Contacts of the strand formed by residues 145 - 152 (chain E) in PDB entry 1XFB


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 PHE 145 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23E  ILE*     3.6    28.9    -      -       +      -
     30E  ILE*     4.4     7.4    -      -       +      -
     76E  GLY*     4.3     5.4    -      -       -      -
     77E  VAL      3.7    22.7    -      -       -      -
     78E  ILE*     3.6    20.2    -      -       +      -
    104E  VAL*     3.6    21.8    -      -       +      -
    105E  VAL      3.2    19.7    -      -       -      -
    106E  GLY*     2.9    43.1    -      -       -      -
    107E  ILE*     3.2     8.3    +      -       -      +
    144E  ASP*     1.3    82.0    -      -       -      +
    146E  ALA*     1.3    62.1    +      -       -      +
    183E  ILE*     3.7     5.3    -      -       -      +
    184E  VAL*     2.9    22.0    -      -       +      +
    186E  ILE*     3.6    35.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 146 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78E  ILE*     5.8     0.2    -      -       -      -
    107E  ILE*     3.2    17.7    -      -       +      +
    109E  VAL*     3.9    17.5    -      -       +      -
    135E  CYS*     5.7     0.4    -      -       -      -
    145E  PHE*     1.3    78.8    -      -       -      +
    147E  LYS*     1.3    61.5    +      -       -      +
    174E  TYR*     3.2    10.8    -      -       +      +
    178E  CYS*     4.1    10.5    -      -       -      -
    183E  ILE*     3.7    15.0    -      -       +      +
    184E  VAL      2.8     7.5    +      -       -      -
    186E  ILE*     2.8    31.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 147 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32E  ALA*     5.1     0.6    -      -       -      +
     34E  ASP*     3.2    33.6    +      -       -      +
     78E  ILE*     4.0    28.9    -      -       +      -
    107E  ILE      3.0     5.1    +      -       -      -
    108E  LYS*     3.4    12.0    -      -       +      +
    109E  VAL*     3.0    27.4    +      -       -      +
    110E  ASP*     3.9     1.9    +      -       -      +
    146E  ALA*     1.3    76.8    -      -       -      +
    148E  TRP*     1.3    64.4    +      -       -      +
    149E  ARG*     4.2    16.9    -      -       -      +
    174E  TYR*     3.3     3.6    -      -       -      -
    186E  ILE*     4.0     9.0    -      -       +      +
    188E  GLU*     2.8    31.2    +      -       +      +
    230E  LYS*     3.0    31.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 148 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109E  VAL*     4.0     3.4    -      -       +      -
    110E  ASP*     3.6    22.7    -      -       +      -
    125E  THR*     3.3    35.4    -      -       +      -
    126E  GLN      3.5     0.7    -      -       -      -
    127E  GLY*     3.4    28.7    -      -       -      -
    128E  LEU*     3.4    38.1    -      -       +      -
    131E  LEU*     4.4     5.2    -      -       +      -
    147E  LYS*     1.3    76.1    -      -       -      +
    149E  ARG*     1.3    64.0    +      -       -      +
    150E  CYS*     3.6    12.2    -      -       -      -
    170E  VAL*     3.3    25.5    -      -       +      +
    171E  LEU*     3.6    18.2    -      -       +      +
    174E  TYR*     3.3    50.3    +      +       +      -
    186E  ILE      3.7     1.8    +      -       -      -
    188E  GLU*     3.3    24.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 149 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108E  LYS*     5.7     2.9    -      -       -      +
    110E  ASP*     3.2    17.1    +      -       -      +
    112E  GLY      5.7     0.2    -      -       -      -
    113E  VAL*     5.6     2.1    -      -       -      +
    125E  THR*     2.8    21.3    +      -       -      +
    147E  LYS*     4.2    11.9    -      -       -      +
    148E  TRP*     1.3    76.0    -      -       -      +
    150E  CYS*     1.3    69.3    +      -       -      +
    151E  VAL*     3.4    31.4    +      -       +      +
    188E  GLU*     3.3    33.2    -      -       +      +
    190E  GLU*     2.4    43.0    +      -       -      +
    192E  LEU*     4.3     7.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 150 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125E  THR*     3.3    10.3    -      -       -      -
    148E  TRP*     3.6    23.3    -      -       -      -
    149E  ARG*     1.3    78.9    -      -       -      +
    151E  VAL*     1.3    66.3    +      -       -      +
    152E  LEU*     5.6     2.0    -      -       +      -
    167E  ASN*     3.3    36.3    -      -       +      +
    170E  VAL*     4.6     2.7    -      -       -      -
    171E  LEU*     3.6    25.8    -      -       +      -
    188E  GLU      3.0    13.2    +      -       -      +
    189E  PRO*     4.5     6.5    -      -       +      -
    190E  GLU*     3.2    21.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 151 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113E  VAL*     4.7    13.1    -      -       +      +
    123E  THR*     3.5    30.7    +      -       -      +
    124E  THR      5.9     0.2    -      -       -      -
    125E  THR*     4.5     1.4    +      -       -      -
    149E  ARG*     3.4    39.3    -      -       +      +
    150E  CYS*     1.3    82.9    -      -       -      +
    152E  LEU*     1.3    72.8    +      -       -      +
    153E  LYS*     5.9     0.2    -      -       +      -
    167E  ASN*     4.2     2.9    +      -       -      +
    190E  GLU      3.4     3.8    -      -       -      +
    192E  LEU*     3.5    40.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 152 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122E  GLU*     5.5     0.9    -      -       -      +
    123E  THR      5.2     0.2    -      -       -      +
    150E  CYS*     5.6     1.6    -      -       +      -
    151E  VAL*     1.3    80.8    -      -       -      +
    153E  LYS*     1.3    61.5    +      -       -      +
    159E  PRO*     5.0     9.2    -      -       +      -
    163E  ALA*     3.8    19.1    -      -       +      +
    164E  ILE*     4.6    13.9    -      -       +      -
    167E  ASN*     3.5    35.0    -      -       +      +
    189E  PRO*     5.6     5.8    -      -       +      -
    190E  GLU      2.8    12.4    +      -       -      +
    191E  ILE*     4.2    13.7    -      -       +      -
    192E  LEU*     2.9    31.6    +      -       -      +
    209E  VAL*     3.3    45.8    -      -       +      -
----------------------------------------------------------
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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