Contacts of the strand formed by residues 64 - 69 (chain K) in PDB entry 1FPY


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 ASP 64 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48K  MET*     3.2    29.8    -      -       +      +
     49K  PHE*     3.5    15.4    +      -       -      +
     50K  ASP*     4.1     5.5    +      -       -      +
     62K  GLU      2.8    12.2    +      -       -      +
     63K  SER*     1.3    70.9    -      -       -      +
     65K  MET*     1.3    60.8    +      -       -      +
     94K  PRO*     3.3    23.4    -      -       -      +
    339L  ARG*     2.7    22.9    +      -       -      +
    344L  ARG*     3.5    22.5    +      -       -      -
   4482L  ADP      5.7     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 65 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48K  MET*     3.4     5.1    -      -       -      +
     49K  PHE*     2.9    50.6    +      -       +      +
     51K  GLY*     4.7     3.3    -      -       -      +
     57K  TRP*     4.7     8.3    -      -       +      +
     62K  GLU      4.9     0.7    -      -       -      +
     63K  SER*     3.4    41.7    +      -       -      +
     64K  ASP*     1.3    75.1    -      -       -      +
     66K  VAL*     1.3    62.6    +      -       -      +
     91K  ILE*     3.8    21.1    -      -       +      -
     92K  LEU      3.3    19.3    -      -       -      +
     93K  GLU*     3.8    22.2    -      -       -      +
     94K  PRO*     4.2     6.3    -      -       +      -
    100K  TYR*     3.6    38.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 66 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45K  GLU      3.4    25.6    -      -       -      +
     46K  GLY*     4.2     0.9    -      -       -      -
     47K  LYS      3.5    10.8    -      -       -      +
     48K  MET*     4.1    12.6    -      -       -      -
     49K  PHE*     4.3     2.0    -      -       -      -
     65K  MET*     1.3    79.8    -      -       -      +
     67K  LEU*     1.3    73.4    +      -       -      +
     68K  MET*     3.5    10.3    +      -       +      +
     90K  ASP      3.2     4.5    -      -       -      +
     91K  ILE*     3.4     4.9    -      -       -      +
     92K  LEU*     3.0    39.9    +      -       +      +
     94K  PRO*     3.8    26.9    -      -       +      -
     97K  LEU*     4.2    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 67 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19K  LEU*     4.3    11.9    -      -       +      -
     21K  PHE*     3.6    24.2    -      -       +      -
     31K  VAL*     4.0    27.6    -      -       +      -
     42K  PHE*     5.2     0.8    -      -       +      -
     46K  GLY*     3.1    15.6    -      -       -      -
     47K  LYS*     2.9    22.5    +      -       +      +
     48K  MET      5.5     0.4    -      -       -      +
     49K  PHE*     3.6    30.7    -      -       +      -
     66K  VAL*     1.3    72.0    -      -       -      +
     68K  MET*     1.3    60.8    +      -       -      +
     69K  PRO*     3.0    12.4    -      -       -      +
     89K  CYS*     3.7    23.1    -      -       +      -
     90K  ASP      3.7     0.4    -      -       -      -
     91K  ILE*     3.5    23.6    -      -       +      -
    180L  PHE*     5.8     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 68 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43K  PHE      3.4    24.0    -      -       -      +
     44K  GLU      3.6    12.1    -      -       -      +
     45K  GLU*     3.4    10.8    -      -       -      +
     46K  GLY*     3.4    22.4    -      -       -      +
     66K  VAL*     3.5     5.8    +      -       +      -
     67K  LEU*     1.3    70.8    -      -       -      +
     69K  PRO*     1.3    76.4    -      -       -      +
     70K  ASP      3.5     0.2    +      -       -      -
     89K  CYS*     3.3     3.1    -      -       -      +
     90K  ASP*     2.7    51.0    +      -       +      +
     92K  LEU*     3.5    37.9    -      -       +      -
     97K  LEU*     4.9     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 69 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42K  PHE*     3.6    45.5    -      -       +      +
     43K  PHE*     4.0    26.9    -      -       +      +
     46K  GLY*     3.8     5.8    -      -       -      -
     67K  LEU      3.0    13.7    -      -       -      +
     68K  MET*     1.3   103.7    -      -       -      +
     70K  ASP*     1.3    58.8    +      -       -      +
     71K  ALA      3.7     2.1    +      -       -      -
     87K  ILE*     3.9    12.8    -      -       +      -
     88K  ARG      3.9     0.7    -      -       -      +
     89K  CYS*     3.8    14.6    -      -       -      -
     90K  ASP*     5.2     0.3    -      -       -      +
----------------------------------------------------------
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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