Contacts of the strand formed by residues 254 - 260 (chain H) 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 254 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164H  THR*     3.4    43.5    -      -       -      +
    165H  ILE*     3.7    15.5    -      -       +      -
    246H  ALA*     4.5     4.9    -      -       +      -
    247H  THR      3.6    10.8    -      -       -      +
    248H  LYS*     4.4     9.0    -      -       +      -
    252H  GLY      4.2     6.7    -      -       -      +
    253H  LYS*     1.3    78.3    -      -       -      +
    255H  ASP*     1.3    72.6    +      -       -      +
    256H  VAL*     3.9    12.5    +      -       +      -
    269H  ILE      3.6     1.6    -      -       -      +
    270H  THR*     3.2     4.7    -      -       -      -
    271H  CYS*     2.9    47.8    +      -       -      +
    272H  ASP      4.1     4.9    -      -       -      +
    273H  VAL*     4.4     0.7    -      -       -      -
    274H  LEU*     3.9    22.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 255 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246H  ALA*     3.1     5.5    -      -       -      +
    247H  THR*     3.0    45.9    +      -       +      +
    249H  LYS*     2.8    36.5    +      -       -      +
    253H  LYS      4.3     0.2    -      -       -      -
    254H  ILE*     1.3    71.4    -      -       -      +
    256H  VAL*     1.3    61.7    +      -       -      +
    257H  SER*     4.0     2.7    +      -       -      +
    268H  VAL*     3.7    20.3    -      -       +      +
    269H  ILE      3.7     1.6    -      -       -      -
    270H  THR*     2.7    27.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 256 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182H  VAL*     4.2    19.3    -      -       +      -
    184H  ILE*     4.9     0.9    -      -       +      -
    207H  VAL*     5.5     0.4    -      -       +      -
    243H  VAL*     3.9    27.6    -      -       +      -
    245H  GLY      3.6     3.1    -      -       -      +
    246H  ALA*     4.3     2.0    -      -       +      +
    254H  ILE*     4.2    12.8    -      -       +      -
    255H  ASP*     1.3    76.3    -      -       -      +
    257H  SER*     1.3    62.8    +      -       -      +
    258H  ILE*     3.8    15.2    +      -       +      +
    268H  VAL*     3.3     4.1    -      -       -      +
    269H  ILE*     2.8    45.7    +      -       +      +
    271H  CYS*     4.3     6.7    -      -       -      -
    274H  LEU*     3.7    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 257 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243H  VAL*     3.4     3.3    -      -       -      +
    244H  THR*     2.8    45.8    +      -       -      -
    245H  GLY      2.7    21.5    +      -       -      +
    255H  ASP*     4.0     3.0    +      -       -      +
    256H  VAL*     1.3    72.7    -      -       -      +
    258H  ILE*     1.3    59.0    +      -       -      +
    267H  GLU      3.5     7.6    -      -       -      -
    268H  VAL*     3.8    16.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 258 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207H  VAL*     4.2     8.1    -      -       +      -
    238H  LYS*     4.3    11.7    -      -       +      -
    241H  THR*     3.6    18.8    -      -       +      -
    242H  LYS      3.2    13.2    -      -       -      +
    243H  VAL*     3.9    17.9    -      -       +      -
    244H  THR*     4.2     2.4    +      -       -      +
    256H  VAL*     4.1    13.5    -      -       +      +
    257H  SER*     1.3    81.2    -      -       -      +
    259H  GLU*     1.3    66.3    +      -       -      +
    266H  ALA*     3.3     5.4    -      -       -      +
    267H  GLU*     2.8    74.4    +      -       +      +
    269H  ILE*     3.7    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 259 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241H  THR*     3.1     8.8    -      -       -      +
    242H  LYS*     2.8    36.7    +      -       +      +
    244H  THR*     3.5    25.9    -      -       +      +
    258H  ILE*     1.3    82.2    -      -       -      +
    260H  ALA*     1.3    66.2    +      -       -      +
    263H  GLY*     4.1     5.7    -      -       -      -
    264H  GLY*     3.3    30.2    +      -       -      +
    265H  LYS      3.7     4.9    -      -       -      -
    266H  ALA*     4.0    14.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 260 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240H  ASN      3.7     8.7    -      -       -      +
    241H  THR*     4.5     2.5    -      -       -      +
    242H  LYS*     4.4     2.9    -      -       -      +
    259H  GLU*     1.3    78.5    -      -       -      +
    261H  ALA*     1.3    61.2    +      -       -      +
    262H  SER*     4.2     7.6    -      -       -      +
    263H  GLY*     2.8    39.3    +      -       -      +
    264H  GLY      2.8    12.8    +      -       -      +
    265H  LYS*     4.1    16.9    +      -       +      +
----------------------------------------------------------
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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