Contacts of the strand formed by residues 54 - 60 (chain A) in PDB entry 1YIT


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 PRO 54 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  ILE*     3.9    20.6    -      -       +      -
     46A  GLU      3.1    12.6    -      -       -      +
     47A  HIS*     4.6     1.3    -      -       -      -
     51A  ARG*     3.8    13.8    +      -       -      -
     53A  ALA*     1.3    91.0    -      -       +      +
     55A  VAL*     1.3    61.0    +      -       -      +
     70A  ALA*     3.6    13.5    +      -       -      +
    159A  VAL*     5.9     0.2    -      -       -      +
    160A  ALA*     3.4    30.2    -      -       +      +
    161A  GLY*     4.2     5.6    -      -       -      +
     52Z  THR      3.7    11.7    -      -       -      +
     53Z  GLY*     3.9    17.5    -      -       -      +
     54Z  ILE*     4.0    10.8    -      -       +      -
     65Z  THR*     4.4     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  LYS*     5.1     0.7    -      -       +      -
     27A  LEU*     3.5    18.4    -      -       +      -
     45A  ILE*     3.6     2.2    -      -       -      -
     46A  GLU*     2.8    54.3    +      -       +      +
     47A  HIS      4.4     1.3    -      -       -      +
     48A  ASP*     4.1    23.3    -      -       +      +
     51A  ARG*     5.5     0.2    -      -       -      +
     54A  PRO*     1.3    75.6    -      -       -      +
     56A  ALA*     1.3    59.9    +      -       -      +
     57A  ALA      4.0     0.2    +      -       -      -
     67A  LEU*     3.4    41.7    -      -       +      -
     68A  ILE      2.9    24.2    -      -       -      +
     69A  LEU*     5.2     0.2    -      -       -      +
     70A  ALA*     3.9     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 56 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  VAL*     4.5     9.6    -      -       +      -
     44A  ASP      3.4     4.5    -      -       -      +
     45A  ILE*     3.6    21.5    -      -       +      -
     55A  VAL*     1.3    72.6    -      -       -      +
     57A  ALA*     1.3    62.1    +      -       -      +
     58A  VAL*     3.5     3.6    +      -       +      -
     67A  LEU*     3.4     3.1    -      -       -      -
     68A  ILE*     2.8    54.4    +      -       +      +
     70A  ALA*     3.6    10.8    -      -       +      +
     74A  VAL*     4.6     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 57 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  VAL*     3.5     4.2    -      -       -      -
     43A  VAL*     2.7    32.7    +      -       +      -
     44A  ASP*     2.8    24.5    +      -       +      +
     46A  GLU*     4.0     9.6    -      -       -      +
     55A  VAL      4.0     0.6    +      -       -      -
     56A  ALA*     1.3    70.7    -      -       -      +
     58A  VAL*     1.3    55.6    +      -       -      +
     65A  ARG*     3.7    30.7    -      -       -      +
     66A  ARG      4.0     1.6    -      -       -      -
     67A  LEU*     3.5    22.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 58 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  GLY*     4.1     6.7    -      -       -      +
     41A  THR      3.7    18.4    -      -       -      +
     42A  VAL*     4.2    12.1    -      -       +      -
     56A  ALA      3.5    10.3    +      -       -      +
     57A  ALA*     1.3    80.4    -      -       -      +
     59A  GLU*     1.3    68.5    +      -       -      +
     60A  PHE*     3.7    29.4    -      -       +      -
     64A  ASP      3.5     3.1    -      -       -      +
     65A  ARG*     3.4     5.8    -      -       -      +
     66A  ARG      3.0    34.6    +      -       -      +
     68A  ILE*     4.1    19.7    -      -       +      -
     80A  LEU*     4.1    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 59 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  GLY*     2.8     3.6    -      -       -      -
     41A  THR*     2.7    39.5    +      -       -      +
     43A  VAL*     3.1    32.9    -      -       +      +
     58A  VAL*     1.3    73.3    -      -       -      +
     60A  PHE*     1.3    65.5    +      -       -      +
     63A  GLY*     5.8     4.8    -      -       -      +
     64A  ASP      3.7     4.3    -      -       -      -
     65A  ARG*     3.7    30.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  ARG*     3.4    35.2    -      -       +      +
     38A  ILE*     3.5    28.9    -      -       +      -
     39A  ALA*     3.4    16.4    -      -       -      +
     40A  GLY*     3.8     5.6    -      -       -      -
     58A  VAL*     3.7    28.7    -      -       +      -
     59A  GLU*     1.3    79.0    -      -       -      +
     61A  GLU*     1.3    62.0    +      -       -      +
     62A  ASP*     3.2    17.5    -      -       -      +
     63A  GLY*     2.9    21.5    +      -       -      -
     64A  ASP*     3.1    24.0    +      -       +      +
     66A  ARG*     4.6    13.2    -      -       +      -
     68A  ILE*     5.1    11.2    -      -       +      -
     80A  LEU*     5.4     3.6    -      -       +      -
     82A  VAL*     4.2    17.0    -      -       +      -
----------------------------------------------------------
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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