Contacts of the strand formed by residues 249 - 253 (chain A) in PDB entry 4K8T


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 ALA 249 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242A  VAL      3.4    13.5    -      -       -      +
    243A  THR*     4.1     3.6    -      -       +      -
    244A  MSE      3.3    13.4    -      -       -      +
    248A  GLY*     1.3    75.2    -      -       -      +
    250A  VAL*     1.3    59.9    +      -       -      +
    251A  ILE*     4.3     6.3    -      -       +      -
    258A  TYR      4.6     0.2    -      -       -      -
    259A  TYR*     3.6     1.7    -      -       -      -
    260A  VAL*     2.9    36.0    +      -       +      +
    278A  PHE*     3.7    35.4    -      -       +      -
    296A  GLY*     5.6     0.2    -      -       -      -
    300A  CYS*     4.1     6.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 250 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  LEU*     3.8    29.6    -      -       +      -
    242A  VAL*     3.0    38.9    +      -       +      +
    244A  MSE      3.9    15.0    -      -       +      -
    249A  ALA*     1.3    75.3    -      -       -      +
    251A  ILE*     1.3    73.5    +      -       -      +
    252A  LEU*     3.5    13.0    -      -       +      +
    257A  ARG*     4.2    11.4    -      -       +      -
    258A  TYR      3.4     8.1    -      -       -      +
    259A  TYR*     3.7    38.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 251 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239A  ILE*     4.3     9.9    -      -       +      -
    240A  ALA      3.4     9.2    -      -       -      +
    241A  ALA*     3.9    12.3    -      -       +      -
    249A  ALA*     4.6     4.7    -      -       +      -
    250A  VAL*     1.3    81.1    -      -       -      +
    252A  LEU*     1.3    63.2    +      -       -      +
    256A  GLU      3.9     0.2    -      -       -      +
    257A  ARG*     3.4     5.2    -      -       -      -
    258A  TYR*     2.8    46.8    +      -       +      +
    260A  VAL*     5.1     3.1    -      -       +      -
    278A  PHE*     4.1    13.5    -      -       +      -
    282A  PHE*     3.6    40.2    -      -       +      -
    292A  LEU*     3.7    37.0    -      -       +      +
    296A  GLY*     4.1     9.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 252 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  LEU*     3.6    48.7    -      -       +      +
    231A  ASN*     5.6     0.2    -      -       -      -
    233A  ILE*     4.7     1.3    -      -       +      -
    234A  ALA*     4.0    19.8    -      -       +      -
    238A  LYS      4.0     0.3    -      -       -      +
    239A  ILE*     3.4     6.1    -      -       -      +
    240A  ALA*     2.8    45.4    +      -       +      +
    242A  VAL*     3.9    11.4    -      -       +      -
    250A  VAL*     3.5    22.4    -      -       +      +
    251A  ILE*     1.3    78.0    -      -       -      +
    253A  LYS*     1.3    61.4    +      -       -      +
    254A  GLY      4.2     0.9    -      -       -      +
    256A  GLU      3.4     5.2    -      -       -      +
    257A  ARG*     3.5    35.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 253 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238A  LYS*     3.6    18.2    -      -       -      +
    239A  ILE*     4.1    17.2    -      -       +      +
    252A  LEU*     1.3    76.3    -      -       -      +
    254A  GLY*     1.3    60.3    +      -       -      +
    255A  ARG      3.1     0.5    +      -       -      -
    256A  GLU*     2.9    57.9    +      -       +      +
    258A  TYR*     5.2     0.6    -      -       +      -
    292A  LEU*     3.8    30.6    -      -       +      +
----------------------------------------------------------
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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