Contacts of the strand formed by residues 555 - 560 (chain A) in PDB entry 3I8E


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 LEU 555 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    507A  GLN*     5.9     0.2    +      -       -      -
    546A  LEU*     5.0     8.0    -      -       +      +
    553A  SER*     3.8    13.7    +      -       -      +
    554A  PRO*     1.3    86.4    -      -       +      +
    556A  CYS*     1.3    67.9    +      -       -      +
    568A  ILE*     5.1     1.6    -      -       +      -
    569A  LEU      4.0    11.9    -      -       -      +
    570A  LYS*     4.9     8.1    -      -       +      +
    571A  LEU*     4.8     4.2    -      -       -      +
    577A  LEU*     5.8     2.2    -      -       +      -
    593A  MET*     4.2    11.6    -      -       +      +
    616A  LEU*     3.5    29.8    -      -       +      -
    617A  ASN      3.4    17.9    -      -       -      +
    618A  ILE*     3.3    42.0    -      -       +      +
    619A  GLU      4.8     3.6    -      -       -      +
    621A  GLY*     4.2    11.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 556 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    509A  VAL*     5.1     5.2    -      -       -      -
    541A  LEU*     6.4     0.2    -      -       -      -
    542A  ASP      3.5     9.4    -      -       -      -
    543A  ILE*     3.4    32.5    -      -       -      -
    555A  LEU*     1.3    83.6    -      -       -      +
    557A  ALA*     1.3    75.2    +      -       -      +
    558A  ILE*     5.3     3.6    -      -       -      -
    568A  ILE*     4.0     2.9    -      -       -      +
    569A  LEU*     2.8    55.0    +      -       +      +
    570A  LYS      4.3     0.9    -      -       -      +
    571A  LEU*     4.3    21.8    -      -       +      -
    593A  MET*     4.7     7.0    -      -       -      -
    616A  LEU*     5.2     1.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 557 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    542A  ASP*     3.7    21.5    +      -       -      +
    556A  CYS*     1.3    83.5    -      -       -      +
    558A  ILE*     1.3    68.6    +      -       -      +
    567A  ARG      3.0    20.6    -      -       -      +
    568A  ILE*     4.1    11.2    -      -       +      -
    569A  LEU*     3.6     5.3    -      -       -      +
    591A  ILE*     4.6     6.6    -      -       +      +
    593A  MET*     5.1     2.7    -      -       +      +
    602A  LEU*     4.1    27.5    -      -       +      +
    616A  LEU*     4.9     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 558 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    509A  VAL*     5.8     0.4    -      -       +      -
    516A  LEU*     5.3     2.2    -      -       +      -
    534A  MET*     3.8    26.2    -      -       -      -
    538A  VAL*     4.0    20.4    -      -       +      -
    540A  CYS      3.2    10.3    -      -       -      +
    541A  LEU*     3.2    38.6    -      -       +      +
    542A  ASP      4.7     0.2    -      -       -      +
    556A  CYS*     5.3     3.6    -      -       -      -
    557A  ALA*     1.3    80.8    -      -       -      +
    559A  GLY*     1.3    54.9    +      -       -      +
    560A  LEU*     3.9    21.1    -      -       +      -
    566A  ALA*     3.4     3.1    -      -       -      +
    567A  ARG*     2.5    46.4    +      -       +      +
    569A  LEU*     4.0    21.3    -      -       +      -
    591A  ILE*     4.6    12.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 559 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    538A  VAL*     4.6     0.2    -      -       -      -
    539A  ALA*     3.2     6.5    +      -       -      +
    540A  CYS*     3.1    40.5    +      -       -      +
    558A  ILE*     1.3    79.7    -      -       -      +
    560A  LEU*     1.3    61.2    +      -       -      -
    565A  SER      3.2    19.3    -      -       -      -
    566A  ALA*     4.2     1.1    -      -       -      -
    567A  ARG*     4.5     1.8    -      -       -      -
    588A  PRO*     4.6     6.1    -      -       -      -
    591A  ILE*     4.9     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 560 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    534A  MET*     4.1    24.0    -      -       +      -
    535A  GLU      4.7     1.3    -      -       -      +
    536A  HIS*     3.3    39.0    -      -       +      +
    537A  GLU      3.0    18.8    -      -       -      +
    538A  VAL*     4.0     3.4    -      -       -      -
    539A  ALA*     3.7     6.3    -      -       -      +
    558A  ILE*     3.9    21.5    -      -       +      -
    559A  GLY*     1.3    73.7    -      -       -      +
    561A  TRP*     1.3    62.9    +      -       -      +
    563A  ASP*     3.3    30.7    -      -       -      +
    564A  ILE*     3.9     9.9    -      -       -      -
    565A  SER*     3.7    10.8    +      -       -      +
    567A  ARG*     4.3    19.7    -      -       +      +
    588A  PRO*     3.5    18.9    -      -       -      +
----------------------------------------------------------
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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