Contacts of the strand formed by residues 173 - 184 (chain B) in PDB entry 3MEU


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 GLU 173 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165B  ARG*     3.5    43.2    +      -       -      +
    166B  VAL      3.6     1.3    -      -       -      +
    167B  LYS*     3.4    31.0    +      -       -      +
    171B  GLY      3.8     6.2    -      -       -      +
    172B  ASP*     1.3    83.2    +      -       -      +
    174B  GLN*     1.3    64.9    +      -       -      +
    209B  ARG*     2.8    40.3    +      -       -      -
    289B  GLU*     4.3     9.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 174 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164B  ALA      3.4     1.0    -      -       -      +
    165B  ARG*     4.3     1.8    -      -       -      -
    166B  VAL*     2.9    38.4    +      -       +      +
    172B  ASP*     4.6    10.0    -      -       -      +
    173B  GLU*     1.3    77.0    +      -       -      +
    175B  TRP*     1.3    81.8    +      -       -      +
    176B  ILE*     3.6    11.1    +      -       +      +
    243B  CYS*     3.6    27.8    -      -       -      +
    244B  PHE      2.9    27.9    +      -       -      -
    245B  TYR*     3.5    25.8    +      -       -      -
      3D  THR*     5.1     6.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 175 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163B  ALA*     3.4    23.8    -      -       +      -
    164B  ALA      3.3     9.0    -      -       -      -
    165B  ARG*     3.4    38.1    -      -       +      +
    174B  GLN*     1.3    84.6    +      -       -      +
    176B  ILE*     1.3    59.8    +      -       -      +
    208B  ARG      3.8    20.6    -      -       -      -
    209B  ARG      3.3    19.5    -      -       -      -
    211B  ILE*     3.6    24.5    -      -       +      -
    235B  LEU*     3.8    22.3    -      -       +      +
    243B  CYS*     3.5     1.7    -      -       -      -
    244B  PHE*     2.9    48.3    +      -       +      +
    288B  LYS*     3.7    22.9    -      -       +      -
    289B  GLU*     2.8    41.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 176 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163B  ALA*     3.4     4.2    -      -       -      -
    164B  ALA*     2.8    44.2    +      -       +      +
    166B  VAL*     3.9    23.6    -      -       +      -
    174B  GLN*     3.8    22.9    -      -       +      +
    175B  TRP*     1.3    79.4    -      -       -      +
    177B  LEU*     1.3    64.0    +      -       -      +
    178B  ALA*     3.6     3.1    +      -       +      -
    192B  VAL*     6.0     0.2    -      -       +      -
    194B  ASP*     3.6    44.2    -      -       +      +
    203B  HIS*     4.7     5.4    -      -       +      +
    242B  THR      3.6     8.3    -      -       -      +
    243B  CYS*     4.0     1.6    -      -       -      -
    244B  PHE*     3.8     6.7    -      -       -      -
      1D  ALA*     3.7    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 177 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  LEU*     3.6    42.2    -      -       +      -
    161B  LYS*     4.6     7.2    -      -       +      -
    162B  VAL      3.7     6.1    -      -       -      +
    176B  ILE*     1.3    72.7    -      -       -      +
    178B  ALA*     1.3    68.0    +      -       -      +
    194B  ASP*     4.0     6.1    -      -       -      +
    195B  ILE*     3.0    35.9    +      -       +      +
    213B  LEU*     3.6    31.4    -      -       +      -
    237B  LEU*     4.3     7.4    -      -       +      -
    242B  THR*     2.8    19.9    +      -       -      +
    244B  PHE*     3.7    13.4    -      -       +      -
    283B  TYR*     3.9    20.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 178 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161B  LYS*     3.5     7.4    -      -       -      +
    162B  VAL*     2.9    32.4    +      -       +      -
    164B  ALA*     4.0    16.2    -      -       +      -
    176B  ILE*     4.4     3.6    -      -       +      +
    177B  LEU*     1.3    78.0    -      -       -      +
    179B  GLU*     1.3    61.4    +      -       -      +
    192B  VAL*     3.9    22.4    -      -       +      -
    193B  ASP      3.2    20.9    -      -       -      +
    194B  ASP*     4.3     2.7    -      -       -      +
    195B  ILE*     4.0     6.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 179 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159B  GLY*     3.4    39.6    +      -       -      +
    160B  ASP      3.4     4.9    -      -       -      +
    161B  LYS*     2.9    25.8    +      -       +      +
    178B  ALA*     1.3    75.8    -      -       -      +
    180B  VAL*     1.3    69.0    +      -       -      +
    181B  VAL*     3.4     2.1    +      -       +      +
    192B  VAL*     3.3     3.4    -      -       -      -
    193B  ASP*     2.8    39.0    +      -       +      +
    195B  ILE*     4.3    12.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 180 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156B  ALA*     3.8    20.9    -      -       +      +
    157B  ARG      3.4    27.4    -      -       -      +
    158B  PRO*     3.5     2.1    -      -       +      +
    159B  GLY*     2.8    26.7    +      -       -      -
    160B  ASP      2.9    12.3    +      -       -      +
    162B  VAL*     3.6    32.1    -      -       +      -
    179B  GLU*     1.3    75.1    -      -       -      +
    181B  VAL*     1.3    62.1    +      -       -      +
    182B  SER      3.8    22.9    -      -       -      +
    190B  TYR*     4.0    15.3    -      -       +      -
    191B  GLU      3.8     4.3    -      -       -      +
    192B  VAL*     4.2     7.2    -      -       +      -
    210B  VAL*     4.9     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 181 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158B  PRO*     3.5    18.7    -      -       -      +
    179B  GLU      4.0     0.9    -      -       -      +
    180B  VAL*     1.3    79.0    -      -       -      +
    182B  SER*     1.3    63.7    +      -       -      +
    191B  GLU*     2.8    30.1    +      -       +      +
    192B  VAL      4.1     0.9    -      -       -      -
    193B  ASP*     3.3    46.4    -      -       +      +
    202B  ARG*     3.6    28.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 182 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158B  PRO*     4.5     7.6    -      -       -      -
    180B  VAL*     3.8     7.9    -      -       -      +
    181B  VAL*     1.3    85.6    -      -       -      +
    183B  TYR*     1.3    66.4    +      -       -      +
    184B  SER*     5.0     1.6    +      -       -      -
    190B  TYR*     3.3     8.8    -      -       -      -
    191B  GLU*     2.8    54.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 183 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155B  VAL*     3.6    41.2    -      -       +      +
    156B  ALA      4.8     2.7    -      -       -      +
    158B  PRO*     5.4     2.9    -      -       +      +
    182B  SER*     1.3    81.2    -      -       -      +
    184B  SER*     1.3    68.4    +      -       -      +
    185B  HIS*     3.5    36.7    +      -       +      -
    188B  ASN*     2.6    40.2    +      -       -      -
    189B  LYS      3.6    17.0    -      -       -      -
    190B  TYR*     4.2    14.6    -      +       +      -
    207B  ARG*     4.2    10.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with SER 184 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182B  SER*     5.0     2.0    +      -       -      -
    183B  TYR*     1.3    76.8    -      -       -      +
    185B  HIS*     1.3    54.3    +      -       -      +
    186B  ALA*     3.1    25.8    +      -       -      +
    187B  THR*     3.3    17.5    +      -       -      +
    188B  ASN*     2.7    36.9    +      -       -      -
    189B  LYS      3.0    11.1    +      -       -      -
----------------------------------------------------------
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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