Contacts of the strand formed by residues 44 - 48 (chain L) in PDB entry 1SY6


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 LYS 44 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109H  TRP*     5.0     0.9    -      -       -      -
     35L  TYR*     3.2     6.0    -      -       -      -
     36L  GLN*     2.6    52.0    +      -       +      +
     38L  LYS*     6.0     6.7    -      -       -      +
     41L  THR*     5.4     8.1    -      -       -      -
     42L  SER      3.8     9.6    -      -       -      +
     43L  PRO*     1.3    79.1    -      -       -      +
     45L  ARG*     1.3    68.8    +      -       -      +
     46L  TRP*     3.1    23.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 45 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103H  HIS*     2.5    42.4    +      -       -      -
    105H  CYS*     3.9    17.8    -      -       +      -
    106H  LEU      3.6    17.7    -      -       -      +
    107H  ASP*     3.7    39.0    +      -       -      +
    108H  TYR*     5.0     7.9    +      -       -      -
    109H  TRP*     4.5     3.4    -      -       -      +
     34L  TRP      4.4     0.2    -      -       -      -
     35L  TYR*     3.6    16.6    -      -       +      -
     43L  PRO      4.3     0.4    +      -       -      -
     44L  LYS*     1.3    72.0    -      -       -      +
     46L  TRP*     1.3    67.1    +      -       -      +
     47L  ILE      5.1     0.9    -      -       -      +
     48L  TYR*     3.4    28.3    +      -       +      -
     54L  ALA*     3.6    36.2    -      -       +      +
     55L  SER*     5.2     3.6    -      -       -      +
     57L  VAL*     4.5     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 46 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34L  TRP*     3.0    19.6    +      -       +      +
     35L  TYR      4.4     0.4    -      -       -      -
     36L  GLN*     3.3    51.8    -      -       +      +
     38L  LYS*     6.1     0.7    -      -       -      -
     44L  LYS*     3.1    22.4    +      -       +      +
     45L  ARG*     1.3    82.9    -      -       -      +
     47L  ILE*     1.3    75.4    +      -       +      +
     53L  LEU*     3.8     0.9    -      -       -      -
     54L  ALA*     3.0    27.1    +      -       -      -
     56L  GLY      5.4     1.8    -      -       -      -
     57L  VAL*     3.5    34.6    -      -       +      +
     58L  PRO*     3.8    24.5    -      -       +      -
     61L  PHE*     3.3    38.2    -      +       -      -
     72L  LEU*     4.7     1.8    -      -       +      -
     80L  GLU      5.9     0.4    -      -       -      -
     85L  TYR*     3.9    16.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 47 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105H  CYS*     5.7     0.2    -      -       -      +
     33L  ASN*     3.3     4.0    -      -       -      +
     34L  TRP*     2.8    43.7    +      -       +      +
     45L  ARG*     5.5     1.4    -      -       -      +
     46L  TRP*     1.3    92.5    +      -       +      +
     48L  TYR*     1.3    63.3    +      -       -      +
     50L  THR*     3.5    30.3    -      -       -      +
     51L  SER*     4.0     6.7    -      -       -      -
     52L  LYS      3.3    10.5    -      -       -      +
     53L  LEU*     3.8    16.4    -      -       +      -
     61L  PHE*     4.7     4.3    -      -       +      -
     62L  ARG      3.9     6.3    -      -       -      +
     63L  GLY*     3.7    22.7    -      -       -      +
     72L  LEU*     3.9    28.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 48 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102H  ASP      5.3     0.2    -      -       -      -
    103H  HIS*     3.4    64.3    +      +       +      +
    105H  CYS*     3.6    13.5    -      -       +      -
     33L  ASN*     3.1     8.5    -      -       -      +
     45L  ARG*     3.4    31.5    +      -       +      +
     47L  ILE*     1.3    76.5    -      -       -      +
     49L  ASP*     1.3    75.6    +      -       +      +
     50L  THR      3.1     2.7    -      -       -      -
     52L  LYS*     2.8    73.3    +      -       +      +
     53L  LEU      3.9     5.5    +      -       -      -
     54L  ALA*     3.9    17.7    -      -       +      -
----------------------------------------------------------
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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