Contacts of the strand formed by residues 297 - 302 (chain K) in PDB entry 1XFB


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 297 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24K  VAL*     3.7    38.4    -      -       +      +
    266K  PRO      3.0    18.3    +      -       -      +
    267K  GLY*     3.8     1.3    -      -       -      -
    268K  VAL      2.8    24.3    +      -       -      -
    296K  TRP*     1.3    75.2    -      -       -      +
    298K  LEU*     1.3    63.1    +      -       -      +
    299K  THR*     3.8     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 298 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    254K  VAL*     4.3     5.8    -      -       +      -
    257K  LEU*     3.9    13.7    -      -       +      -
    268K  VAL*     3.6    17.3    -      -       +      -
    270K  PHE*     4.0    11.4    -      -       +      -
    284K  LEU*     3.3     4.1    -      -       -      +
    287K  ILE*     3.4    25.8    -      -       +      -
    288K  ASN*     2.8    35.8    +      -       -      +
    294K  ARG*     3.5    39.7    -      -       +      +
    296K  TRP*     3.4    34.5    +      -       +      +
    297K  ALA*     1.3    77.2    -      -       -      +
    299K  THR*     1.3    64.2    +      -       -      +
    339K  ALA      4.2     1.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 299 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24K  VAL*     4.3    20.2    -      -       +      +
     25K  ALA      5.0     0.7    -      -       -      +
     26K  PRO*     6.2     0.2    -      -       +      -
     27K  GLY      5.5     1.3    -      -       -      +
     28K  LYS      3.0    30.2    +      -       -      +
     29K  GLY*     3.5     2.1    -      -       -      -
    268K  VAL      3.2    10.0    +      -       -      -
    269K  THR*     4.5     9.2    -      -       -      +
    270K  PHE*     3.1    31.2    +      -       -      +
    284K  LEU*     3.8     9.4    -      -       -      +
    297K  ALA*     3.8     6.0    -      -       +      -
    298K  LEU*     1.3    81.1    -      -       -      +
    300K  PHE*     1.3    83.2    +      -       -      +
    339K  ALA*     3.8    22.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 300 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28K  LYS      4.1     1.6    -      -       -      -
     29K  GLY*     3.2    25.6    -      -       -      -
     30K  ILE*     2.8    53.3    +      -       -      +
     73K  CYS      3.5    14.1    -      -       -      -
     74K  ILE*     4.2     7.2    -      -       +      -
    269K  THR*     3.9     5.3    -      -       -      -
    270K  PHE      3.6     4.5    -      -       -      +
    284K  LEU*     3.7    10.3    -      -       +      -
    299K  THR*     1.3    95.1    +      -       -      +
    301K  SER*     1.3    58.2    +      -       -      +
    302K  TYR*     3.3    38.8    -      +       +      -
    306K  LEU*     3.8    17.0    -      -       +      -
    332K  ALA      4.4     5.2    -      -       -      -
    335K  ASN*     3.5    43.7    -      -       +      -
    336K  GLY*     3.9     3.4    -      -       -      -
    339K  ALA*     4.4     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 301 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30K  ILE*     3.4    28.5    -      -       -      +
     32K  ALA*     4.4     1.2    -      -       -      +
     78K  ILE*     3.7     5.2    -      -       -      +
    186K  ILE*     4.9     0.3    -      -       -      +
    230K  LYS*     3.3    38.0    +      -       -      +
    269K  THR*     3.2    33.9    +      -       -      -
    270K  PHE      2.7    13.3    +      -       -      +
    271K  LEU*     3.8     4.9    -      -       -      -
    272K  SER      4.3     0.2    +      -       -      -
    300K  PHE*     1.3    70.8    -      -       -      +
    302K  TYR*     1.3    60.6    +      -       -      +
    303K  GLY      4.1     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 302 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30K  ILE      3.3     7.7    +      -       -      +
     31K  LEU*     4.2     0.3    -      -       -      +
     32K  ALA*     2.9    27.0    +      -       -      -
    233K  MET*     3.2    16.6    -      -       +      +
    270K  PHE*     3.5    22.4    -      -       +      -
    271K  LEU      4.1     0.7    -      -       -      -
    272K  SER*     3.5    21.8    -      -       -      -
    280K  ALA*     3.1    41.1    +      -       +      -
    284K  LEU*     3.5     9.3    -      -       +      +
    300K  PHE*     3.3    27.5    -      +       +      -
    301K  SER*     1.3    75.6    -      -       -      +
    303K  GLY*     1.3    61.4    -      -       -      +
    305K  ALA*     3.4    20.6    -      -       +      -
    306K  LEU*     3.7    23.1    -      -       +      +
    335K  ASN*     3.5    31.9    -      -       -      -
----------------------------------------------------------
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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