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


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 ARG 40 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6E  PHE*     3.7    16.6    -      -       -      -
     35E  GLY*     2.9     4.5    -      -       -      -
     36E  ASP*     2.9    51.7    +      -       +      +
     38E  GLN      4.7     2.5    -      -       -      +
     39E  GLY*     1.3    77.7    -      -       -      +
     41E  VAL*     1.3    61.7    +      -       -      +
     66E  MET*     3.7    40.5    -      -       +      +
     67E  VAL      3.5     4.0    -      -       -      +
     68E  GLU*     2.6    64.3    +      -       -      +
    112E  LEU      3.6     2.0    -      -       -      +
    113E  ALA      4.0     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 41 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33E  VAL*     4.6     4.7    -      -       +      -
     34E  VAL      3.1     9.4    -      -       -      +
     35E  GLY*     4.0     0.9    -      -       -      -
     40E  ARG*     1.3    73.6    -      -       -      +
     42E  GLY*     1.3    59.7    +      -       -      +
     66E  MET*     3.3     5.9    -      -       -      +
     67E  VAL*     2.8    38.1    +      -       +      +
     69E  VAL*     3.8    20.2    -      -       +      -
    109E  ILE*     3.5    15.7    -      -       +      +
    112E  LEU*     3.4    11.9    -      -       +      +
    113E  ALA*     3.1    50.0    -      -       +      +
    136E  MET*     4.5     6.1    -      -       -      -
    139E  LEU*     4.3    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 42 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32E  VAL      3.7     1.0    -      -       -      +
     33E  VAL*     3.4     6.9    -      -       -      +
     34E  VAL*     2.5    38.3    +      -       -      -
     41E  VAL*     1.3    76.8    -      -       -      +
     43E  LEU*     1.3    60.1    +      -       -      -
     62E  ALA*     3.8     8.4    -      -       -      +
     65E  ASN      2.8    16.8    -      -       -      -
     66E  MET*     3.7     9.4    -      -       -      -
    136E  MET*     4.0     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 43 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11E  ILE*     4.9     1.8    -      -       +      -
     31E  LEU*     3.4    21.1    -      -       +      -
     32E  VAL      3.2    14.4    -      -       -      +
     33E  VAL*     4.5     8.1    -      -       +      +
     42E  GLY*     1.3    74.1    -      -       -      +
     44E  GLY*     1.3    70.9    +      -       -      +
     61E  TYR      4.1     1.0    -      -       -      +
     62E  ALA*     3.3    10.7    +      -       -      -
     65E  ASN*     3.4    21.5    +      -       -      +
    109E  ILE*     4.4     9.0    -      -       +      -
    132E  ALA*     3.9    25.8    -      -       +      -
    133E  TYR*     3.9    33.6    +      -       +      -
    136E  MET*     3.4    40.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 44 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30E  ALA      3.4     1.4    -      -       -      +
     31E  LEU*     3.2     5.5    -      -       -      +
     32E  VAL*     2.5    45.2    +      -       -      +
     43E  LEU*     1.3    77.8    -      -       -      +
     45E  PHE*     1.3    61.3    +      -       -      -
     46E  GLY      4.1     0.7    -      -       -      -
     58E  ALA*     3.8     6.3    -      -       -      -
     61E  TYR*     4.2     2.5    -      -       -      -
     62E  ALA*     3.3    23.5    -      -       -      +
    133E  TYR*     5.2     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 45 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1079A    G      4.2    16.4    -      -       -      -
   1080A    A      4.0     8.1    -      -       -      -
     12E  LEU*     5.1     4.3    -      -       +      -
     14E  ARG*     4.1    16.6    -      -       +      -
     29E  GLY*     3.8    11.7    -      -       -      -
     30E  ALA      3.1    36.8    -      -       -      -
     31E  LEU*     3.6    23.1    -      -       +      -
     44E  GLY*     1.3    72.6    -      -       -      -
     46E  GLY*     1.3    58.5    -      -       -      +
     47E  LYS*     3.4    38.3    +      -       -      -
     58E  ALA*     4.4     1.7    -      -       -      +
     61E  TYR*     4.4    12.8    -      -       -      +
    129E  ILE*     3.4    34.5    -      -       +      -
    133E  TYR*     4.3    18.8    +      +       +      +
----------------------------------------------------------
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Residues in contact with GLY 46 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29E  GLY*     3.6     1.0    -      -       -      -
     30E  ALA*     2.9    32.6    +      -       -      +
     45E  PHE*     1.3    74.5    -      -       -      +
     47E  LYS*     1.3    65.3    +      -       -      -
     54E  ALA*     3.6    11.7    -      -       -      +
     57E  LYS*     4.5     3.1    -      -       -      -
     58E  ALA*     3.7    20.0    -      -       -      +
     61E  TYR*     4.4    11.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 47 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1077A    G      2.7    34.4    +      -       -      -
   1079A    G      4.2     8.9    +      -       -      -
   1080A    A      3.5    23.8    +      -       -      +
   1081A    G      4.7     6.7    +      -       -      +
     27E  ARG*     4.3    17.9    -      -       -      +
     28E  PHE      2.9    13.7    -      -       -      +
     29E  GLY*     4.2     7.9    -      -       -      -
     45E  PHE*     3.4    38.5    +      -       +      -
     46E  GLY*     1.3    79.0    -      -       -      +
     48E  ALA*     1.3    64.8    +      -       -      +
     54E  ALA*     4.1     1.1    -      -       -      +
     57E  LYS*     3.5    17.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 48 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1072A    G      4.4     0.9    -      -       -      +
     27E  ARG*     4.0     8.7    -      -       -      +
     28E  PHE*     3.0    27.6    +      -       -      +
     47E  LYS*     1.3    77.3    -      -       -      +
     49E  PRO*     1.3    77.5    -      -       +      +
     50E  GLU      3.2     1.7    +      -       -      +
     53E  LEU*     3.5    27.1    -      -       +      -
     54E  ALA*     3.6    11.2    -      -       -      +
     57E  LYS*     3.4    17.0    -      -       -      +
----------------------------------------------------------
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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