Contacts of the strand formed by residues 273 - 282 (chain M) in PDB entry 6LTJ


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 ILE 273 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    268M  ILE      3.7     1.0    -      -       -      +
    269M  HIS*     3.4     3.8    -      -       -      +
    270M  VAL      2.9    35.0    +      -       -      +
    271M  GLY*     5.8     0.2    -      -       -      -
    272M  ASN*     1.3    91.1    -      -       -      +
    274M  SER*     1.3    63.8    +      -       -      +
    275M  LEU      4.2     0.2    -      -       -      -
    303M  LEU*     4.7     7.4    -      -       +      -
    307M  PHE*     3.7    21.2    -      -       +      -
    353M  LEU*     4.0    31.0    -      -       +      -
    354M  GLU      3.5     6.1    -      -       -      +
    355M  THR*     4.3    13.7    -      -       +      -
    361M  MET*     4.6     0.2    -      -       -      -
     38R  ARG*     5.6     4.7    -      -       -      -
     41R  PHE*     3.8    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 274 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    268M  ILE      3.4     4.5    -      -       -      -
    269M  HIS*     3.5    18.0    +      -       -      +
    273M  ILE*     1.3    75.0    -      -       -      +
    275M  LEU*     1.3    60.4    +      -       -      +
    276M  VAL*     4.1    13.0    -      -       -      +
    352M  LEU      3.5     0.5    -      -       -      +
    353M  LEU*     2.8    26.2    -      -       -      -
    354M  GLU*     2.9    24.8    +      -       -      +
    356M  LEU*     3.6    31.7    -      -       -      +
    361M  MET*     4.0     9.9    -      -       -      -
    364M  LYS*     4.7     1.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 275 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266M  LEU*     3.6     4.3    -      -       +      +
    267M  ASN*     3.5     1.4    +      -       -      -
    268M  ILE*     2.9    45.6    +      -       +      +
    273M  ILE      4.2     0.4    -      -       -      -
    274M  SER*     1.3    72.6    +      -       -      +
    276M  VAL*     1.3    78.1    +      -       -      +
    277M  ASP*     4.8     5.6    -      -       +      +
    297M  LEU*     4.8     5.4    -      -       +      -
    301M  LEU*     4.2    20.9    -      -       +      -
    303M  LEU*     4.3     9.6    -      -       +      -
    307M  PHE*     4.2    14.1    -      -       +      -
    311M  ILE*     3.8    31.9    -      -       +      -
    351M  PRO*     3.8    28.3    -      -       +      -
    352M  LEU      3.6     6.5    -      -       -      +
    353M  LEU*     4.1    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 276 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265M  LYS*     6.4     0.7    -      -       +      -
    266M  LEU      3.1     8.7    -      -       -      +
    267M  ASN*     3.3    23.8    -      -       +      +
    274M  SER*     4.1    13.2    -      -       -      +
    275M  LEU*     1.3    82.6    -      -       -      +
    277M  ASP*     1.3    68.5    +      -       -      +
    350M  CYS      3.9     1.2    -      -       -      +
    351M  PRO*     3.5     0.7    -      -       -      +
    352M  LEU*     2.9    48.0    +      -       +      +
    354M  GLU*     5.3     4.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 277 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265M  LYS*     3.2     6.4    -      -       -      +
    266M  LEU*     2.9    54.0    +      -       -      +
    275M  LEU*     4.8     4.4    -      -       -      +
    276M  VAL*     1.3    81.3    -      -       -      +
    278M  GLN*     1.3    64.1    +      -       -      +
    279M  PHE*     3.5    15.3    -      -       -      -
    297M  LEU*     3.8    11.8    -      -       -      +
    350M  CYS      3.5     7.6    -      -       -      +
    351M  PRO*     3.3    26.4    -      -       +      +
    487O  ARG*     2.8    23.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 278 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263M  ILE*     3.3    39.6    -      -       +      +
    264M  ILE      3.2     8.1    -      -       -      +
    265M  LYS*     3.7    26.8    -      -       +      +
    277M  ASP*     1.3    82.0    -      -       -      +
    279M  PHE*     1.3    66.2    +      -       -      +
    348M  GLN*     3.7    41.2    +      -       -      +
    349M  TRP*     3.1    38.0    -      -       +      +
    350M  CYS      4.3     2.0    +      -       -      -
    487O  ARG*     3.5     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 279 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263M  ILE*     4.4     0.4    -      -       -      -
    264M  ILE*     2.9    59.2    +      -       +      +
    266M  LEU*     3.9    14.6    -      -       +      -
    277M  ASP*     3.5    26.2    -      -       -      -
    278M  GLN*     1.3    80.2    -      -       -      +
    280M  GLU*     1.3    72.9    +      -       -      +
    281M  TRP*     3.8    22.9    -      +       +      -
    293M  PHE*     3.3    35.2    -      +       -      -
    315M  ILE*     4.2     7.4    -      -       +      -
    341M  ARG*     5.8     0.4    -      -       -      +
    349M  TRP*     3.8    10.5    -      -       -      -
    487O  ARG*     3.4    17.5    -      -       -      +
    494O  VAL*     3.6    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 280 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261M  ARG*     3.4    29.2    +      -       +      +
    262M  VAL      3.5     6.7    -      -       -      +
    263M  ILE*     4.4     2.0    -      -       +      +
    279M  PHE*     1.3    74.5    -      -       -      +
    281M  TRP*     1.3    59.3    +      -       -      +
    333M  LEU*     4.3    15.7    -      -       +      +
    341M  ARG*     3.2    24.8    +      -       -      +
    349M  TRP*     3.7    22.4    -      -       +      -
    491O  ALA*     4.5     4.5    -      -       -      +
    492O  GLY*     2.5    44.3    +      -       -      +
    493O  ASP*     4.5     0.7    -      -       -      +
    494O  VAL*     3.0    33.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 281 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261M  ARG*     3.1     5.0    -      -       -      +
    262M  VAL*     2.9    35.4    +      -       +      +
    264M  ILE*     4.4    15.7    -      -       +      -
    279M  PHE*     3.8    15.3    -      +       +      +
    280M  GLU*     1.3    78.1    -      -       -      +
    282M  ASP*     1.3    79.6    +      -       -      +
    283M  MET*     3.3     3.3    +      -       +      +
    288M  ASN*     3.7    25.1    -      -       +      +
    289M  SER      3.7     4.0    -      -       -      -
    290M  PRO*     3.7    39.9    -      -       +      -
    293M  PHE*     3.9    22.7    -      +       +      -
    315M  ILE*     4.5     4.5    -      -       +      -
    319M  LEU*     3.8    32.2    -      -       +      +
    493O  ASP*     3.5     7.1    -      -       -      +
    494O  VAL*     3.5    17.9    -      -       +      -
    495O  CYS*     3.4    25.1    -      -       -      -
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Residues in contact with ASP 282 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259M  ASP*     3.1    22.3    -      -       -      +
    260M  GLN      2.9    18.5    +      -       -      -
    261M  ARG*     3.8     6.9    -      -       +      +
    281M  TRP*     1.3    76.5    +      -       -      +
    283M  MET*     1.3    65.8    +      -       -      +
    284M  SER*     2.9    24.7    +      -       -      -
    285M  GLU*     3.8    11.3    +      -       +      +
    288M  ASN*     2.7    26.6    +      -       -      +
    454O  ASN*     3.1    17.0    +      -       -      -
    457O  LYS*     4.1     3.1    -      -       -      -
    493O  ASP*     2.9    33.9    +      -       +      +
----------------------------------------------------------
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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