Contacts of the strand formed by residues 615 - 620 (chain A) in PDB entry 1XMI


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 615 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    447A  LYS      4.6     4.7    +      -       -      +
    448A  ILE*     3.8    23.1    -      -       +      -
    449A  GLU*     6.3     0.8    -      -       -      +
    452A  GLN*     4.5    11.1    +      -       -      +
    453A  LEU      3.3     2.0    +      -       -      -
    454A  LEU*     3.3     7.5    -      -       +      +
    455A  ALA      3.0    23.0    +      -       -      -
    613A  ALA*     3.6     4.4    -      -       -      +
    614A  ASP*     1.3    86.5    -      -       +      +
    616A  ILE*     1.3    64.2    +      -       -      +
    627A  TYR*     3.4    44.6    +      -       +      +
    628A  GLY*     3.4    22.2    -      -       -      +
    629A  THR*     4.6     9.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 616 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454A  LEU*     3.9     2.5    -      -       -      -
    455A  ALA*     3.3     9.2    -      -       +      +
    610A  LEU*     3.6    49.1    -      -       +      +
    613A  ALA*     4.0     7.2    -      -       +      +
    615A  LYS*     1.3    79.3    -      -       -      +
    617A  LEU*     1.3    59.6    +      -       -      +
    618A  ILE*     4.2     6.5    -      -       +      -
    626A  PHE*     3.7    27.6    -      -       +      -
    627A  TYR*     3.4     9.7    -      -       -      -
    628A  GLY      2.7    43.7    +      -       -      +
    629A  THR      3.9     2.0    -      -       -      -
    630A  PHE*     3.8    22.2    -      -       -      +
    633A  LEU*     3.8    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 617 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    444A  ILE*     4.6     6.7    -      -       +      -
    445A  ASN      4.9     4.3    -      -       -      +
    446A  PHE*     4.4    19.7    -      -       +      -
    454A  LEU*     4.1    13.0    -      -       +      -
    455A  ALA      2.9    10.3    +      -       -      +
    456A  VAL*     3.4     9.8    -      -       +      +
    457A  ALA      3.0    25.1    +      -       -      +
    467A  LEU*     3.9    26.0    -      -       +      -
    616A  ILE*     1.3    74.6    -      -       -      +
    618A  ILE*     1.3    70.6    +      -       -      +
    619A  LEU*     3.6    27.8    +      -       +      -
    624A  SER*     3.4    26.9    -      -       -      +
    626A  PHE      3.4     9.4    -      -       -      +
    627A  TYR*     4.2    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 618 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    455A  ALA      5.7     0.4    -      -       -      +
    457A  ALA*     3.4    29.6    -      -       +      +
    458A  GLY*     4.9     2.0    -      -       -      -
    610A  LEU*     4.2    11.7    -      -       +      -
    616A  ILE*     4.4     7.4    -      -       +      -
    617A  LEU*     1.3    75.2    -      -       -      +
    619A  LEU*     1.3    63.6    +      -       -      +
    624A  SER*     3.7     3.8    -      -       -      -
    625A  TYR*     2.8    53.7    +      -       +      -
    626A  PHE*     2.8    28.6    +      -       +      +
    633A  LEU*     4.0    14.6    -      -       +      -
    640A  PHE*     3.6    37.9    -      -       +      -
    643A  LYS*     4.7     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 619 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    441A  LEU*     4.3     9.6    -      -       +      -
    444A  ILE*     3.9    20.4    -      -       +      -
    456A  VAL*     4.0    22.0    -      -       +      -
    457A  ALA      2.8    12.5    +      -       -      +
    458A  GLY*     3.4    19.6    -      -       -      -
    459A  SER      4.4     0.9    +      -       -      -
    462A  ALA*     3.7    24.1    -      -       +      +
    463A  GLY      3.8    28.7    -      -       -      +
    464A  LYS*     4.0     3.1    -      -       +      +
    467A  LEU*     4.6     5.2    -      -       +      -
    617A  LEU*     3.6    29.5    +      -       +      -
    618A  ILE*     1.3    79.5    -      -       -      +
    620A  HIS*     1.3    62.6    +      -       -      +
    622A  GLY      4.8     1.3    -      -       -      -
    623A  SER      3.3    13.0    -      -       -      +
    624A  SER*     4.3     0.2    -      -       -      -
    643A  LYS*     5.5     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 620 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    459A  SER*     5.0    11.3    +      -       -      -
    462A  ALA*     4.5     1.6    -      -       -      -
    618A  ILE      4.1     0.2    +      -       -      -
    619A  LEU*     1.3    74.6    +      -       -      +
    621A  GLU*     1.3   100.4    +      -       +      +
    622A  GLY      3.1     0.9    -      -       -      -
    623A  SER*     2.8    31.2    +      -       -      +
    625A  TYR*     4.1    24.2    -      +       +      -
    643A  LYS*     3.8    21.7    +      -       -      +
----------------------------------------------------------
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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