.4     2.1    -      -       -      -
    188G  GLU*     2.5    59.1    +      -       +      +
    189G  ALA      4.0    16.9    +      -       -      +
    190G  ALA*     4.6     2.7    -      -       +      +
    199G  ASP*     1.3    72.5    -      -       -      +
    201G  LEU*     1.3    58.9    +      -       -      +
    202G  VAL*     3.8     9.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 201 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27G  THR*     3.3     5.9    -      -       -      +
     28G  LEU*     2.6    64.5    +      -       +      +
     31G  LEU*     3.8    13.4    -      -       +      +
     36G  GLY      4.0     4.5    -      -       -      +
     39G  LEU*     4.1     9.2    -      -       +      -
     40G  GLY      4.0    18.8    -      -       -      +
    185G  TYR*     3.7    37.0    -      -       +      -
    186G  ASN      3.7     1.8    -      -       -      +
    187G  VAL*     3.8    16.4    -      -       +      -
    199G  ASP      4.0     1.4    -      -       -      -
    200G  LYS*     1.3    71.9    -      -       -      +
    202G  VAL*     1.3    62.3    +      -       -      +
    203G  ILE*     3.8    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 202 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25G  LYS*     4.4    26.7    -      -       +      +
     26G  VAL      3.5    13.0    -      -       -      +
     27G  THR*     4.1    17.9    -      -       +      +
    184G  ALA      3.7     0.2    -      -       -      +
    185G  TYR*     3.3     3.8    -      -       -      -
    186G  ASN*     3.1    40.9    +      -       +      +
    188G  GLU*     4.1    20.4    -      -       -      +
    200G  LYS*     4.2     9.6    -      -       +      +
    201G  LEU*     1.3    78.0    -      -       -      +
    203G  ILE*     1.3    61.4    +      -       -      +
    204G  GLU*     3.5     3.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 203 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24G  ALA      4.1     0.3    -      -       -      +
     25G  LYS*     3.7     1.0    -      -       -      -
     26G  VAL*     3.1    41.7    +      -       +      +
     28G  LEU*     4.0     8.5    -      -       +      -
     39G  LEU      5.0     0.2    -      -       -      +
     40G  GLY*     5.3     1.6    -      -       -      +
     43G  LEU*     3.8    19.3    -      -       +      -
     44G  ARG      6.1     0.4    -      -       -      +
     47G  LEU*     4.6    13.2    -      -       +      -
    183G  ILE*     4.1    23.6    -      -       +      -
    184G  ALA      3.7     3.8    -      -       -      +
    185G  TYR*     4.1    10.3    -      -       +      -
    201G  LEU*     3.8    34.7    +      -       +      -
    202G  VAL*     1.3    70.3    -      -       -      +
    204G  GLU*     1.3    58.3    +      -       -      +
    205G  MET*     3.5    12.8    +      -       +      +
    217G  ILE*     3.8    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 204 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23G  HIS*     4.4    16.7    +      -       +      -
     24G  ALA      3.9     4.0    -      -       -      +
     25G  LYS*     3.7    31.7    -      -       +      +
    182G  ARG*     3.8    21.9    +      -       -      +
    183G  ILE*     3.7     1.2    -      -       -      -
    184G  ALA*     2.6    47.9    +      -       +      +
    186G  ASN*     5.0     9.3    +      -       -      +
    202G  VAL*     3.5     4.6    +      -       +      +
    203G  ILE*     1.3    70.3    -      -       -      +
    205G  MET*     1.3    65.0    +      -       -      +
   1090I  ASN*     5.6     2.7    -      -       -      +
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Residues in contact with MET 205 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23G  HIS*     3.2    22.2    -      -       -      +
     24G  ALA      3.3    23.7    +      -       -      +
     26G  VAL*     4.8    15.9    -      -       +      -
     47G  LEU*     4.1    20.9    -      -       +      -
    180G  VAL*     4.7     7.2    -      -       +      -
    182G  ARG*     3.3     6.7    -      -       -      -
    183G  ILE*     3.6    18.8    -      -       +      +
    203G  ILE*     3.5     8.9    +      -       +      +
    204G  GLU*     1.3    76.4    -      -       -      +
    206G  GLU*     1.3    60.5    +      -       -      +
    207G  THR*     3.5    21.5    -      -       -      +
    211G  ILE      5.6     1.1    -      -       -      +
    213G  PRO*     4.1    40.4    -      -       +      +
    216G  ALA*     4.3    11.9    -      -       +      -
    217G  ILE*     5.1     3.1    -      -       +      +
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Residues in contact with GLU 206 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22G  THR*     3.7    20.8    +      -       -      -
     23G  HIS*     3.1    29.4    +      -       -      +
    180G  VAL*     3.4     1.6    -      -       -      -
    181G  GLU*     2.6    49.8    +      -       +      +
    182G  ARG*     2.6    58.3    +      -       +      +
    183G  ILE*     4.5     0.4    -      -       -      +
    205G  MET*     1.3    73.5    -      -       -      +
    207G  THR*     1.3    58.3    +      -       -      +
   1133I  LYS*     4.9    11.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 207 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22G  THR*     2.9    39.7    +      -       -      +
     23G  HIS*     4.0     1.9    -      -       -      +
    179G  PRO*     3.4    20.4    -      -       +      +
    180G  VAL*     4.1     6.9    -      -       +      +
    181G  GLU*     5.4     2.0    -      -       -      -
    205G  MET*     3.5    27.4    -      -       -      +
    206G  GLU*     1.3    79.9    -      -       -      +
    208G  ASN*     1.3    68.1    +      -       -      +
    209G  GLY*     3.5    11.2    -      -       -      +
    210G  THR      4.0     0.4    -      -       -      +
    211G  ILE*     3.8    31.9    +      -       +      +
    213G  PRO*     5.6     1.2    -      -       -      +
----------------------------------------------------------
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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