Contacts of the strand formed by residues 252 - 257 (chain A) in PDB entry 1L6O


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 252 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251A  MSE      1.3    85.2    -      -       -      +
    253A  ILE*     1.3    74.3    +      -       -      +
    254A  THR*     5.6     0.9    -      -       -      +
    305A  LEU*     4.1    22.7    -      -       +      -
    313A  GLU*     6.1     0.7    -      -       -      +
    337A  THR*     5.2     6.1    -      -       -      -
    338A  VAL      3.7    10.3    -      -       -      +
    339A  ALA*     4.6     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 253 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251A  MSE      4.0    15.2    +      -       +      -
    252A  ILE*     1.3    80.6    -      -       -      +
    254A  THR*     1.4    65.2    -      -       -      +
    255A  VAL*     3.6    23.5    -      -       +      +
    297A  ARG*     4.3    24.7    -      -       +      +
    336A  LEU      3.6     1.2    -      -       -      +
    337A  THR*     3.0     4.7    -      -       -      -
    338A  VAL*     2.7    52.7    +      -       +      +
    340A  LYS*     4.0    22.4    -      -       +      -
    285C  SER*     4.4    17.7    -      -       -      +
    287C  MSE      4.4     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 254 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252A  ILE*     5.6     1.6    -      -       -      +
    253A  ILE*     1.4    72.0    -      -       -      +
    255A  VAL*     1.3    73.9    +      -       -      +
    256A  THR*     5.2     1.1    -      -       +      +
    297A  ARG*     3.8    15.1    +      -       -      -
    335A  VAL*     4.2    17.3    -      -       +      -
    336A  LEU      3.4     1.8    -      -       -      -
    337A  THR*     2.8    22.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 255 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253A  ILE*     3.6    21.8    -      -       +      -
    254A  THR*     1.3    83.5    -      -       -      +
    256A  THR*     1.3    60.0    +      -       -      +
    257A  LEU*     4.3    20.4    -      -       +      -
    295A  ASP*     4.2     8.1    -      -       -      +
    297A  ARG*     3.4    29.6    -      -       +      +
    298A  ILE*     3.7    31.0    -      -       +      -
    334A  ILE      3.8     1.6    -      -       -      +
    335A  VAL*     3.1     7.8    -      -       -      -
    336A  LEU*     2.5    52.9    +      -       +      +
    338A  VAL*     6.0     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 256 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    254A  THR*     4.2     1.7    +      -       +      -
    255A  VAL*     1.3    73.3    -      -       -      +
    257A  LEU*     1.3    73.6    +      -       -      +
    258A  ASN      3.9     0.9    +      -       -      -
    295A  ASP*     4.8     7.8    -      -       -      +
    297A  ARG*     4.5     4.7    +      -       -      +
    333A  PRO*     4.5     8.1    -      -       -      +
    334A  ILE      3.6     7.1    +      -       -      -
    335A  VAL*     3.7    18.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 257 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    255A  VAL*     4.3    10.5    -      -       +      +
    256A  THR*     1.3    82.6    +      -       -      +
    258A  ASN*     1.3    60.5    +      -       -      +
    259A  MSE      3.5    20.5    +      -       -      -
    265A  LEU*     3.8    25.4    -      -       +      -
    291A  ALA*     3.4    30.1    -      -       +      +
    292A  VAL*     4.2    10.8    -      -       +      +
    295A  ASP*     4.3    13.7    -      -       +      -
    333A  PRO*     4.0     6.1    -      -       -      +
    334A  ILE*     2.9    35.8    +      -       +      +
    336A  LEU*     4.1    25.6    -      -       +      -
----------------------------------------------------------
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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