Contacts of the strand formed by residues 615 - 622 (chain A) in PDB entry 4IQJ


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 615 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294A  ARG      3.8     7.3    +      -       -      +
    295A  ILE*     4.6     5.8    -      -       +      -
    296A  PRO*     3.3    33.7    -      -       +      -
    402A  TYR*     3.6    32.1    -      -       +      -
    405A  ILE*     4.4    13.7    -      -       +      -
    406A  VAL*     6.2     0.2    -      -       +      -
    461A  MET*     4.4    12.5    -      -       -      -
    580A  VAL*     3.7     7.1    -      -       -      +
    581A  ILE*     3.2    49.1    +      -       +      +
    614A  LEU*     1.3    73.7    -      -       -      +
    616A  LYS*     1.3    61.8    +      -       -      +
    617A  MET*     3.5    37.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 616 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402A  TYR*     4.7     0.7    +      -       -      -
    461A  MET*     4.6     7.7    -      -       +      +
    463A  ASP*     3.7    23.3    +      -       -      +
    492A  ILE*     3.4    34.5    -      -       +      -
    579A  VAL      3.5     6.3    -      -       -      +
    606A  MET*     3.2    26.7    -      -       -      +
    609A  VAL*     5.1     5.8    -      -       +      -
    610A  GLU*     3.4    40.8    -      -       +      +
    614A  LEU      3.5     7.4    +      -       -      +
    615A  LEU*     1.3    77.3    -      -       -      +
    617A  MET*     1.3    77.9    +      -       -      +
    618A  ASP*     3.0    35.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 617 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402A  TYR*     3.1    29.8    -      -       +      +
    405A  ILE*     5.7     1.1    -      -       -      -
    406A  VAL*     3.9    14.4    -      -       -      -
    409A  TYR*     2.8    26.2    -      -       -      +
    464A  ILE      4.2    10.8    -      -       -      +
    577A  ALA      4.0     0.7    -      -       -      -
    579A  VAL*     2.9    34.6    +      -       +      +
    581A  ILE*     4.2    17.9    -      -       +      -
    615A  LEU*     3.5    27.4    -      -       +      -
    616A  LYS*     1.3   101.4    -      -       -      +
    618A  ASP*     1.3    72.5    +      -       -      +
    619A  PHE*     3.6    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 618 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    463A  ASP*     3.5     6.9    -      -       -      +
    464A  ILE      4.3     6.1    +      -       -      -
    465A  ASP*     2.7    35.1    -      -       -      +
    466A  THR*     2.9    28.2    +      -       -      +
    577A  ALA*     3.3    14.6    -      -       +      +
    606A  MET*     3.6    14.8    -      -       -      +
    616A  LYS*     3.0    28.5    +      -       -      -
    617A  MET*     1.3    82.7    -      -       -      +
    619A  PHE*     1.3    63.1    +      -       -      +
    620A  LEU*     3.3    10.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 619 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    409A  TYR*     3.2    49.4    -      +       -      -
    464A  ILE      6.1     0.2    -      -       -      -
    466A  THR*     3.4     6.3    -      -       -      -
    468A  PHE*     3.7    25.6    -      +       +      -
    473A  ARG*     3.3    28.0    +      -       +      +
    476A  VAL*     4.6     8.7    -      -       +      -
    477A  ILE*     3.5    33.7    -      -       +      -
    480A  VAL*     4.5    10.3    -      -       +      -
    576A  ALA      3.9     0.7    -      -       -      +
    577A  ALA*     3.1    23.9    +      -       -      +
    579A  VAL*     3.8    24.7    -      -       +      -
    581A  ILE*     5.6     0.9    -      -       +      -
    617A  MET*     3.6    20.9    -      -       +      -
    618A  ASP*     1.3    76.2    -      -       -      +
    620A  LEU*     1.3    61.2    +      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
    424A  ARG*     2.9    50.7    -      -       -      +
    465A  ASP*     4.3     0.7    -      -       +      -
    466A  THR      2.8    15.6    +      -       -      +
    467A  ASP*     3.3    15.7    -      -       -      +
    468A  PHE      2.7    32.4    +      -       -      +
    473A  ARG*     4.0     2.2    -      -       -      -
    576A  ALA*     6.0     0.7    -      -       -      -
    577A  ALA*     3.9    15.3    -      -       +      -
    618A  ASP*     3.3    30.5    -      -       +      +
    619A  PHE*     1.3    75.0    -      -       -      +
    621A  GLY*     1.3    58.9    +      -       -      +
    622A  LEU*     3.6     2.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 621 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    468A  PHE      3.5     7.0    -      -       -      -
    470A  ASP*     3.7    23.9    -      -       -      +
    473A  ARG*     3.4    18.8    -      -       -      +
    620A  LEU*     1.3    73.6    -      -       -      +
    622A  LEU*     1.3    61.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 622 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    467A  ASP*     4.3    12.1    -      -       +      +
    468A  PHE      3.0    12.3    +      -       -      +
    470A  ASP*     3.2    21.4    +      -       -      +
    620A  LEU*     4.7     4.3    -      -       +      +
    621A  GLY*     1.3    76.6    -      -       -      +
    623A  ARG*     1.3    67.9    +      -       -      +
    624A  THR*     3.5    11.2    -      -       -      +
    625A  LEU*     3.8    13.4    +      -       +      -
    626A  THR      3.7     8.5    +      -       -      -
    668A  PHE*     4.3    22.2    -      -       +      -
    821A  TYR*     4.3    20.4    -      -       +      +
    824A  LEU*     4.1    26.2    -      -       +      -
----------------------------------------------------------
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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