Contacts of the strand formed by residues 241 - 250 (chain A) in PDB entry 1LEK


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 241 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  ASP*     3.3    34.5    -      -       +      -
    207A  GLY      3.5     6.8    +      -       -      -
    208A  PHE*     2.9    58.1    +      -       +      -
    209A  TYR*     3.7    26.0    -      +       -      -
    211A  ALA*     3.8    28.9    -      -       +      -
    233A  THR*     3.8     9.9    -      -       +      -
    234A  ARG*     3.3     9.0    -      -       -      +
    235A  PRO*     3.7    35.0    -      -       +      -
    236A  ALA*     4.4     3.7    -      -       -      +
    239A  GLY      3.8     9.4    -      -       -      -
    240A  THR*     1.3    76.1    +      -       -      +
    242A  GLN*     1.3    64.2    +      -       -      +
     53B  ASP*     5.4     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 242 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  TRP*     3.3    12.7    -      -       -      -
    205A  ALA      3.3    14.8    -      -       -      +
    206A  LEU*     3.6    20.0    -      -       +      +
    207A  GLY      5.0     0.7    -      -       -      +
    208A  PHE*     3.4     4.9    -      -       -      -
    233A  THR*     3.6     1.7    -      -       -      +
    234A  ARG*     2.6    80.0    +      -       +      +
    236A  ALA*     4.8     8.4    -      -       +      +
    241A  PHE*     1.3    76.8    -      -       -      +
    243A  LYS*     1.3    65.0    +      -       -      +
     10B  TYR*     3.1    18.7    -      -       +      -
     11B  SER      3.4    24.0    +      -       -      -
     12B  ARG      4.6     3.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 243 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  TRP*     3.7     4.8    -      -       -      -
    205A  ALA*     3.0    29.1    +      -       +      +
    208A  PHE*     4.0     8.5    -      -       +      -
    213A  ILE*     4.0    20.2    -      -       +      +
    215A  LEU*     3.8    25.8    -      -       +      +
    230A  LEU*     4.5    22.4    -      -       -      +
    231A  VAL*     2.9    38.2    +      -       -      +
    232A  GLU*     3.8     3.4    -      -       -      +
    233A  THR*     3.3    33.3    +      -       -      +
    234A  ARG*     5.4     0.2    -      -       -      +
    242A  GLN*     1.3    80.6    -      -       -      +
    244A  TRP*     1.3    69.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 244 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202A  ARG*     3.2    38.1    -      -       +      -
    203A  CYS      3.0    13.7    -      -       -      +
    204A  TRP*     3.5    42.4    -      +       +      -
    215A  LEU*     3.8     4.5    -      -       -      -
    229A  GLU*     3.3    36.1    -      -       -      -
    230A  LEU*     3.3    22.0    -      -       -      +
    231A  VAL*     3.4    46.4    +      -       +      +
    234A  ARG*     3.7    11.8    -      -       -      +
    243A  LYS*     1.3    79.3    -      -       -      +
    245A  ALA*     1.3    66.8    +      -       -      +
    246A  SER*     3.4    24.0    -      -       -      -
     99B  MET*     4.4    13.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 245 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203A  CYS*     2.8    34.4    +      -       +      +
    215A  LEU*     3.9    22.9    -      -       +      +
    217A  TRP*     2.9    17.0    +      -       +      +
    228A  MET*     3.9    24.0    -      -       +      -
    229A  GLU      3.2     9.4    -      -       -      +
    230A  LEU*     3.9     5.4    -      -       +      -
    243A  LYS*     6.0     0.2    -      -       -      -
    244A  TRP*     1.3    77.2    -      -       -      +
    246A  SER*     1.3    61.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 246 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200A  THR*     4.3    12.8    -      -       -      +
    201A  LEU      3.0    14.8    -      -       -      -
    202A  ARG*     4.0    13.1    +      -       -      -
    217A  TRP*     3.9     2.0    -      -       -      +
    228A  MET*     2.9     9.6    -      -       -      +
    229A  GLU*     2.6    49.6    +      -       -      +
    244A  TRP*     3.4    21.1    -      -       -      -
    245A  ALA*     1.3    75.3    -      -       -      +
    247A  VAL*     1.3    62.1    +      -       -      +
    248A  VAL*     6.1     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 247 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200A  THR*     3.7     0.8    -      -       -      -
    201A  LEU*     2.8    36.2    +      -       +      +
    217A  TRP*     3.7    39.3    -      -       +      -
    224A  LEU*     3.8    26.2    -      -       +      -
    227A  ASP*     4.4    15.3    -      -       +      +
    228A  MET*     4.4     8.5    -      -       +      +
    246A  SER*     1.3    75.6    -      -       -      +
    248A  VAL*     1.3    74.9    +      -       -      +
    249A  VAL*     3.6    18.2    +      -       +      -
    257A  TYR*     4.6     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 248 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194A  ARG*     3.8    38.1    -      -       -      +
    198A  LYS*     3.4    32.3    -      -       +      -
    199A  VAL      3.4    10.3    -      -       -      +
    200A  THR*     4.2     8.1    -      -       +      +
    227A  ASP      5.0     5.0    +      -       -      +
    246A  SER*     6.1     0.9    -      -       -      +
    247A  VAL*     1.3    81.3    -      -       -      +
    249A  VAL*     1.3    64.1    +      -       -      +
    250A  PRO*     4.7     0.9    -      -       -      +
    257A  TYR*     5.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 249 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198A  LYS*     3.0     7.5    -      -       -      +
    199A  VAL*     2.7    63.0    +      -       +      +
    201A  LEU*     3.6    17.9    -      -       +      -
    247A  VAL*     3.6    18.6    -      -       +      -
    248A  VAL*     1.3    79.3    -      -       -      +
    250A  PRO*     1.3    73.9    -      -       +      +
    254A  GLU*     4.1    10.1    -      -       +      -
    257A  TYR*     3.5    40.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 250 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197A  ASP      4.8     1.1    -      -       -      +
    198A  LYS*     3.9    11.4    -      -       +      -
    248A  VAL      4.7     0.4    -      -       -      +
    249A  VAL*     1.3    91.2    -      -       +      +
    251A  LEU*     1.3    70.2    +      -       -      +
    252A  GLY      3.3     0.2    +      -       -      -
    253A  LYS*     2.8    49.8    +      -       +      +
    254A  GLU*     3.6     3.1    -      -       -      +
    257A  TYR*     3.6    17.3    -      -       +      +
----------------------------------------------------------
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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