Contacts of the strand formed by residues 140 - 149 (chain A) in PDB entry 5FL6


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 LEU 140 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  TYR*     4.1     2.7    -      -       -      -
     91A  LEU*     4.9     2.7    -      -       +      -
    121A  VAL*     5.0     9.4    -      -       +      -
    122A  HIS      3.3    15.5    -      -       -      +
    123A  LEU*     3.9    19.7    -      -       +      -
    130A  VAL*     4.4    18.4    -      -       +      -
    133A  ALA*     4.1    10.0    +      -       +      +
    134A  LEU*     4.0    31.6    -      -       +      -
    135A  GLY      5.9     0.2    -      -       -      +
    136A  ARG      4.9     0.2    +      -       -      -
    138A  GLY      4.0     4.0    -      -       -      -
    139A  GLY*     1.3    83.3    -      -       -      +
    141A  ALA*     1.3    61.5    +      -       -      +
    142A  VAL*     5.7     0.4    -      -       +      -
    199A  LEU*     4.0    22.7    -      -       +      -
    205A  ALA*     6.0     0.4    -      -       +      -
    207A  GLY      4.0     3.9    +      -       -      +
    208A  VAL*     3.5    22.4    -      -       +      -
    209A  ILE*     3.1    22.3    +      -       -      +
    268A  Y0R      5.9     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 141 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  MET*     4.1    16.2    -      -       +      -
     82A  LEU*     4.3    11.9    -      -       +      -
     88A  TYR*     3.6    29.1    -      -       +      -
    121A  VAL*     3.7     0.2    -      -       -      -
    122A  HIS*     2.8    43.0    +      -       -      +
    140A  LEU*     1.3    74.5    -      -       -      +
    142A  VAL*     1.3    63.4    +      -       -      +
    143A  LEU*     5.9     0.2    -      -       +      -
    208A  VAL*     4.6     0.2    -      -       -      -
    209A  ILE*     3.3    12.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 142 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  HIS*     3.7    24.9    -      -       +      -
    120A  VAL      3.3     7.9    -      -       -      +
    121A  VAL*     4.3    15.7    -      -       +      -
    140A  LEU*     5.7     0.4    -      -       +      -
    141A  ALA*     1.3    79.0    -      -       -      +
    143A  LEU*     1.3    68.3    +      -       -      +
    199A  LEU*     5.2     4.0    -      -       +      -
    208A  VAL*     3.9    19.1    -      -       +      -
    209A  ILE      2.9     8.3    +      -       -      +
    210A  TRP*     3.3    42.5    -      -       +      -
    211A  THR*     3.0    28.8    +      -       -      +
    268A  Y0R      4.2     9.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 143 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  LEU*     3.4    34.8    -      -       +      -
     50A  LEU*     4.4     8.7    -      -       +      -
     53A  PHE*     5.8     0.4    -      -       +      -
     80A  MET*     4.1    24.9    -      -       +      -
     82A  LEU*     4.5     1.6    -      -       +      -
    118A  ILE      3.6     1.0    -      -       -      +
    119A  HIS*     3.3     4.9    -      -       -      -
    120A  VAL*     2.9    42.5    +      -       +      +
    122A  HIS*     3.7    23.6    -      -       +      -
    141A  ALA*     5.8     0.4    -      -       +      -
    142A  VAL*     1.3    76.1    -      -       -      +
    144A  ALA*     1.3    59.7    +      -       -      +
    185A  LEU*     4.2    21.9    -      -       +      +
    189A  PHE*     5.7     0.9    -      -       +      -
    211A  THR*     3.5    17.0    -      -       +      +
    213A  PHE*     4.1    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 144 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  GLU*     3.6    22.9    -      -       -      +
    118A  ILE      3.2     4.7    -      -       -      -
    119A  HIS*     3.7    10.1    -      -       +      +
    143A  LEU*     1.3    75.0    -      -       -      +
    145A  ALA*     1.3    59.8    +      -       -      +
    185A  LEU*     5.4     0.7    -      -       -      -
    210A  TRP*     4.2    10.3    -      -       +      -
    211A  THR      2.8    14.7    +      -       -      +
    212A  VAL*     3.3    18.1    -      -       +      +
    213A  PHE*     3.0    31.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  GLU*     3.3     5.6    -      -       -      +
    118A  ILE*     2.9    47.6    +      -       +      +
    144A  ALA*     1.3    74.9    -      -       -      +
    146A  PHE*     1.3    68.5    +      -       -      +
    147A  LEU      3.8     0.2    +      -       -      -
    185A  LEU*     4.4     1.8    -      -       +      -
    186A  PRO*     3.5    36.8    -      -       +      -
    212A  VAL*     5.6     0.4    -      -       -      -
    213A  PHE*     4.0     8.7    -      -       +      +
    215A  GLN      4.7     0.9    -      -       -      +
    217A  VAL*     4.3     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  ILE*     4.9     0.2    -      -       +      -
    105A  SER*     3.8     7.2    -      -       -      -
    107A  HIS*     3.3    42.0    -      -       +      -
    109A  VAL*     3.8    19.1    -      -       +      -
    114A  PHE*     3.4    56.3    -      +       +      -
    116A  ALA      3.6     1.8    -      -       -      -
    117A  GLU*     3.5    22.7    -      -       -      -
    145A  ALA*     1.3    74.5    -      -       -      +
    147A  LEU*     1.3    62.6    +      -       -      +
    148A  GLU      4.1     0.2    -      -       -      -
    193A  PHE*     6.6     0.2    -      +       -      -
    212A  VAL*     3.9    21.5    -      -       +      -
    213A  PHE      4.5    11.4    +      -       -      -
    214A  ASN      5.6     0.9    -      -       -      -
    215A  GLN      5.0     0.8    +      -       -      -
    216A  THR*     3.5    18.3    -      -       +      +
    217A  VAL*     2.9    26.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  LEU*     4.4    12.8    -      -       +      -
    114A  PHE*     4.2     0.5    -      -       -      +
    115A  PRO*     3.2    23.8    -      -       -      +
    116A  ALA*     2.8    46.2    +      -       +      +
    117A  GLU*     4.1     3.1    -      -       -      +
    118A  ILE*     4.0    14.4    -      -       +      -
    145A  ALA      4.1     0.2    -      -       -      +
    146A  PHE*     1.3    77.7    -      -       -      +
    148A  GLU*     1.3    61.3    +      -       -      +
    157A  TYR*     3.3    35.9    -      -       +      +
    217A  VAL*     3.4    21.1    -      -       +      +
    219A  LEU*     3.9    28.0    -      -       +      -
    224A  LEU*     4.6     4.7    -      -       +      -
    227A  LEU*     4.7     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  HIS*     4.9     4.2    +      -       -      -
    114A  PHE*     3.6    28.7    -      -       +      -
    115A  PRO*     4.3    11.5    -      -       +      +
    147A  LEU*     1.3    77.7    -      -       -      +
    149A  GLU*     1.3    64.5    +      -       -      +
    216A  THR*     2.7    38.0    +      -       -      +
    217A  VAL      2.8     9.1    +      -       -      +
    218A  MET*     3.3    13.1    -      -       -      +
    219A  LEU*     2.8    26.9    +      -       -      +
    224A  LEU*     4.1     6.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  PRO*     4.8     4.1    -      -       +      +
    148A  GLU*     1.3    75.1    -      -       -      +
    150A  GLY*     1.3    70.6    -      -       -      +
    218A  MET*     3.5    10.7    -      -       -      +
    219A  LEU      3.2     4.9    -      -       -      -
    221A  ALA*     3.6    36.6    +      -       -      +
    224A  LEU*     3.8    14.3    -      -       +      +
----------------------------------------------------------
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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