Contacts of the strand formed by residues 381 - 387 (chain C) in PDB entry 1ZMD


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 TYR 381 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    371C  GLU*     2.6    50.3    +      -       +      +
    374C  LEU*     3.8    32.8    -      -       +      -
    375C  LYS*     3.2    30.2    -      -       +      -
    379C  ILE*     3.1    27.6    -      -       +      +
    380C  GLU*     1.3    78.7    -      -       -      +
    382C  LYS*     1.3    74.9    +      -       -      +
    383C  VAL*     3.7    12.9    -      -       +      +
    407C  LEU*     4.0    11.0    -      -       +      -
    408C  GLY      3.2    15.0    -      -       -      +
    410C  LYS*     4.0     4.4    -      -       -      +
    416C  LEU*     4.5     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 382 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381C  TYR*     1.3    79.0    -      -       -      +
    383C  VAL*     1.3    64.7    +      -       -      +
    406C  ILE      3.6     0.3    -      -       -      +
    407C  LEU*     3.4     6.6    -      -       -      -
    408C  GLY*     2.7    37.1    +      -       -      +
    409C  GLN      3.8    16.8    -      -       -      -
    410C  LYS*     4.0    27.6    +      -       +      +
    413C  ASP*     2.7    36.3    +      -       -      +
    466C  ALA*     3.3    27.1    +      -       -      +
    467C  SER      3.5    13.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 383 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    371C  GLU*     4.1     9.4    -      -       -      +
    381C  TYR*     3.7    26.2    -      -       +      +
    382C  LYS*     1.3    79.5    -      -       -      +
    384C  GLY*     1.3    62.7    +      -       -      +
    385C  LYS*     3.7    34.3    +      -       +      -
    405C  LYS*     4.3    13.5    -      -       +      -
    406C  ILE      3.4     7.2    -      -       -      +
    407C  LEU*     3.9     5.8    -      -       +      -
    465C  ALA      4.7     2.1    -      -       -      +
    466C  ALA*     4.2     8.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 384 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    383C  VAL*     1.3    75.6    -      -       -      +
    385C  LYS*     1.3    63.0    +      -       -      +
    404C  VAL      3.7     0.9    -      -       -      +
    405C  LYS*     3.5     3.1    -      -       -      -
    406C  ILE      2.8    34.5    +      -       -      -
    462C  ALA*     3.6    11.2    -      -       -      +
    465C  ALA*     4.0     5.6    -      -       -      -
    466C  ALA*     3.6    25.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 385 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221C  GLU*     2.6    41.5    +      -       -      +
    371C  GLU*     5.7     0.4    -      -       -      -
    383C  VAL*     3.7    24.2    -      -       +      -
    384C  GLY*     1.3    79.6    -      -       -      +
    386C  PHE*     1.3    64.5    +      -       -      +
    387C  PRO*     4.5     2.9    -      -       +      +
    403C  MET*     4.3    18.6    -      -       -      -
    404C  VAL      3.3     5.8    -      -       -      +
    405C  LYS*     4.3     7.2    -      -       +      +
    462C  ALA*     4.4     2.0    -      -       -      -
    465C  ALA*     4.3    12.3    -      -       -      +
    471C  SER*     5.3     1.4    -      -       -      -
    474C  PHE*     4.8     7.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 386 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    385C  LYS*     1.3    76.9    -      -       -      +
    387C  PRO*     1.3    79.0    -      -       -      +
    388C  PHE      3.9     0.2    +      -       -      -
    390C  ALA*     3.5    32.5    -      -       +      -
    391C  ASN*     3.9     6.5    -      -       -      -
    403C  MET*     3.3     3.9    -      -       -      +
    404C  VAL*     2.9    32.2    +      -       -      +
    457C  GLU      5.1     0.4    -      -       -      -
    458C  ALA*     3.6    41.6    -      -       +      +
    461C  GLU*     3.4    22.2    -      -       +      -
    462C  ALA*     3.9     9.6    -      -       +      +
    471C  SER*     3.0    31.2    -      -       -      -
    473C  ASN*     3.9    11.4    -      -       +      -
    474C  PHE*     3.7    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 387 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    385C  LYS*     4.5     1.1    -      -       +      +
    386C  PHE*     1.3   102.4    -      -       +      +
    388C  PHE*     1.3    65.4    +      -       -      +
    389C  ALA*     4.0    12.1    -      -       +      +
    390C  ALA*     3.0    19.6    +      -       +      +
    402C  GLY      3.4    11.9    -      -       -      +
    403C  MET*     3.8     4.7    -      -       +      -
    458C  ALA*     5.5     0.2    -      -       -      -
    474C  PHE*     3.9    48.2    -      -       +      -
----------------------------------------------------------
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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