Contacts of the strand formed by residues 5 - 12 (chain B) 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 ILE 5 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  PRO*     1.3    82.8    -      -       -      +
      6B  ASP*     1.3    66.5    +      -       -      +
     31B  LYS*     5.9     1.3    -      -       -      +
     33B  VAL*     4.5    11.4    -      -       +      -
    113B  VAL*     5.8     3.6    -      -       +      -
    115B  VAL*     5.2     4.0    -      -       +      -
    137B  GLN*     3.5    18.4    -      -       +      +
    138B  VAL      3.1     3.4    +      -       -      +
    139B  ILE*     3.2    49.6    -      -       +      -
    140B  ASP*     3.0    24.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 6 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  ILE*     1.3    81.5    -      -       -      +
      7B  ALA*     1.3    67.5    +      -       -      +
     31B  LYS*     3.1    44.6    +      -       -      +
     33B  VAL*     4.3     5.9    -      -       -      +
    139B  ILE*     4.7     2.2    -      -       -      -
    140B  ASP*     3.0    21.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 7 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  ASP*     1.3    80.2    -      -       -      +
      8B  ASP*     1.3    63.1    +      -       -      +
      9B  VAL      4.0     8.3    -      -       -      +
     10B  THR*     4.2     9.2    -      -       -      +
     31B  LYS*     3.3    24.5    -      -       +      +
     33B  VAL*     3.4    25.1    -      -       +      -
    139B  ILE*     4.6     0.7    -      -       +      -
    140B  ASP      2.9     6.3    +      -       -      +
    141B  THR*     3.1    22.0    -      -       -      -
    142B  LYS*     3.2     8.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 8 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  ALA*     1.3    74.4    -      -       -      +
      9B  VAL*     1.3    61.0    +      -       -      +
     29B  GLY      4.8     2.6    -      -       -      +
     30B  PHE*     3.5    32.2    -      -       +      -
     31B  LYS*     2.8    41.4    +      -       -      +
    141B  THR*     3.1     1.0    +      -       -      -
    142B  LYS*     3.1    33.1    -      -       +      +
    143B  ASN*     2.9    32.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 9 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  ALA*     4.0     0.8    -      -       -      +
      8B  ASP*     1.3    85.9    -      -       -      +
     10B  THR*     1.3    71.0    +      -       -      +
     11B  VAL*     4.0     3.4    -      -       +      +
     25B  ALA*     4.5    14.6    -      -       +      -
     30B  PHE*     3.6    35.7    -      -       +      -
     31B  LYS      3.2     3.2    +      -       -      +
     32B  THR*     3.5    10.1    -      -       +      +
     33B  VAL*     3.1    24.9    +      -       -      +
    141B  THR*     3.8     0.2    -      -       -      -
    143B  ASN*     3.6     8.1    -      -       +      +
    145B  LEU*     4.5     8.5    -      -       +      -
    339B  VAL*     5.0     2.9    -      -       +      -
    342B  MET*     3.8    39.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 10 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  ALA*     4.2     0.7    -      -       -      +
      9B  VAL*     1.3    73.3    -      -       -      +
     11B  VAL*     1.3    56.9    +      -       -      +
     12B  ILE*     3.9     1.5    +      -       +      -
     33B  VAL*     3.0    29.1    -      -       +      +
     35B  ILE*     3.6    25.8    -      -       +      -
    127B  VAL*     4.0    18.8    -      -       +      -
    139B  ILE*     3.3     7.7    -      -       +      +
    141B  THR*     3.1    33.3    -      -       -      +
    143B  ASN      3.0     7.6    +      -       -      -
    144B  ILE*     3.4     5.1    -      -       -      +
    145B  LEU      2.7    30.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 11 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  VAL*     4.0     3.5    -      -       +      -
     10B  THR*     1.3    73.8    -      -       -      +
     12B  ILE*     1.3    62.1    +      -       -      +
     13B  GLY      3.5     5.8    +      -       -      +
     18B  GLY*     3.6    31.2    -      -       -      +
     22B  ALA*     3.8    20.6    -      -       +      +
     32B  THR*     4.7     2.9    -      -       +      -
     33B  VAL      3.0    14.5    +      -       -      +
     34B  CYS*     3.6    20.6    -      -       +      -
     35B  ILE*     3.0    25.8    +      -       -      +
    145B  LEU*     3.2    29.2    -      -       +      +
    147B  ALA*     4.1     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 12 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  THR*     4.6     2.5    -      -       +      +
     11B  VAL*     1.3    71.2    -      -       -      +
     13B  GLY*     1.3    58.2    +      -       -      +
     35B  ILE*     3.8     9.6    -      -       +      +
    119B  GLY*     4.4     7.4    -      -       -      -
    121B  ILE*     4.0    13.2    -      -       +      -
    127B  VAL*     4.2    18.6    -      -       +      -
    144B  ILE*     3.8    25.8    -      -       +      -
    145B  LEU      2.9     9.8    +      -       -      +
    146B  ILE*     4.5     8.7    -      -       +      -
    147B  ALA      2.9    28.2    +      -       -      -
    148B  THR*     3.3     9.7    +      -       +      +
    287B  LEU*     3.8    22.0    -      -       +      -
    480B  FAD      3.4    42.2    -      -       +      +
----------------------------------------------------------
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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