Contacts of the strand formed by residues 403 - 409 (chain D) 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 MET 403 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221D  GLU*     4.0    22.9    -      -       +      +
    222D  ILE*     3.7    27.5    -      -       +      +
    225D  ASN*     4.4    11.7    -      -       -      +
    385D  LYS*     3.8    30.5    -      -       +      -
    386D  PHE      3.3    16.8    -      -       -      +
    387D  PRO*     3.9     6.5    -      -       +      -
    388D  PHE*     3.8     6.4    -      -       -      -
    402D  GLY*     1.3    77.6    -      -       -      +
    404D  VAL*     1.3    65.2    +      -       -      +
    405D  LYS*     3.8    18.2    -      -       +      -
    419D  HIS      3.8     0.9    -      -       -      +
    420D  ILE*     3.5     1.2    -      -       -      -
    421D  LEU*     2.7    41.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 404 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    385D  LYS*     3.3     6.4    -      -       -      +
    386D  PHE      3.0    28.3    +      -       -      +
    388D  PHE*     3.8    22.9    -      -       +      -
    403D  MET*     1.3    80.0    -      -       -      +
    405D  LYS*     1.3    61.2    +      -       -      +
    406D  ILE*     4.2     8.1    -      -       +      -
    419D  HIS      3.4     8.1    -      -       -      +
    420D  ILE*     4.0     9.9    -      -       +      -
    428D  MET*     4.0    13.0    -      -       -      -
    458D  ALA*     3.8    29.4    -      -       +      +
    459D  PHE*     4.0    24.9    -      -       +      -
    462D  ALA*     3.5    15.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 405 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219D  ASP*     2.6    38.0    +      -       -      -
    221D  GLU*     2.6    33.9    +      -       -      +
    222D  ILE*     4.6     3.1    -      -       -      -
    371D  GLU*     2.8    20.9    +      -       -      +
    383D  VAL*     3.9    26.2    -      -       +      -
    384D  GLY      3.4     2.9    -      -       -      +
    385D  LYS*     4.1     4.5    -      -       +      -
    403D  MET*     3.8    20.4    -      -       +      -
    404D  VAL*     1.3    73.5    -      -       -      +
    406D  ILE*     1.3    64.8    +      -       -      +
    407D  LEU*     4.1    13.2    -      -       +      -
    417D  GLY      3.9     0.5    -      -       -      +
    418D  ALA*     3.5     4.0    -      -       -      -
    419D  HIS*     2.7    52.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 406 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    382D  LYS      3.7     0.5    -      -       -      +
    383D  VAL*     3.4     5.5    -      -       -      +
    384D  GLY      2.7    37.2    +      -       -      +
    404D  VAL*     4.2     2.7    -      -       +      -
    405D  LYS*     1.3    80.8    -      -       -      +
    407D  LEU*     1.3    67.9    +      -       -      +
    408D  GLY      4.1     0.2    +      -       -      -
    415D  VAL*     4.4     6.1    -      -       +      -
    417D  GLY      3.6     3.4    -      -       -      +
    418D  ALA*     3.9    14.4    -      -       +      -
    442D  CYS*     3.9    19.7    -      -       -      -
    459D  PHE*     3.7    21.1    -      -       +      -
    462D  ALA*     3.7    28.9    -      -       +      +
    463D  ASN*     3.4    41.3    -      -       -      +
    466D  ALA*     4.1     5.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 407 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219D  ASP*     5.0     0.7    -      -       -      +
    369D  LYS      3.3    25.8    -      -       -      +
    370D  SER      3.7     1.1    -      -       -      -
    371D  GLU*     3.6    43.7    -      -       +      +
    374D  LEU*     3.9    20.6    -      -       +      -
    381D  TYR*     4.3     4.0    -      -       +      -
    382D  LYS      3.4     2.7    -      -       -      +
    383D  VAL*     3.7    23.1    -      -       +      -
    405D  LYS*     4.1    11.9    -      -       +      -
    406D  ILE*     1.3    80.5    -      -       -      +
    408D  GLY*     1.3    51.2    +      -       -      +
    415D  VAL*     3.6     2.4    -      -       -      +
    416D  LEU*     2.6    33.7    +      -       -      -
    417D  GLY      2.9    18.8    +      -       -      +
    419D  HIS*     3.9    13.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 408 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381D  TYR*     3.2     6.0    -      -       -      -
    382D  LYS*     2.7    47.0    +      -       -      +
    406D  ILE      4.1     1.2    -      -       -      -
    407D  LEU*     1.3    74.6    -      -       -      +
    409D  GLN*     1.3    63.5    +      -       -      -
    414D  ARG      3.2     9.6    -      -       -      -
    416D  LEU*     4.2     1.1    -      -       -      -
    442D  CYS*     4.0    19.5    -      -       -      -
    466D  ALA*     5.2     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 409 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    379D  ILE*     4.3     1.6    -      -       +      -
    380D  GLU*     2.7    27.8    +      -       -      +
    382D  LYS*     3.8     2.4    -      -       -      -
    408D  GLY*     1.3    71.4    -      -       -      -
    410D  LYS*     1.3    72.7    +      -       -      +
    411D  SER*     2.6    37.7    +      -       -      +
    412D  THR*     3.0    29.5    +      -       +      +
    413D  ASP*     3.0    22.2    +      -       -      -
    414D  ARG*     2.8    16.4    +      -       +      +
    416D  LEU*     3.7    25.2    -      -       +      +
   2013D  SO4      2.9    35.8    +      -       -      +
----------------------------------------------------------
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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