Contacts of the strand formed by residues 195 - 201 (chain A) in PDB entry 3DLX


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 195 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  GOL      4.8     4.6    +      -       -      -
    158A  PRO*     3.3    28.3    -      -       -      +
    161A  TYR*     6.5     0.2    -      -       +      -
    191A  GLU*     3.2     2.6    -      -       -      -
    192A  PHE      2.9    31.4    +      -       -      +
    193A  ASN      3.2     3.7    +      -       -      +
    194A  GLY*     1.3    78.5    -      -       -      +
    196A  HIS*     1.3    73.1    +      -       -      +
    197A  PHE*     3.3    27.3    -      -       +      -
    431A  SER      3.7    14.6    +      -       -      -
    432A  SER*     6.1     0.2    -      -       -      -
    433A  ALA*     5.0    14.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158A  PRO*     4.1     6.2    -      -       -      +
    161A  TYR*     3.6    42.7    +      -       +      +
    189A  VAL*     3.6    22.7    -      -       +      -
    190A  ARG      3.7     1.1    -      -       -      -
    191A  GLU*     4.0    23.6    -      -       +      +
    194A  GLY      4.9     2.9    +      -       -      -
    195A  GLN*     1.3    86.4    +      -       -      +
    197A  PHE*     1.3    66.9    +      -       -      +
    161C  TYR*     2.6    29.5    +      -       -      -
    196C  HIS*     3.3    41.3    +      +       -      -
----------------------------------------------------------
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Residues in contact with PHE 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  TYR*     3.9    16.8    -      -       +      -
    157A  THR      3.4     7.9    -      -       -      +
    158A  PRO*     3.4    40.6    -      -       +      -
    161A  TYR*     5.2     0.4    -      -       -      -
    189A  VAL*     3.3     6.8    -      -       -      +
    190A  ARG      2.9    32.5    +      -       -      +
    192A  PHE*     3.6    34.3    -      +       +      -
    195A  GLN*     3.3    44.9    -      -       +      -
    196A  HIS*     1.3    73.1    -      -       -      +
    198A  ILE*     1.3    66.3    +      -       -      +
    151B  GLY      4.1     3.6    -      -       -      -
    153B  PRO*     3.3    35.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  TYR*     3.3     5.0    -      -       -      -
    157A  THR*     2.8    44.9    +      -       +      +
    159A  THR      3.3    22.7    -      -       -      +
    160A  GLY      4.0     8.1    -      -       -      -
    161A  TYR*     4.4     9.9    -      -       +      +
    165A  VAL*     4.0    12.6    -      -       +      -
    166A  GLN*     3.4    31.6    -      -       +      -
    187A  ARG*     3.9    19.3    -      -       +      -
    188A  GLU      3.2     5.8    -      -       -      +
    189A  VAL*     3.7     8.5    -      -       +      -
    197A  PHE*     1.3    80.7    -      -       -      +
    199A  LEU*     1.3    61.7    +      -       -      +
    200A  GLU*     3.7    23.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 199 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154A  ALA*     3.9    27.4    -      -       +      -
    155A  PHE      3.6    13.2    -      -       -      +
    156A  TYR*     3.4    43.1    -      -       +      +
    187A  ARG*     3.6    23.6    -      -       -      +
    188A  GLU*     3.0    40.1    +      -       +      +
    198A  ILE*     1.3    71.8    -      -       -      +
    200A  GLU*     1.3    59.5    +      -       -      +
    201A  GLU*     5.0     7.5    -      -       +      +
    156B  TYR*     4.1     7.9    -      -       +      -
    190B  ARG*     3.8    19.7    -      -       -      +
    192B  PHE*     4.5     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 200 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  THR*     6.0     0.2    -      -       -      -
    137A  PRO*     5.3     0.5    -      -       -      +
    140A  THR*     3.4    26.8    +      -       +      +
    144A  ARG*     3.7    26.7    +      -       -      -
    154A  ALA*     3.2     4.3    -      -       -      +
    155A  PHE*     2.9    53.5    +      -       +      +
    157A  THR*     3.6    20.1    -      -       +      +
    159A  THR      4.9     0.3    -      -       -      +
    165A  VAL*     4.0     9.2    -      -       -      +
    187A  ARG*     3.5    31.1    +      -       -      -
    198A  ILE*     3.7    16.7    -      -       +      +
    199A  LEU*     1.3    73.0    -      -       -      +
    201A  GLU*     1.3    63.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  ARG*     2.7    43.1    +      -       -      +
    153A  PRO      3.4    10.6    -      -       -      +
    154A  ALA*     4.4     7.0    -      -       +      -
    155A  PHE*     5.1     1.1    -      -       -      -
    199A  LEU*     5.0     7.0    -      -       +      +
    200A  GLU*     1.3    77.3    +      -       -      +
    202A  ALA*     1.3    66.8    -      -       -      +
    192B  PHE*     3.5    25.9    -      -       +      -
    193B  ASN*     4.6     8.7    -      -       -      +
----------------------------------------------------------
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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