Contacts of the strand formed by residues 151 - 161 (chain A) in PDB entry 3DB3


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 TRP 151 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  ASP*     3.5    25.6    -      -       +      -
    143A  ALA      3.5    11.9    -      -       -      -
    144A  ARG*     3.5    49.4    -      -       +      +
    149A  GLY      4.2     6.8    +      -       -      -
    150A  ALA*     1.3    73.9    -      -       -      +
    152A  PHE*     1.3    66.9    +      -       -      +
    153A  GLU*     5.0     1.0    -      -       -      +
    202A  ARG      4.0     7.2    -      -       -      -
    203A  ASP      3.4    34.8    -      -       -      -
    204A  VAL*     4.0     1.8    -      -       -      -
    205A  ARG*     3.2    57.5    -      -       +      +
    224A  MSE      3.8    20.1    -      -       -      +
    237A  PHE*     5.8     0.3    -      -       -      +
    238A  TRP*     2.8    36.7    +      -       -      +
    240A  ASP*     3.5    21.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  ASP*     3.3     6.2    -      -       -      -
    143A  ALA*     2.7    40.0    +      -       -      -
    145A  ASP*     3.9     9.2    -      -       +      -
    148A  MSE      3.9    12.1    -      -       +      -
    150A  ALA*     3.3    30.7    -      -       +      -
    151A  TRP*     1.3    76.5    -      -       -      +
    153A  GLU*     1.3    70.5    +      -       -      +
    154A  ALA*     3.4     1.4    +      -       -      +
    188A  TYR*     3.7    21.8    -      +       +      -
    191A  TYR*     4.0    17.7    -      +       +      -
    237A  PHE*     3.8    33.7    -      +       +      -
      9B  M3L      3.7    49.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 153 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  VAL      3.6     5.8    -      -       -      -
    142A  ASP*     3.5     9.4    +      -       -      +
    151A  TRP      5.0     1.2    -      -       -      +
    152A  PHE*     1.3    82.8    -      -       -      +
    154A  ALA*     1.3    60.3    +      -       -      +
    188A  TYR*     3.8     5.5    -      -       -      +
    189A  ASP*     3.1    28.3    +      -       +      +
    190A  ASP*     4.3    17.4    +      -       -      +
    207A  ARG*     3.4    33.4    -      -       -      +
    238A  TRP*     6.1     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 154 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140A  TYR*     3.4     1.2    -      -       -      -
    141A  VAL*     2.8    34.5    +      -       +      +
    143A  ALA*     3.8    18.6    -      -       +      -
    152A  PHE      4.0     0.7    -      -       -      +
    153A  GLU*     1.3    77.2    -      -       -      +
    155A  GLN*     1.3    62.0    +      -       -      +
    186A  VAL*     3.7    20.4    -      -       +      -
    187A  LYS      3.2    16.2    -      -       -      +
    188A  TYR*     4.0     4.7    -      -       +      -
    189A  ASP*     3.6     7.9    -      -       -      -
    207A  ARG*     3.1    10.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138A  ASN*     3.0    44.3    +      -       -      +
    139A  GLU      3.4    14.8    -      -       -      +
    140A  TYR*     3.7    31.7    +      -       +      -
    141A  VAL      4.6     0.2    -      -       -      +
    154A  ALA*     1.3    76.8    -      -       -      +
    156A  VAL*     1.3    68.5    +      -       -      +
    157A  VAL*     3.4     3.1    +      -       -      +
    186A  VAL*     3.4     5.1    -      -       -      -
    187A  LYS*     2.8    66.7    +      -       -      +
    189A  ASP*     4.3     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 156 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  TYR*     4.5     4.7    -      -       +      -
    136A  LYS      3.4    24.5    -      -       -      +
    137A  VAL*     4.0     3.3    -      -       -      +
    138A  ASN*     2.6    32.4    +      -       -      +
    139A  GLU      3.1    13.2    +      -       -      +
    141A  VAL*     4.1    24.7    -      -       +      -
    155A  GLN*     1.3    72.3    -      -       -      +
    157A  VAL*     1.3    60.5    +      -       -      +
    158A  ARG      3.7    20.2    -      -       -      +
    159A  VAL*     3.7    17.9    -      -       +      -
    184A  TYR*     4.1    20.2    -      -       +      -
    185A  HIS      3.7     5.4    -      -       -      +
    186A  VAL*     4.2     7.2    -      -       +      -
    204A  VAL*     5.0     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  VAL*     3.4    18.9    -      -       -      +
    138A  ASN*     5.7     3.1    -      -       -      +
    155A  GLN      3.6    13.0    -      -       -      +
    156A  VAL*     1.3    74.3    -      -       -      +
    158A  ARG*     1.3    63.9    +      -       +      +
    185A  HIS      2.7    19.1    +      -       -      +
    186A  VAL      4.1     1.8    -      -       -      -
    187A  LYS*     3.7    41.1    -      -       +      +
    196A  VAL*     4.2    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  TRP      3.3    27.1    +      -       -      -
    128A  ASP*     4.0    12.2    +      -       -      +
    130A  THR*     2.8    32.5    +      -       -      +
    137A  VAL*     3.8     9.4    -      -       +      -
    156A  VAL*     3.7     5.4    -      -       -      +
    157A  VAL*     1.3    81.9    -      -       +      +
    159A  VAL*     1.3    64.0    +      -       -      +
    160A  THR*     3.8     9.7    -      -       -      +
    185A  HIS*     2.8    54.0    +      -       +      +
    196A  VAL*     6.0     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  THR*     3.3     9.9    +      -       -      +
    131A  GLU      3.0    35.7    +      -       -      +
    132A  LEU*     5.3     0.9    -      -       -      -
    133A  GLY      4.5     9.9    -      -       -      +
    135A  TYR      3.8    17.0    -      -       -      +
    136A  LYS*     4.6     0.4    -      -       -      -
    137A  VAL*     3.9    20.5    -      -       +      +
    156A  VAL*     3.7    20.0    -      -       +      -
    158A  ARG*     1.3    79.6    -      -       -      +
    160A  THR*     1.3    61.5    -      -       -      +
    182A  VAL*     3.2    31.4    -      -       +      -
    183A  ILE      3.6     2.2    -      -       -      -
    184A  TYR*     3.8    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  TRP*     3.7    23.7    -      -       -      +
    129A  GLU*     3.4    14.1    -      -       -      +
    130A  THR      3.6    15.0    -      -       -      +
    131A  GLU*     4.0     4.3    -      -       -      +
    158A  ARG*     3.8    10.7    -      -       -      +
    159A  VAL*     1.3    80.1    -      -       -      +
    161A  ARG*     1.3    62.8    +      -       -      +
    182A  VAL*     3.2     9.0    -      -       -      +
    183A  ILE*     2.9    37.6    +      -       -      +
    185A  HIS*     2.9    33.3    +      -       +      +
    198A  GLN*     5.5     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 161 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  GLU*     2.9    31.2    +      -       +      +
    131A  GLU*     4.0    15.0    -      -       +      -
    160A  THR*     1.3    75.8    -      -       -      +
    162A  LYS*     1.3    66.1    +      -       -      +
    181A  ASP      4.8     0.2    -      -       -      -
    182A  VAL*     4.8     6.5    -      -       +      +
    183A  ILE*     5.1     0.2    -      -       -      -
----------------------------------------------------------
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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