Contacts of the strand formed by residues 50 - 57 (chain A) in PDB entry 3CY2


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 GLY 50 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  SER*     3.2     2.9    -      -       -      -
     47A  GLY      2.8    34.4    +      -       -      +
     48A  GLY      3.2     1.0    -      -       -      -
     49A  PHE*     1.3    86.4    -      -       -      +
     51A  SER*     1.3    63.4    +      -       -      -
     68A  HIS      3.2     9.6    -      -       -      -
     69A  VAL*     4.9     0.4    -      -       -      -
     70A  GLU*     4.9     9.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  LEU*     3.9    17.7    -      -       -      +
     45A  GLY      3.4     5.8    -      -       -      -
     46A  SER*     3.6    10.6    -      -       -      -
     49A  PHE*     3.6     3.5    -      -       -      -
     50A  GLY*     1.3    76.8    +      -       -      -
     52A  VAL*     1.3    62.5    +      -       -      +
     53A  TYR*     4.1    13.9    +      -       -      -
     67A  LYS*     3.6     1.0    -      -       -      +
     68A  HIS*     2.8    40.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  LEU*     3.6     2.8    -      -       -      +
     44A  LEU*     2.7    32.5    +      -       +      -
     45A  GLY      2.8    32.1    +      -       -      +
     49A  PHE*     4.2     1.3    -      -       +      -
     51A  SER*     1.3    74.1    -      -       -      +
     53A  TYR*     1.3    60.2    +      -       -      +
     65A  ALA*     3.9    25.8    -      -       +      -
     66A  ILE      3.3    13.0    -      -       -      +
     67A  LYS*     4.2     5.2    -      -       +      -
    120A  LEU*     5.5     0.2    -      -       +      -
    501A  MB9      3.4    64.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  VAL*     4.0    17.5    -      -       +      -
     41A  GLY      3.7    11.7    -      -       -      -
     42A  PRO      3.4     5.2    -      -       -      +
     43A  LEU*     3.6    44.7    -      -       +      +
     44A  LEU*     3.8     5.7    -      -       -      +
     51A  SER*     4.1    11.9    -      -       -      -
     52A  VAL*     1.3    75.7    -      -       -      +
     54A  SER*     1.3    69.3    +      -       -      +
     65A  ALA*     3.3     7.1    -      -       -      +
     66A  ILE*     2.8    38.2    +      -       +      +
     68A  HIS*     3.6    35.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with SER 54 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  VAL*     3.9     1.2    -      -       -      -
     41A  GLY*     2.6    31.0    +      -       -      -
     42A  PRO*     2.8    31.1    +      -       -      +
     44A  LEU*     3.5    26.3    -      -       -      +
     53A  TYR*     1.3    77.5    -      -       -      +
     55A  GLY*     1.3    52.8    +      -       -      +
     64A  VAL      3.9     2.7    -      -       -      -
     66A  ILE*     4.5     0.4    -      -       -      +
    122A  ARG*     3.2    28.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  GLN      3.2    13.2    -      -       -      -
     41A  GLY      4.3     0.4    -      -       -      -
     53A  TYR      3.8     0.4    +      -       -      -
     54A  SER*     1.3    76.5    +      -       -      +
     56A  ILE*     1.3    62.9    +      -       -      +
     64A  VAL*     2.9    43.0    +      -       -      -
     66A  ILE*     4.1     8.5    -      -       -      -
    122A  ARG*     2.9    12.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 56 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  TYR*     3.4     5.3    -      -       -      -
     39A  GLN*     2.9    47.1    +      -       +      +
     55A  GLY*     1.3    80.5    -      -       -      +
     57A  ARG*     1.3    65.7    +      -       -      +
     58A  VAL*     3.3     1.9    +      -       -      -
     61A  ASN*     3.3    49.8    -      -       +      +
     62A  LEU      3.4     4.3    -      -       -      +
     63A  PRO*     4.9     1.6    -      -       +      -
     64A  VAL*     3.8     0.4    -      -       -      +
    122A  ARG*     4.3     9.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 57 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  GLN*     4.1    10.8    -      -       -      +
     38A  TYR*     3.5    40.1    +      -       +      -
     56A  ILE*     1.3    70.0    -      -       -      +
     58A  VAL*     1.3    61.4    +      -       -      +
     59A  SER*     3.1    25.4    +      -       -      +
     60A  ASP*     3.2    31.5    +      -       -      +
     61A  ASN*     2.8    31.4    +      -       -      -
     62A  LEU*     2.9    43.3    +      -       +      +
     64A  VAL*     4.2     3.7    -      -       +      +
    107A  LEU*     4.4    20.8    +      -       -      +
----------------------------------------------------------
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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