Contacts of the strand formed by residues 203 - 208 (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 ASP 203 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179D  GLU*     3.0    18.4    +      -       +      +
    180D  LYS*     3.5    26.9    -      -       +      +
    181D  MET      2.9    24.7    +      -       -      +
    201D  GLY      3.8     1.4    +      -       -      +
    202D  ALA*     1.3    69.6    -      -       -      +
    204D  VAL*     1.3    58.5    +      -       -      +
    205D  THR*     5.0     0.3    +      -       -      -
    236D  LYS*     2.6    36.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 204 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181D  MET*     3.5    33.2    -      -       +      +
    183D  VAL*     3.9    17.0    -      -       +      -
    194D  GLY*     3.6    21.5    -      -       -      +
    198D  GLN*     3.7    17.6    -      -       +      +
    202D  ALA*     3.5    20.0    +      -       +      +
    203D  ASP*     1.3    77.7    +      -       -      +
    205D  THR*     1.3    68.4    +      -       -      +
    234D  GLY      4.1     3.2    +      -       -      +
    235D  PHE*     4.1    19.0    -      -       +      -
    236D  LYS*     3.1    31.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 205 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180D  LYS*     5.3     6.9    -      -       -      -
    181D  MET      3.2     7.6    +      -       -      -
    182D  VAL*     3.4    14.9    -      -       -      +
    183D  VAL*     2.8    24.1    +      -       -      +
    203D  ASP*     5.0     2.3    +      -       -      -
    204D  VAL*     1.3    79.7    -      -       -      +
    206D  ALA*     1.3    71.7    +      -       -      +
    207D  VAL*     4.6     6.1    -      -       +      -
    236D  LYS*     3.2    36.1    -      -       +      +
    237D  PHE      4.6     0.4    -      -       -      +
    238D  LYS*     4.3    24.9    -      -       +      +
    269D  ILE*     5.4     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 206 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183D  VAL*     3.1    26.9    -      -       +      +
    185D  GLY      4.4     2.0    -      -       -      +
    186D  ALA*     4.3    12.8    -      -       +      -
    190D  GLY      5.5     0.7    -      -       -      +
    205D  THR*     1.3    74.5    -      -       -      +
    207D  VAL*     1.3    61.6    -      -       -      +
    208D  GLU*     4.0     0.7    +      -       -      +
    235D  PHE*     4.0    19.5    -      -       +      -
    236D  LYS      2.9     7.7    +      -       -      -
    237D  PHE*     3.4    16.8    -      -       +      +
    238D  LYS*     2.8    25.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 207 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182D  VAL*     5.0     5.6    -      -       +      -
    183D  VAL      2.8    10.0    +      -       -      +
    184D  ILE*     3.8     0.7    -      -       -      -
    185D  GLY*     2.8    26.9    +      -       -      -
    186D  ALA      4.8     0.2    -      -       -      -
    205D  THR*     4.6     4.9    -      -       +      -
    206D  ALA*     1.3    73.9    -      -       -      +
    208D  GLU*     1.3    54.5    +      -       -      +
    238D  LYS*     3.4    22.4    -      -       +      -
    241D  THR*     3.4    44.9    -      -       +      +
    243D  VAL*     4.2    24.2    -      -       +      -
    258D  ILE*     4.4     6.7    -      -       +      -
    269D  ILE*     4.3    23.3    -      -       +      -
    481D  NAI      3.5     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 208 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186D  ALA*     2.7    39.4    +      -       +      -
    206D  ALA      4.0     0.8    +      -       -      +
    207D  VAL*     1.3    73.2    -      -       -      +
    209D  PHE*     1.3    56.5    +      -       -      +
    210D  LEU*     2.8    35.0    +      -       -      +
    212D  HIS      3.5    21.1    -      -       -      +
    238D  LYS      2.8     9.1    +      -       -      -
    239D  LEU*     3.3    13.4    -      -       +      -
    240D  ASN      2.7    32.4    +      -       -      -
    241D  THR      2.9     9.1    +      -       -      -
    481D  NAI      2.6    50.7    +      -       -      -
----------------------------------------------------------
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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