Contacts of the strand formed by residues 834 - 841 (chain I) 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 GLN 834 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    762I  ASN*     4.1    18.4    -      -       +      +
    832I  HIS*     5.6     1.8    -      -       +      -
    833I  ILE*     1.3    81.4    -      -       -      +
    835I  GLU*     1.3    60.4    -      -       -      +
    836I  LEU*     4.1    18.9    -      -       +      +
    921I  PRO*     5.0     7.4    -      -       -      +
    924I  VAL*     4.5    19.2    -      -       -      +
   1052I  VAL      3.8     0.3    -      -       -      +
   1053I  TYR*     3.4     3.6    -      -       -      -
   1054I  LEU*     2.9    40.8    +      -       +      +
   1055I  ALA*     4.7     0.2    -      -       -      +
   1056I  VAL*     4.7    13.3    -      -       +      +
   1058I  ARG*     3.8    29.2    -      -       -      +
   1241I  ASP*     5.2     3.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 835 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    758I  ARG*     3.3    46.1    +      -       -      +
    762I  ASN*     4.6     0.4    +      -       -      -
    834I  GLN*     1.3    74.1    -      -       -      +
    836I  LEU*     1.3    65.7    +      -       -      +
    837I  ALA*     3.9     3.1    +      -       +      +
   1051I  LYS*     3.3    40.2    +      -       +      +
   1052I  VAL      3.8     4.3    -      -       -      +
   1053I  TYR*     3.4    31.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 836 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    834I  GLN*     4.1    27.6    -      -       +      +
    835I  GLU*     1.3    77.6    -      -       -      +
    837I  ALA*     1.3    63.2    +      -       -      +
    883I  LEU*     3.7    23.8    -      -       +      -
    918I  LEU*     4.0    18.7    -      -       +      +
    919I  ARG      4.1     8.5    -      -       -      +
    920I  VAL*     4.3     0.9    -      -       -      -
    921I  PRO*     3.7    31.9    -      -       +      -
   1050I  VAL      3.9     0.7    -      -       -      +
   1051I  LYS*     3.5     2.2    -      -       -      -
   1052I  VAL*     2.9    43.7    +      -       +      +
   1054I  LEU*     3.8    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 837 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    835I  GLU*     3.9     5.3    +      -       +      +
    836I  LEU*     1.3    76.1    -      -       -      +
    838I  CYS*     1.3    65.1    +      -       -      +
    839I  VAL*     5.0    10.5    -      -       +      -
    918I  LEU*     3.6    15.6    -      -       -      +
   1049I  ILE*     5.1     2.5    -      -       +      -
   1050I  VAL      3.8     3.1    -      -       -      -
   1051I  LYS*     4.4    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 838 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    837I  ALA*     1.3    77.7    -      -       -      +
    839I  VAL*     1.3    60.4    +      -       -      +
    850I  ILE*     5.8     2.5    -      -       -      +
    884I  VAL*     3.7    24.7    -      -       +      -
    886I  LYS*     3.7    30.3    -      -       -      -
    918I  LEU*     3.7    35.4    -      -       +      -
   1048I  LYS      4.1     0.5    -      -       -      +
   1049I  ILE*     3.6     1.2    -      -       -      +
   1050I  VAL*     2.9    41.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 839 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    837I  ALA*     5.0     6.7    -      -       +      -
    838I  CYS*     1.3    79.1    -      -       -      +
    840I  SER*     1.3    59.8    +      -       -      +
    841I  ARG*     3.4    46.9    -      -       +      +
    848I  GLU*     3.6     1.6    -      -       -      +
    850I  ILE*     5.4     0.4    -      -       -      -
    886I  LYS*     3.2    27.1    -      -       -      +
   1046I  VAL*     3.8    11.7    -      -       +      -
   1048I  LYS      3.8     4.0    -      -       -      -
   1049I  ILE*     3.8    27.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 840 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    839I  VAL*     1.3    73.1    -      -       -      +
    841I  ARG*     1.3    60.0    +      -       -      +
    848I  GLU*     3.2    29.8    +      -       -      +
    850I  ILE*     3.7    20.1    -      -       -      +
    886I  LYS*     4.5     0.4    -      -       -      -
   1046I  VAL*     3.7     2.8    -      -       -      +
   1047I  LEU*     2.5    42.5    +      -       -      +
   1048I  LYS*     2.9    31.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 841 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    839I  VAL*     3.4    36.0    -      -       +      +
    840I  SER*     1.3    73.5    -      -       -      +
    842I  ASP*     1.3    61.6    +      -       -      +
    843I  THR*     3.6    22.7    +      -       +      +
    847I  PRO*     4.4     0.3    -      -       -      +
    848I  GLU*     2.8    45.5    +      -       -      +
    886I  LYS*     6.0     2.0    -      -       -      +
   1045I  GLY      3.6     8.5    -      -       -      +
   1046I  VAL*     4.3     5.6    -      -       +      +
   1047I  LEU*     4.6     1.1    -      -       -      -
    256J  ASP*     2.8    54.8    +      -       -      +
    257J  GLY      5.5     1.8    -      -       -      +
----------------------------------------------------------
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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