Contacts of the strand formed by residues 617 - 622 (chain A) in PDB entry 3K5M


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 TYR 617 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    543A  TYR*     4.2    16.6    -      +       -      -
    550A  PHE*     3.6    28.0    -      +       -      -
    598A  PHE*     4.8    11.2    -      +       -      -
    601A  PHE*     3.5    20.0    -      +       +      -
    602A  LEU      3.4    15.9    -      -       -      +
    603A  MET*     3.6    11.4    -      -       +      -
    604A  PRO*     4.0     3.6    -      -       -      -
    615A  LYS      4.8     1.3    -      -       -      -
    616A  ARG*     1.3    85.1    -      -       -      +
    618A  ALA*     1.3    66.7    +      -       -      +
    630A  VAL*     5.0     3.4    -      -       +      -
    632A  LYS*     2.9    71.2    +      -       +      +
    634A  LEU*     3.6    10.0    -      -       -      +
    912P    A      4.6     1.6    -      -       -      -
    913P    G      2.7    28.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 618 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    601A  PHE*     3.5     9.4    -      -       -      -
    602A  LEU*     2.7    35.0    +      -       +      -
    617A  TYR*     1.3    80.7    -      -       -      +
    619A  GLY*     1.3    59.1    +      -       -      +
    630A  VAL      3.2    12.6    -      -       -      +
    631A  PHE*     3.7    22.7    -      -       +      -
    634A  LEU*     3.9     2.0    -      -       +      +
    653A  TYR*     3.7    26.9    -      -       +      -
    657A  PHE*     3.9     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 619 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    598A  PHE*     3.6    21.1    -      -       -      -
    600A  ARG      3.2    11.9    -      -       -      -
    601A  PHE*     4.3     0.2    -      -       -      -
    618A  ALA*     1.3    77.8    -      -       -      +
    620A  LEU*     1.3    61.7    +      -       -      -
    629A  MET*     3.2     7.1    -      -       -      +
    630A  VAL      2.9    32.3    +      -       -      -
    657A  PHE*     3.8     9.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 620 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    598A  PHE*     3.6     3.5    -      -       -      -
    599A  CYS*     3.1    45.3    +      -       -      -
    600A  ARG*     2.9    11.4    +      -       +      +
    619A  GLY*     1.3    74.1    -      -       -      -
    621A  ILE*     1.3    62.3    +      -       -      +
    627A  GLN*     3.5    43.7    -      -       +      +
    628A  ARG      3.7     3.8    -      -       -      +
    629A  MET*     3.4    24.7    -      -       +      -
    654A  LEU*     3.8    16.6    -      -       +      -
    657A  PHE*     3.9    33.8    -      -       +      +
    658A  ARG*     4.2     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 621 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    559A  GLU*     5.7     0.7    -      -       -      +
    596A  THR*     3.8    16.2    -      -       +      +
    597A  HIS      4.0    15.7    -      -       -      +
    598A  PHE*     3.4    35.9    -      -       +      -
    599A  CYS*     4.7     0.2    -      -       -      -
    620A  LEU*     1.3    74.4    -      -       -      +
    622A  GLN*     1.3    67.1    +      -       -      +
    623A  GLU*     3.5    30.6    +      -       +      +
    627A  GLN*     3.1     6.2    -      -       -      -
    628A  ARG*     2.8    63.3    +      -       -      +
    630A  VAL*     4.0    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 622 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    559A  GLU*     3.7    40.6    +      -       +      +
    597A  HIS      5.1     0.8    +      -       -      -
    599A  CYS*     4.6    10.8    -      -       -      -
    620A  LEU      4.3     0.8    +      -       -      -
    621A  ILE*     1.3    75.5    -      -       -      +
    623A  GLU*     1.3    64.4    +      -       -      +
    624A  GLY      2.8    26.2    +      -       -      +
    625A  ASP*     3.8     4.2    -      -       -      +
    626A  LYS      2.7    30.7    +      -       -      +
    627A  GLN*     3.3    25.1    -      -       +      +
----------------------------------------------------------
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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