Contacts of the strand formed by residues 98 - 106 (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 SER 98 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90E  GLU      5.1     0.5    -      -       -      +
     91E  VAL*     3.7     8.1    +      -       -      +
     94E  THR*     4.4     7.8    +      -       -      +
     96E  SER*     2.7    28.4    +      -       -      -
     97E  LEU*     1.3    80.0    -      -       -      +
     99E  ALA*     1.3    64.3    +      -       -      +
    120E  GLN*     4.3     9.9    -      -       -      -
    121E  VAL      3.2     7.6    -      -       -      -
    122E  SER*     3.5    11.4    -      -       -      -
    201E  FMT      3.4    22.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 99 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90E  GLU*     4.0    18.4    -      -       +      +
     91E  VAL*     4.2     4.7    -      -       +      +
     98E  SER*     1.3    77.9    -      -       -      +
    100E  SER*     1.3    62.0    +      -       -      +
    101E  PHE*     3.8    26.3    -      -       +      -
    120E  GLN*     3.5     5.8    +      -       -      +
    121E  VAL      2.9    30.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 100 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99E  ALA*     1.3    75.0    -      -       -      +
    101E  PHE*     1.3    73.3    +      -       -      +
    118E  VAL*     6.2     2.0    -      -       -      -
    119E  LEU      3.4     9.4    -      -       -      -
    120E  GLN*     4.1    10.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 101 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86E  VAL*     3.5    44.0    -      -       +      -
     87E  PRO*     4.9     0.9    -      -       +      -
     90E  GLU*     3.6    36.1    -      -       +      -
     91E  VAL*     4.0    14.8    -      -       +      -
     99E  ALA*     3.8    35.0    -      -       +      -
    100E  SER*     1.3    80.2    -      -       -      +
    102E  ASN*     1.3    59.0    +      -       -      +
    103E  ALA*     3.6     7.4    -      -       +      +
    117E  LEU      3.3     1.6    -      -       -      +
    118E  VAL*     3.3     6.5    -      -       -      +
    119E  LEU*     2.7    52.4    +      -       +      +
    121E  VAL*     4.1    12.1    -      -       +      -
     93F  ALA      6.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 102 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8E  TYR*     5.5     1.4    +      -       -      -
     10E  GLU*     5.9     2.2    +      -       -      -
    100E  SER      4.3     0.2    -      -       -      -
    101E  PHE*     1.3    70.6    -      -       -      +
    103E  ALA*     1.3    58.9    +      -       -      +
    116E  SER*     3.6    11.9    +      -       -      -
    117E  LEU      3.5     2.0    -      -       -      +
    118E  VAL*     3.3    27.2    -      -       +      +
     93F  ALA      3.4    15.7    +      -       -      +
     94F  THR*     3.6     2.8    -      -       +      -
     95F  PRO*     3.2    47.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 103 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84E  ALA*     4.1    23.1    -      -       +      -
     86E  VAL*     5.1     5.6    -      -       +      -
    101E  PHE*     4.7    12.6    -      -       +      -
    102E  ASN*     1.3    72.0    -      -       -      +
    104E  PRO*     1.3    68.7    -      -       +      +
    105E  LEU*     3.5     0.5    +      -       -      +
    116E  SER*     3.2     2.6    -      -       -      -
    117E  LEU*     2.7    44.9    +      -       +      +
    119E  LEU*     4.8     5.2    -      -       +      -
    206E  FMT      4.3     8.5    -      -       -      +
     92F  LEU      5.6     0.2    -      -       -      +
     93F  ALA      4.6     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 104 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83E  GLU      4.3     0.9    -      -       -      +
     84E  ALA*     4.5     0.7    -      -       -      +
    102E  ASN      3.6     8.3    -      -       -      +
    103E  ALA*     1.3    83.2    -      -       +      +
    105E  LEU*     1.3    65.0    +      -       -      +
    106E  LEU*     3.8     5.9    +      -       +      +
    112E  PRO*     5.3     5.2    -      -       +      -
    115E  ALA      3.6     8.3    -      -       -      +
    116E  SER*     4.2     4.7    -      -       -      -
    206E  FMT      3.0    24.2    +      -       -      +
     92F  LEU*     3.2    35.2    -      -       +      +
     93F  ALA      4.1     0.4    -      -       -      -
     94F  THR      3.7    20.2    -      -       -      +
     95F  PRO*     4.4     4.9    -      -       +      -
     97F  LEU*     3.8    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 105 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9E  ALA*     5.1     3.1    -      -       +      -
     12E  VAL*     5.1     2.2    -      -       +      -
     67E  VAL      5.2     0.7    -      -       -      +
     69E  VAL*     3.7    33.9    -      -       +      -
     81E  LEU*     5.6     0.9    -      -       +      -
     82E  GLY*     4.0    15.0    -      -       -      +
     83E  GLU*     3.7    10.3    -      -       -      +
     84E  ALA*     4.0    20.2    -      -       +      +
    103E  ALA      4.3     0.7    -      -       -      +
    104E  PRO*     1.3    73.3    -      -       -      +
    106E  LEU*     1.3    61.0    +      -       -      +
    112E  PRO*     3.4     5.7    -      -       -      +
    113E  THR*     2.9    33.8    +      -       -      +
    115E  ALA*     2.9    38.3    +      -       +      +
    116E  SER*     4.1    11.4    -      -       -      +
    117E  LEU*     3.8    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 106 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80E  PHE*     3.8     0.2    -      -       -      -
     82E  GLY*     3.3     4.7    -      -       -      -
     83E  GLU*     2.9    44.8    +      -       +      +
    104E  PRO*     4.4    10.1    -      -       +      +
    105E  LEU*     1.3    76.2    -      -       -      +
    107E  ASP*     1.3    68.6    +      -       -      +
    110E  LYS*     3.8    35.7    -      -       +      +
    111E  GLN      3.3     2.2    -      -       -      +
    112E  PRO*     3.7    28.0    -      -       +      -
    113E  THR*     3.8     3.4    -      -       -      -
    206E  FMT      4.4    14.8    -      -       -      +
     60F  ASP*     4.4    11.7    -      -       +      +
     92F  LEU*     4.0    29.4    -      -       +      -
----------------------------------------------------------
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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