Contacts of the strand formed by residues 255 - 265 (chain C) in PDB entry 1LWU


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 HIS 255 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247C  ASP*     6.3     2.2    -      -       +      -
    248C  LEU      3.5     7.0    -      -       -      +
    249C  THR*     3.2    24.0    +      -       -      +
    253C  ASN*     3.3    47.3    +      -       -      -
    254C  THR*     1.3    75.3    -      -       -      +
    256C  ARG*     1.3    64.2    +      -       -      +
    257C  TYR*     5.7     1.0    -      -       -      -
    283C  ASP*     4.4     2.9    -      -       -      +
    379C  MET*     5.2     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 256 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247C  ASP*     3.8     2.8    -      -       -      +
    248C  LEU*     3.2    30.1    +      -       -      +
    254C  THR*     3.9    12.6    +      -       +      +
    255C  HIS*     1.3    78.1    -      -       -      +
    257C  TYR*     1.3    62.5    +      -       -      +
    283C  ASP*     2.8    47.1    +      -       -      +
    284C  ALA*     4.0     9.6    -      -       +      -
    370C  TRP*     3.1    56.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 257 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245C  ARG*     3.7    19.0    +      -       -      -
    246C  ILE      3.1    12.6    -      -       -      +
    247C  ASP*     3.5    14.8    -      -       -      +
    255C  HIS      5.7     0.7    -      -       -      -
    256C  ARG*     1.3    79.4    -      -       -      +
    258C  ALA*     1.3    57.2    +      -       -      +
    259C  ASP*     2.8    39.5    -      -       -      -
    281C  ASP*     2.5    27.5    +      -       +      -
    282C  GLY*     3.1    29.7    -      -       -      -
    283C  ASP*     2.9    30.4    +      -       -      -
    284C  ALA*     3.0    26.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 258 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244C  LEU      3.8     0.3    -      -       -      +
    245C  ARG*     3.4     0.5    -      -       -      -
    246C  ILE*     2.9    36.8    +      -       +      +
    248C  LEU*     5.3     0.2    -      -       +      -
    257C  TYR*     1.3    76.3    -      -       -      +
    259C  ASP*     1.3    70.3    +      -       -      +
    260C  TYR*     4.0    10.1    -      -       +      -
    279C  TYR*     4.1    10.3    -      -       +      -
    281C  ASP      3.9     5.6    -      -       -      -
    282C  GLY*     4.3     0.4    -      -       -      -
    284C  ALA*     3.9     2.7    -      -       +      +
    367C  TRP*     4.0    36.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 259 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243C  ARG*     3.1    21.5    +      -       -      +
    244C  LEU      3.3     8.1    -      -       -      +
    245C  ARG*     3.0    32.5    +      -       -      +
    257C  TYR*     2.8    30.3    -      -       -      -
    258C  ALA*     1.3    91.6    -      -       -      +
    260C  TYR*     1.3    73.0    +      -       -      +
    279C  TYR*     3.4     5.0    -      -       -      -
    280C  LEU*     3.0    34.6    +      -       +      -
    281C  ASP*     3.0    18.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 260 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242C  TYR      3.9     0.3    -      -       -      +
    243C  ARG*     3.4     2.0    -      -       -      -
    244C  LEU*     2.7    56.4    +      -       +      +
    246C  ILE*     4.4     2.5    -      -       +      -
    258C  ALA*     4.0    16.6    -      -       +      -
    259C  ASP*     1.3    93.3    -      -       -      +
    261C  GLY*     1.3    62.6    +      -       -      +
    263C  PHE*     4.0     1.5    -      -       +      +
    276C  TYR*     3.4    41.7    -      +       +      -
    278C  MET      3.4     8.5    -      -       -      -
    279C  TYR*     3.6    11.7    -      +       -      -
    280C  LEU*     3.8     2.0    -      -       -      -
    286C  ASN*     3.1    45.2    +      -       -      -
    287C  ALA      3.5     1.4    +      -       -      -
    288C  PHE*     3.2    49.8    +      +       +      -
    367C  TRP*     3.9     4.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLY 261 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    260C  TYR*     1.3    70.3    -      -       -      +
    262C  HIS*     1.3    58.2    +      -       -      -
    263C  PHE      2.9    13.5    +      -       -      -
    276C  TYR*     3.1     4.3    -      -       -      +
    277C  SER*     2.8    31.0    +      -       -      -
    278C  MET      3.2     2.6    +      -       -      -
    280C  LEU*     2.9    27.9    -      -       -      +
    387C  MET*     3.5    17.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 262 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241C  ALA*     3.8    19.5    -      -       +      +
    242C  TYR      3.0    15.8    +      -       -      +
    261C  GLY*     1.3    70.3    -      -       -      +
    263C  PHE*     1.3    67.9    +      -       -      +
    264C  LYS*     3.5     6.1    +      -       -      +
    275C  PHE*     3.6    23.8    -      -       +      -
    276C  TYR*     4.0     0.4    -      -       -      -
    277C  SER*     2.9    38.6    -      -       -      +
    280C  LEU*     5.9     0.4    -      -       +      -
    387C  MET*     3.2    28.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 263 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194C  ILE*     5.6     3.4    -      -       +      -
    233C  ILE*     4.2    13.7    -      -       +      -
    237C  THR*     3.6    31.2    -      -       +      +
    240C  GLN      5.5     0.2    -      -       -      +
    242C  TYR*     2.8    20.6    +      -       -      +
    244C  LEU*     3.3    48.5    -      -       +      +
    260C  TYR      4.0     2.9    -      -       -      +
    261C  GLY      2.9     4.8    +      -       -      -
    262C  HIS*     1.3    80.0    -      -       -      +
    264C  LYS*     1.3    69.4    +      -       -      +
    265C  LEU*     3.9    17.7    -      -       +      -
    274C  LEU*     3.2    29.2    -      -       +      -
    275C  PHE      3.2     9.2    -      -       -      -
    276C  TYR*     4.1     7.4    -      +       +      -
    288C  PHE*     5.4     0.7    -      +       -      -
    333C  TRP*     4.6    10.1    -      +       -      -
    382C  MET*     4.7     9.0    -      -       +      -
    384C  LEU*     3.8    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 264 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237C  THR*     3.4    26.5    -      -       -      +
    238C  GLY*     4.9    12.0    -      -       -      +
    262C  HIS      3.7     4.5    -      -       -      +
    263C  PHE*     1.3    81.0    -      -       -      +
    265C  LEU*     1.3    82.4    +      -       -      +
    266C  THR*     4.9    10.0    -      -       +      +
    274C  LEU*     4.2     0.7    -      -       -      +
    275C  PHE*     2.9    64.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 265 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230C  ASN*     4.3    15.9    -      -       -      +
    233C  ILE*     3.5    33.9    -      -       +      -
    234C  HIS*     2.5    38.7    +      -       +      +
    237C  THR*     3.5     5.2    +      -       -      -
    238C  GLY*     5.7     0.9    +      -       -      -
    263C  PHE*     3.9     9.2    -      -       +      -
    264C  LYS*     1.3    94.7    -      -       -      +
    266C  THR*     1.3    62.3    +      -       -      +
    272C  TYR*     4.3    16.6    -      -       +      +
    273C  ARG      3.1    13.9    -      -       -      +
    274C  LEU*     3.9     4.5    -      -       -      -
    333C  TRP*     3.3    40.6    -      -       +      +
----------------------------------------------------------
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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