Contacts of the strand formed by residues 40 - 48 (chain F) in PDB entry 1C9T


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 HIS 40 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32F  SER*     2.8    26.9    +      -       -      +
     33F  LEU      3.7     5.2    -      -       -      -
     34F  ASN*     4.1     4.6    -      -       -      +
     39F  TYR*     1.3    87.4    -      -       -      +
     41F  PHE*     1.3    62.7    +      -       -      +
     42F  CYS      2.8    27.4    +      -       -      -
     43F  GLY*     4.3     1.6    -      -       -      -
     66F  ARG*     5.6     3.1    -      -       -      +
     73F  ILE*     4.9    16.7    -      -       +      +
    140F  GLY*     6.2     0.2    -      -       -      -
    141F  TRP*     3.8    43.4    -      +       +      +
    193F  GLY*     3.0    31.4    +      -       -      -
     36L  LYS*     3.8    19.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 41 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33F  LEU*     3.1    46.0    +      -       +      -
     34F  ASN      3.6     3.6    -      -       -      -
     37F  SER*     3.1    31.9    -      -       -      -
     39F  TYR*     3.7    19.5    -      -       +      -
     40F  HIS*     1.3    79.1    -      -       -      +
     42F  CYS*     1.3    88.1    +      -       +      +
     58F  CYS*     2.9    29.8    -      -       -      -
     60F  LYS*     3.4    35.9    -      -       +      -
     63F  ILE*     4.0     8.3    -      -       +      -
    193F  GLY*     4.4     2.2    -      -       -      -
     35L  VAL*     3.7     7.0    -      -       +      -
     36L  LYS*     3.3    31.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 42 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33F  LEU*     2.9    25.2    +      -       +      -
     40F  HIS*     2.8    24.0    +      -       -      -
     41F  PHE*     1.3   110.6    -      -       +      +
     43F  GLY*     1.3    64.8    +      -       -      +
     58F  CYS*     2.0    55.0    -      -       +      -
    193F  GLY      4.1     6.5    -      -       -      -
    195F  SER*     3.6     7.2    -      -       -      +
     35L  VAL*     3.9    10.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 43 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30F  GLN*     4.3     8.3    -      -       -      -
     31F  VAL      3.2    14.6    -      -       -      -
     32F  SER*     4.5     0.2    -      -       -      -
     33F  LEU*     3.5    12.9    -      -       -      +
     40F  HIS*     4.3     3.8    -      -       -      -
     42F  CYS*     1.3    76.0    -      -       -      +
     44F  GLY*     1.3    58.3    +      -       -      -
     54F  SER*     3.0    18.0    +      -       -      -
    193F  GLY      4.5     1.8    +      -       -      -
    194F  ASP*     4.8     0.9    +      -       -      -
    195F  SER      2.9    12.5    +      -       -      -
    196F  GLY*     3.6     7.1    -      -       -      -
    197F  GLY*     4.2     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 44 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29F  TYR      3.8     0.9    -      -       -      +
     30F  GLN*     3.8     3.4    +      -       -      -
     31F  VAL*     3.1    37.9    +      -       -      -
     33F  LEU*     5.1     0.4    -      -       -      -
     43F  GLY*     1.3    74.2    -      -       -      -
     45F  SER*     1.3    64.6    +      -       -      -
     52F  VAL*     4.2     3.8    -      -       -      -
     53F  VAL      3.4     9.0    -      -       -      -
     54F  SER*     4.1     2.0    -      -       -      -
    196F  GLY      3.2    14.9    +      -       -      -
    197F  GLY*     4.2     1.8    -      -       -      -
    198F  PRO*     4.3     4.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 45 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29F  TYR*     3.4     6.3    -      -       -      -
     31F  VAL*     4.8     0.4    -      -       -      -
     44F  GLY*     1.3    74.8    -      -       -      -
     46F  LEU*     1.3    62.6    +      -       -      +
     47F  ILE      3.4     0.3    +      -       -      -
     52F  VAL*     3.2     6.9    -      -       -      +
     53F  VAL*     2.9    48.0    +      -       -      +
    121F  ILE*     3.9    20.0    -      -       -      -
    196F  GLY      4.3     0.9    +      -       -      -
    197F  GLY      4.5     0.7    -      -       -      -
    198F  PRO*     2.8    36.8    -      -       -      +
    209F  LEU*     3.7     5.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 46 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29F  TYR*     2.9    17.5    +      -       -      +
     31F  VAL*     4.3     7.5    -      -       +      +
     45F  SER*     1.3    70.0    -      -       -      +
     47F  ILE*     1.3    58.5    +      -       -      +
     48F  ASN      3.3    28.9    -      -       -      +
     49F  SER      4.0     9.4    -      -       -      +
     51F  TRP      3.4     9.2    -      -       -      +
     52F  VAL*     4.1    13.9    -      -       +      +
     67F  LEU*     3.7    16.6    -      -       +      -
    108F  LEU*     4.5     1.3    -      -       +      -
    112F  ALA*     4.3     1.8    -      -       +      -
    114F  LEU*     4.0    16.2    -      -       +      -
    118F  VAL*     3.3    34.8    -      -       +      -
    119F  ALA      4.0    10.8    -      -       -      +
    120F  SER*     3.2     4.0    -      -       -      -
    121F  ILE*     2.9    29.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 47 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45F  SER      3.4     1.3    +      -       -      +
     46F  LEU*     1.3    75.3    -      -       -      +
     48F  ASN*     1.3    72.6    +      -       +      +
     51F  TRP*     3.0    14.3    +      -       +      +
     53F  VAL*     3.4    42.2    -      -       +      +
    105F  LEU*     4.5     3.1    -      -       +      -
    120F  SER*     3.6    10.4    +      -       -      -
    121F  ILE*     3.9    12.5    -      -       +      +
    123F  LEU*     3.7    42.6    -      -       +      -
    209F  LEU*     4.5     4.5    -      -       +      -
    238F  ILE*     3.9    16.8    -      -       +      -
    242F  ILE*     4.4    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 48 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242B  ILE      4.6     3.4    +      -       -      -
    243B  ALA*     3.7    26.9    +      -       +      +
     46F  LEU*     3.3    10.0    -      -       -      +
     47F  ILE*     1.3    89.2    -      -       +      +
     49F  SER*     1.3    79.2    +      -       -      +
     50F  GLN*     2.7    11.8    +      -       -      +
     51F  TRP*     2.9    43.3    +      -       -      +
    114F  LEU*     4.7     0.7    -      -       -      -
    120F  SER*     3.7    13.0    -      -       -      +
    242F  ILE*     4.4     9.3    -      -       -      +
----------------------------------------------------------
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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