Contacts of the strand formed by residues 449 - 457 (chain A) in PDB entry 1QFM


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 449 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    441A  PHE*     4.3    25.6    -      -       +      +
    442A  TYR      3.4     3.1    -      -       -      -
    443A  PRO*     3.9    36.8    -      -       +      -
    447A  GLY      3.3     7.2    +      -       -      +
    448A  THR*     1.3    74.4    -      -       -      +
    450A  ILE*     1.3    59.4    +      -       -      +
    451A  PRO*     4.1     2.1    -      -       -      +
    510A  TYR*     5.5     1.4    -      -       -      -
    514A  TRP*     3.5    18.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 450 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    441A  PHE*     3.2     4.5    -      -       -      -
    442A  TYR*     2.7    73.7    +      -       +      +
    444A  SER*     4.0     2.5    -      -       -      -
    448A  THR*     3.7    20.9    -      -       +      +
    449A  LYS*     1.3    76.5    -      -       -      +
    451A  PRO*     1.3    73.2    -      -       -      +
    503A  ASN      3.5    25.6    -      -       -      +
    504A  ILE*     3.9     4.7    -      -       -      -
    505A  ARG*     4.3     0.9    -      -       -      +
    514A  TRP*     3.7    20.6    -      -       +      -
    529A  ASP*     3.6    32.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 451 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357A  VAL*     4.1    10.1    -      -       +      -
    439A  GLN*     4.1     7.0    -      -       -      +
    440A  ILE      3.4     7.4    -      -       -      +
    441A  PHE*     3.7    17.3    -      -       +      -
    449A  LYS      4.1     2.2    -      -       -      +
    450A  ILE*     1.3    94.5    -      -       +      +
    452A  MET*     1.3    59.6    +      -       -      +
    502A  ALA*     3.8     0.3    -      -       -      -
    503A  ASN*     2.8    54.5    +      -       +      +
    510A  TYR*     3.5    33.7    -      -       +      +
    514A  TRP*     4.0    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 452 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    438A  VAL      3.8     0.5    -      -       -      +
    439A  GLN*     3.4     4.3    -      -       -      +
    440A  ILE*     2.9    42.3    +      -       +      +
    442A  TYR*     3.9    22.0    -      -       +      -
    451A  PRO*     1.3    77.2    -      -       -      +
    453A  PHE*     1.3    73.4    +      -       -      +
    454A  ILE*     4.1     4.9    -      -       +      -
    470A  LEU*     3.9    28.0    -      -       -      -
    500A  ALA*     3.9     8.3    -      -       -      -
    501A  VAL      3.2    13.2    -      -       -      +
    502A  ALA*     4.2     2.5    -      -       -      -
    503A  ASN*     4.4     0.9    -      -       -      -
    533A  ALA*     3.8    22.9    -      -       -      +
    536A  TYR*     3.6    31.0    -      -       +      -
    537A  LEU*     3.9    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 453 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357A  VAL*     3.5    49.8    -      -       +      -
    358A  LYS*     4.5     9.6    -      -       +      -
    379A  VAL*     5.2     4.9    -      -       +      -
    401A  PHE*     3.6    35.7    -      +       +      -
    437A  THR*     4.4     9.2    -      -       +      -
    438A  VAL      3.4     4.9    -      -       -      -
    439A  GLN*     3.7    31.6    -      -       +      -
    452A  MET*     1.3    73.9    -      -       -      +
    454A  ILE*     1.3    62.1    +      -       -      +
    455A  VAL*     4.3     1.6    -      -       +      -
    480A  ILE      4.2     4.9    -      -       -      -
    482A  PRO*     3.7    23.1    -      -       +      -
    500A  ALA*     3.2     5.2    -      -       -      -
    501A  VAL*     2.9    40.3    +      -       +      +
    503A  ASN*     3.8    11.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 454 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    436A  GLN      3.6     1.6    -      -       -      +
    437A  THR*     3.4     2.8    -      -       -      -
    438A  VAL*     2.8    45.8    +      -       +      +
    440A  ILE*     4.1    11.2    -      -       +      -
    452A  MET*     4.1    13.0    -      -       +      +
    453A  PHE*     1.3    79.7    -      -       -      +
    455A  VAL*     1.3    62.7    +      -       -      +
    456A  HIS*     4.0     7.4    -      -       +      -
    498A  VAL*     3.6    27.8    -      -       +      -
    499A  LEU      3.3     5.2    -      -       -      +
    500A  ALA*     4.5     1.3    -      -       +      -
    536A  TYR*     4.1    14.1    -      -       +      -
    537A  LEU*     3.9    18.2    -      -       +      -
    542A  TYR*     3.7    43.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 455 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    401A  PHE*     3.7    31.4    -      -       +      -
    402A  LEU*     4.0    26.5    -      -       +      -
    435A  TYR*     4.8     4.3    -      -       +      -
    436A  GLN      3.3     8.5    -      -       -      +
    437A  THR*     3.6    17.9    -      -       +      +
    453A  PHE      5.3     0.4    -      -       -      -
    454A  ILE*     1.3    76.1    -      -       -      +
    456A  HIS*     1.3    66.8    +      -       -      +
    489A  LEU*     4.6    11.4    -      -       +      -
    492A  VAL*     4.4     6.6    -      -       +      +
    498A  VAL*     3.7     1.4    -      -       -      -
    499A  LEU*     2.8    58.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 456 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    435A  TYR*     3.5     7.4    -      -       -      -
    436A  GLN*     2.8    68.1    +      -       +      +
    438A  VAL*     4.7     5.8    -      -       +      +
    454A  ILE*     4.0    24.7    -      -       +      -
    455A  VAL*     1.3    76.8    -      -       -      +
    457A  LYS*     1.3    85.8    +      -       -      +
    458A  LYS*     4.9     2.7    -      -       -      -
    459A  GLY      5.2     1.8    -      -       -      -
    460A  ILE*     3.6    30.0    -      -       +      +
    462A  LEU*     6.0     0.9    -      -       +      -
    492A  VAL*     4.5     7.4    -      -       -      -
    497A  GLY      4.7     0.9    -      -       -      +
    498A  VAL*     4.1    13.5    -      -       +      -
    542A  TYR*     4.0    16.6    +      +       -      -
----------------------------------------------------------
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Residues in contact with LYS 457 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    434A  ASP*     3.6     9.4    -      -       +      +
    435A  TYR*     3.7    25.1    -      -       +      -
    456A  HIS*     1.3    91.5    +      -       -      +
    458A  LYS*     1.3    66.2    +      -       -      +
    459A  GLY      3.6     0.2    +      -       -      -
    460A  ILE*     3.3    28.0    -      -       +      +
    466A  HIS*     6.1     1.1    +      -       -      -
    492A  VAL*     3.8    24.6    +      -       +      +
    493A  ARG*     4.9     8.6    +      -       -      +
    496A  GLY*     3.7    26.8    +      -       -      -
    497A  GLY      5.1     1.5    +      -       -      -
    709A  ILE*     4.7     8.5    -      -       -      +
----------------------------------------------------------
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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