Contacts of the strand formed by residues 362 - 366 (chain A) in PDB entry 1CX4


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 SER 362 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300A  GLN*     4.1     5.5    +      -       -      -
    302A  ILE*     3.4    11.2    -      -       -      -
    303A  ALA*     3.7     3.1    -      -       -      +
    304A  GLN*     3.0    25.2    +      -       -      +
    321A  ILE*     3.3     8.0    -      -       -      +
    322A  THR*     2.8    45.5    +      -       -      +
    324A  LYS*     5.8     3.5    -      -       -      -
    361A  ALA*     1.3    75.9    -      -       -      +
    363A  ALA*     1.3    63.1    +      -       -      +
    364A  HIS*     4.1    14.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 363 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300A  GLN*     3.6     0.9    -      -       -      -
    301A  ILE*     2.7    34.1    +      -       +      -
    302A  ILE*     3.1    29.7    +      -       +      +
    319A  VAL*     3.9    10.8    -      -       +      -
    320A  ARG      3.3     6.1    -      -       -      -
    321A  ILE*     3.6    21.8    -      -       +      -
    348A  PHE*     3.9     9.4    -      -       +      -
    362A  SER*     1.3    76.4    -      -       -      +
    364A  HIS*     1.3    60.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 364 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298A  GLY*     3.4    24.9    -      -       -      +
    299A  GLU      3.2     5.2    -      -       -      +
    300A  GLN*     3.6    44.3    +      -       +      +
    301A  ILE*     4.3     5.4    -      -       -      +
    319A  VAL*     3.5     3.6    -      -       -      +
    320A  ARG*     2.9    40.9    +      -       +      +
    322A  THR*     4.5     8.7    +      -       -      +
    362A  SER*     4.1    14.9    -      -       -      -
    363A  ALA*     1.3    76.5    +      -       -      +
    365A  ALA*     1.3    65.2    +      -       -      +
    366A  ILE*     5.2     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 365 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295A  TYR*     3.9    12.8    -      -       +      -
    296A  ASN      3.6    20.2    -      -       -      +
    297A  ASP*     4.1     0.3    -      -       -      +
    298A  GLY*     2.9    25.8    +      -       -      -
    299A  GLU      3.0    10.1    +      -       -      +
    301A  ILE*     4.3     6.3    -      -       +      +
    318A  GLU      3.9     4.0    -      -       -      -
    364A  HIS*     1.3    75.7    -      -       -      +
    366A  ILE*     1.3    61.3    +      -       -      +
    367A  GLY      3.8     3.6    -      -       -      +
    369A  VAL*     3.4    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 366 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297A  ASP*     3.7     6.3    -      -       -      +
    317A  GLY*     4.9     0.9    -      -       -      -
    318A  GLU*     2.9    64.5    +      -       +      +
    320A  ARG*     3.7    38.4    -      -       +      -
    341A  ARG*     6.2     0.7    -      -       +      -
    364A  HIS*     4.6     0.7    -      -       +      +
    365A  ALA*     1.3    74.4    -      -       -      +
    367A  GLY*     1.3    65.2    +      -       -      +
    368A  THR      4.0     0.7    +      -       -      +
    369A  VAL*     4.1     0.9    -      -       -      +
----------------------------------------------------------
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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