Contacts of the strand formed by residues 410 - 415 (chain B) in PDB entry 4LT6


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 410 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    404B  LEU*     3.2    60.3    -      -       +      +
    405B  GLU*     4.0     9.6    -      -       -      +
    407B  ASN*     3.5    31.0    +      -       +      +
    408B  GLU      3.5     2.4    -      -       -      +
    409B  PHE*     1.3    78.3    -      -       -      +
    411B  THR*     1.3    64.6    +      -       -      +
    412B  LEU      3.9    21.8    -      -       -      +
    413B  ALA*     5.0     0.4    -      -       +      -
    440B  ILE*     4.2     9.2    -      -       +      -
    441B  ILE      3.8     4.0    -      -       -      +
    442B  PHE*     3.7    21.5    -      -       +      -
    443B  ARG*     5.0     1.2    -      -       -      +
    455B  LEU*     3.6    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 411 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  LYS*     5.1     5.5    +      -       -      -
    330B  THR*     4.8     7.4    +      -       -      -
    331B  SER*     4.1     4.2    +      -       -      -
    405B  GLU*     5.7     5.0    -      -       -      +
    410B  ILE*     1.3    76.4    -      -       -      +
    412B  LEU*     1.3    65.6    +      -       +      +
    441B  ILE*     3.2    24.1    +      -       +      -
    442B  PHE      4.0     6.4    +      -       -      -
    443B  ARG*     3.6    23.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 412 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331B  SER*     3.3    21.8    -      -       -      +
    334B  THR*     3.6    37.2    -      -       +      -
    335B  VAL*     4.4     5.4    -      -       +      -
    370B  TYR*     3.8    24.2    -      -       +      +
    405B  GLU*     5.7     0.7    -      -       -      -
    410B  ILE*     3.8     6.7    -      -       -      +
    411B  THR*     1.3    85.2    -      -       +      +
    413B  ALA*     1.3    62.0    +      -       -      +
    414B  HIS*     3.7    28.5    -      -       +      +
    439B  GLY      4.8     0.7    -      -       -      +
    440B  ILE*     3.4     6.1    -      -       -      -
    441B  ILE*     3.2    45.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 413 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331B  SER*     2.8    29.3    +      -       -      +
    332B  THR*     4.8     3.3    +      -       -      +
    401B  VAL*     3.7    30.7    -      -       +      +
    404B  LEU*     4.0    35.0    -      -       +      -
    405B  GLU*     4.4     4.4    -      -       +      +
    410B  ILE*     5.0     0.4    -      -       +      -
    412B  LEU*     1.3    74.5    -      -       -      +
    414B  HIS*     1.3    60.6    +      -       -      +
    415B  VAL      4.1     1.0    +      -       -      -
    438B  LEU*     4.9     2.9    -      -       +      -
    439B  GLY      3.5     6.1    -      -       -      +
    440B  ILE*     4.7     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 414 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233B  ARG      5.9     1.2    +      -       -      -
    234B  GLY      5.0     4.4    +      -       -      -
    235B  ILE*     5.7     0.2    -      -       -      +
    242B  PHE*     4.0    15.2    -      +       -      -
    332B  THR*     5.7     2.0    -      -       -      -
    335B  VAL*     3.4    34.9    -      -       +      +
    339B  GLU*     5.9     1.1    -      -       -      -
    366B  PHE*     3.7    23.7    -      +       -      -
    369B  LYS*     5.3     6.1    -      -       +      -
    370B  TYR*     2.5    40.2    +      +       +      +
    412B  LEU*     3.7    11.0    -      -       +      -
    413B  ALA*     1.3    75.1    -      -       -      +
    415B  VAL*     1.3    77.5    +      -       -      +
    416B  ASN*     5.2     1.0    -      -       -      -
    417B  PRO*     5.5     0.2    -      -       -      +
    437B  PHE      3.7     1.0    -      -       -      +
    438B  LEU*     3.3     6.3    -      -       -      +
    439B  GLY      2.9    34.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 415 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240B  LEU*     3.8    32.5    -      -       +      +
    242B  PHE*     3.6    12.0    -      -       +      -
    332B  THR*     5.1     4.0    -      -       +      +
    397B  ILE*     3.4    34.5    -      -       +      -
    401B  VAL*     3.8    20.2    -      -       +      -
    413B  ALA      4.1     0.4    -      -       -      -
    414B  HIS*     1.3    86.2    -      -       -      +
    416B  ASN*     1.3    66.7    +      -       -      +
    417B  PRO*     3.2    11.1    -      -       -      +
    436B  TRP*     5.5     2.5    -      -       +      -
    437B  PHE      3.6     4.0    -      -       -      +
    438B  LEU*     3.6    23.6    -      -       +      +
----------------------------------------------------------
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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