Contacts of the strand formed by residues 45 - 53 (chain E) in PDB entry 4IHB


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 VAL 45 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7E  LEU      3.7    11.2    -      -       -      +
      8E  TYR*     4.0    14.6    -      -       +      -
     36E  LYS*     5.0     0.7    +      -       -      -
     38E  ILE*     3.4    21.4    -      -       -      +
     43E  ASN      3.4     9.4    +      -       -      +
     44E  PRO*     1.3    76.5    -      -       -      +
     46E  TRP*     1.3    63.2    +      -       -      +
     47E  ASN*     4.4    13.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 46 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6E  ILE*     3.6    23.1    -      -       +      +
      7E  LEU      2.8     7.9    +      -       -      -
      8E  TYR*     3.9    14.4    -      -       -      -
      9E  ALA*     3.6    28.9    -      -       +      -
     22E  ALA*     3.1    34.6    +      -       +      -
     23E  TYR*     3.9     7.2    -      -       -      -
     24E  CYS*     4.2     7.4    -      -       +      -
     35E  THR*     3.3    25.6    +      -       +      -
     36E  LYS*     3.1    47.4    +      -       +      +
     38E  ILE*     3.4    17.2    -      -       +      +
     44E  PRO*     3.6    20.6    -      -       +      -
     45E  VAL*     1.3    74.3    -      -       -      +
     47E  ASN*     1.3    71.5    +      -       -      +
     48E  GLU*     3.3     5.1    +      -       -      +
     69E  VAL*     4.5     9.6    -      -       +      -
    117E  LEU*     3.6    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 47 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5E  PHE*     5.6     3.4    -      -       -      -
      6E  ILE      3.1     6.4    +      -       -      -
      7E  LEU*     3.0    34.7    +      -       +      +
     45E  VAL*     4.5    13.0    -      -       +      -
     46E  TRP*     1.3    79.8    -      -       -      +
     48E  GLU*     1.3    59.7    +      -       -      +
     49E  GLY      4.4     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 48 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4E  VAL      3.7     0.5    -      -       -      +
      5E  PHE*     3.3     6.9    -      -       -      -
      6E  ILE      2.9    31.5    +      -       -      +
      7E  LEU*     5.2     0.2    -      -       -      +
     35E  THR*     3.4     9.5    -      -       +      -
     36E  LYS*     2.6    62.3    +      -       -      +
     46E  TRP*     3.6     5.7    -      -       +      +
     47E  ASN*     1.3    77.3    -      -       -      +
     49E  GLY*     1.3    59.8    +      -       -      +
     50E  PHE*     3.6    23.1    -      -       +      -
    204E  FMT      2.5    32.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 49 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3E  ARG*     6.0     0.2    -      -       -      -
      4E  VAL      3.4     5.6    -      -       -      -
      5E  PHE*     3.6    22.0    -      -       -      -
     47E  ASN      4.4     0.4    +      -       -      -
     48E  GLU*     1.3    73.1    -      -       -      +
     50E  PHE*     1.3    77.1    +      -       -      -
     51E  GLU*     5.8     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 50 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2E  LEU      3.7     0.7    -      -       -      +
      3E  ARG*     3.4     4.6    -      -       -      +
      4E  VAL*     2.8    41.6    +      -       +      +
      6E  ILE*     3.5    32.1    -      -       +      -
     26E  ALA*     5.5     0.9    -      -       +      -
     33E  LYS*     3.6    34.3    -      -       +      -
     34E  ARG*     3.5    26.5    -      -       -      -
     35E  THR*     3.7    13.0    -      -       +      -
     48E  GLU*     3.6    37.2    -      -       +      -
     49E  GLY*     1.3    79.7    -      -       -      -
     51E  GLU*     1.3    65.9    +      -       -      +
     52E  TRP*     3.8    13.5    -      +       +      -
    202E  FMT      3.6    14.1    -      -       -      -
    204E  FMT      4.1     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 51 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1E  MET*     3.3    38.5    -      -       +      +
      2E  LEU      3.3     2.2    -      -       -      -
      3E  ARG*     3.7    31.1    +      -       +      +
     33E  LYS*     3.2    24.0    +      -       -      +
     49E  GLY      5.8     0.2    -      -       -      -
     50E  PHE*     1.3    80.5    -      -       -      +
     52E  TRP*     1.3    60.0    +      -       -      +
     53E  ASP      3.9     1.6    +      -       -      -
    124E  THR*     4.0     6.2    -      -       -      +
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Residues in contact with TRP 52 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1E  MET*     3.7     4.0    -      -       -      -
      2E  LEU*     2.9    54.5    +      -       +      +
      4E  VAL*     3.5    30.1    -      -       +      -
     26E  ALA*     3.7    40.4    -      -       +      -
     28E  PHE*     3.4    49.2    +      +       +      +
     29E  ALA*     5.7     0.2    -      -       +      -
     31E  VAL*     3.0    37.6    +      -       +      +
     33E  LYS*     3.5    26.4    -      -       +      +
     50E  PHE*     3.8    14.6    -      +       +      -
     51E  GLU*     1.3    72.9    -      -       -      +
     53E  ASP*     1.3    66.0    +      -       -      +
     54E  LEU*     3.2     2.4    +      -       -      -
     65E  LEU*     3.9     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 53 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      0E  PHE      4.7     1.0    -      -       -      +
      1E  MET*     3.7    22.1    -      -       +      +
     28E  PHE*     6.0     0.7    -      -       -      -
     51E  GLU      3.9     3.6    +      -       -      -
     52E  TRP*     1.3    69.9    -      -       -      +
     54E  LEU*     1.3    73.0    +      -       -      +
     55E  LYS*     3.4    47.0    +      -       -      +
----------------------------------------------------------
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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