Contacts of the strand formed by residues 56 - 62 (chain H) in PDB entry 1I94


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 56 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    636A    A      4.1    31.0    -      -       +      +
     52H  GLU*     4.8     1.8    -      -       -      -
     53H  VAL*     3.4    27.0    +      -       -      +
     54H  ASP*     3.6     2.6    -      -       +      -
     55H  GLY*     1.3    81.0    -      -       -      +
     57H  PRO*     1.3    68.0    -      -       -      +
     58H  TYR*     3.6     3.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 57 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    636A    A      4.9    17.3    -      -       -      +
     27H  PRO*     4.1     4.5    -      -       -      +
     28H  ALA*     3.8    26.6    +      -       +      -
     51H  VAL      3.8     7.2    -      -       -      +
     52H  GLU*     4.9     1.8    -      -       +      -
     55H  GLY      4.2     1.2    -      -       -      -
     56H  LYS*     1.3    78.3    -      -       -      +
     58H  TYR*     1.3    60.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 58 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25H  GLU*     4.3    17.3    -      -       +      -
     26H  VAL      3.2    17.7    -      -       -      +
     27H  PRO*     4.8     0.7    -      -       +      -
     28H  ALA*     3.9     9.0    -      -       -      +
     50H  ARG*     4.2     2.9    -      -       -      +
     51H  VAL*     2.9    35.2    +      -       +      +
     53H  VAL*     5.1    11.0    -      -       +      -
     56H  LYS      4.3     4.5    -      -       -      +
     57H  PRO*     1.3    76.0    -      -       -      +
     59H  LEU*     1.3    61.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 59 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24H  THR      3.2     2.4    -      -       -      +
     25H  GLU*     2.9     7.2    -      -       -      -
     26H  VAL*     2.5    47.8    +      -       +      +
     27H  PRO      5.1     0.7    -      -       -      +
     28H  ALA*     4.9     9.4    -      -       +      -
     32H  LYS*     6.5     0.9    -      -       +      -
     33H  GLU*     6.4     2.2    -      -       +      -
     48H  TYR*     5.1     9.9    -      -       +      -
     49H  GLU      4.5     5.6    -      -       -      -
     50H  ARG*     5.1     2.0    -      -       -      +
     58H  TYR*     1.3    74.7    -      -       -      +
     60H  ARG*     1.3    62.4    +      -       -      +
     61H  ILE*     3.5     2.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 60 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23H  SER*     5.2     7.2    -      -       -      -
     24H  THR      3.3     7.4    -      -       -      -
     25H  GLU*     4.3     4.3    -      -       +      +
     47H  GLY      3.5     1.4    -      -       -      +
     48H  TYR*     2.9    26.7    -      -       -      -
     49H  GLU*     3.3    20.4    +      -       +      +
     51H  VAL*     4.7    12.2    -      -       +      +
     58H  TYR      4.2     0.4    +      -       -      -
     59H  LEU*     1.3    70.3    -      -       -      +
     61H  ILE*     1.3    61.4    +      -       -      +
     62H  HIS*     3.7     1.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 61 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13H  ILE*     6.0     7.0    -      -       +      -
     23H  SER*     2.8     4.3    -      -       -      -
     24H  THR*     2.5    46.0    +      -       -      +
     36H  LEU*     6.3     2.2    -      -       +      -
     45H  ILE*     5.6     6.5    -      -       +      -
     47H  GLY      3.6     4.5    -      -       -      -
     48H  TYR*     4.3     6.7    -      -       +      +
     59H  LEU*     3.5     3.1    +      -       +      +
     60H  ARG*     1.3    74.4    -      -       -      +
     62H  HIS*     1.3    59.3    +      -       -      +
     63H  LEU*     3.3     4.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 62 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22H  GLU      3.7     2.9    -      -       -      +
     23H  SER*     3.5    14.4    -      -       -      -
     45H  ILE*     3.5     5.1    -      -       -      +
     46H  LYS*     3.0    32.7    +      -       +      -
     47H  GLY      2.6    26.2    +      -       -      +
     60H  ARG*     3.7     1.8    +      -       +      +
     61H  ILE*     1.3    69.3    -      -       -      +
     63H  LEU*     1.3    62.8    +      -       -      +
----------------------------------------------------------
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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