Contacts of the strand formed by residues 254 - 260 (chain B) in PDB entry 1ZMC


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 254 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164B  THR*     3.0    40.6    -      -       +      +
    165B  ILE*     3.9    17.9    -      -       +      -
    246B  ALA*     4.6     2.7    -      -       +      -
    247B  THR      3.5    12.6    -      -       -      +
    248B  LYS*     4.4    10.8    -      -       +      -
    252B  GLY      4.0     6.3    -      -       -      +
    253B  LYS*     1.3    80.7    -      -       -      +
    255B  ASP*     1.3    71.9    +      -       -      +
    256B  VAL*     4.4     6.3    -      -       +      -
    269B  ILE      3.5     1.7    -      -       -      +
    270B  THR*     3.1     6.2    -      -       -      -
    271B  CYS*     2.9    47.5    +      -       -      +
    272B  ASP      3.9     8.5    -      -       -      +
    274B  LEU*     4.1    21.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 255 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246B  ALA*     3.1     4.5    -      -       -      +
    247B  THR*     2.8    50.4    +      -       -      +
    249B  LYS*     2.8    42.1    +      -       +      +
    253B  LYS      4.3     0.2    -      -       -      -
    254B  ILE*     1.3    71.2    -      -       -      +
    256B  VAL*     1.3    62.1    +      -       -      +
    257B  SER*     4.0     2.2    +      -       -      +
    268B  VAL*     3.7    22.4    -      -       +      +
    269B  ILE      3.5     1.6    -      -       -      -
    270B  THR*     2.9    15.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 256 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182B  VAL*     4.2    18.4    -      -       +      -
    184B  ILE*     5.3     0.2    -      -       +      -
    207B  VAL*     5.9     0.2    -      -       +      -
    243B  VAL*     3.5    33.0    -      -       +      -
    245B  GLY      3.7     4.3    -      -       -      +
    246B  ALA*     3.9     9.2    -      -       +      -
    254B  ILE*     4.4     3.4    -      -       +      -
    255B  ASP*     1.3    74.8    -      -       -      +
    257B  SER*     1.3    63.2    +      -       -      +
    258B  ILE*     3.7     9.8    +      -       +      +
    268B  VAL*     3.3     4.9    -      -       -      -
    269B  ILE*     2.7    50.7    +      -       +      +
    271B  CYS*     4.3    13.0    -      -       -      -
    274B  LEU*     4.0    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 257 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243B  VAL*     3.4     4.3    -      -       -      +
    244B  THR*     2.8    41.4    +      -       -      -
    245B  GLY*     2.7    20.9    +      -       -      +
    246B  ALA*     5.5     0.3    -      -       -      -
    255B  ASP*     4.0     3.0    +      -       -      +
    256B  VAL*     1.3    73.2    -      -       -      +
    258B  ILE*     1.3    65.7    +      -       -      +
    267B  GLU      3.7     6.1    -      -       -      -
    268B  VAL*     4.0    13.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 258 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207B  VAL*     4.3     8.5    -      -       +      -
    238B  LYS*     4.0    19.1    -      -       +      -
    241B  THR*     3.5    24.2    -      -       +      -
    242B  LYS      3.3     4.5    -      -       -      +
    243B  VAL*     4.0    23.1    -      -       +      -
    244B  THR      4.3     0.9    -      -       -      +
    256B  VAL*     4.2    13.5    -      -       +      +
    257B  SER*     1.3    82.0    -      -       -      +
    259B  GLU*     1.3    63.7    +      -       -      +
    265B  LYS      3.7     0.4    -      -       -      +
    266B  ALA*     3.3     4.0    -      -       -      +
    267B  GLU*     2.6    75.7    +      -       +      +
    268B  VAL      4.5     0.4    -      -       -      +
    269B  ILE*     4.2    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 259 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241B  THR*     3.1     9.8    -      -       -      +
    242B  LYS*     2.8    54.6    +      -       -      -
    244B  THR*     3.6    20.1    +      -       -      +
    258B  ILE*     1.3    79.6    -      -       -      +
    260B  ALA*     1.3    67.2    +      -       -      +
    263B  GLY*     4.4     1.1    -      -       -      -
    264B  GLY*     3.1    31.0    +      -       -      +
    265B  LYS*     3.7     5.8    -      -       -      -
    266B  ALA*     4.6    11.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 260 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240B  ASN      3.6     7.6    -      -       -      +
    241B  THR*     4.4     1.8    -      -       -      +
    242B  LYS*     4.0     4.6    -      -       -      -
    259B  GLU*     1.3    79.3    -      -       -      +
    261B  ALA*     1.3    60.3    +      -       -      +
    262B  SER*     4.2    10.5    -      -       -      +
    263B  GLY*     2.8    32.0    +      -       -      +
    264B  GLY      2.8    14.7    +      -       -      +
    265B  LYS*     4.1    21.7    +      -       +      +
----------------------------------------------------------
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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