Contacts of the strand formed by residues 297 - 302 (chain G) 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 G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24G  VAL*     3.7    37.5    -      -       +      +
    266G  PRO      3.0    17.6    +      -       -      +
    267G  GLY*     3.8     1.8    -      -       -      -
    268G  VAL*     2.8    24.4    +      -       -      +
    296G  TRP*     1.3    74.8    -      -       -      +
    298G  LEU*     1.3    63.5    +      -       -      +
    299G  THR*     3.8     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 298 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    254G  VAL*     4.3     5.8    -      -       +      -
    257G  LEU*     3.9    14.1    -      -       +      -
    268G  VAL*     3.6    17.9    -      -       +      -
    270G  PHE*     4.0    10.3    -      -       +      -
    284G  LEU*     3.3     4.8    -      -       -      +
    287G  ILE*     3.4    25.4    -      -       +      -
    288G  ASN*     2.8    35.2    +      -       -      +
    294G  ARG*     3.5    40.4    -      -       +      +
    296G  TRP*     3.4    32.9    +      -       +      +
    297G  ALA*     1.3    77.4    -      -       -      +
    299G  THR*     1.3    63.1    +      -       -      +
    339G  ALA      4.2     1.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 299 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24G  VAL*     4.3    20.4    -      -       +      +
     25G  ALA      5.0     0.7    -      -       -      +
     26G  PRO*     6.2     0.2    -      -       +      -
     27G  GLY      5.5     0.9    -      -       -      +
     28G  LYS      3.0    30.4    +      -       -      +
     29G  GLY*     3.5     2.1    -      -       -      -
    268G  VAL      3.2     9.6    +      -       -      -
    269G  THR*     4.2     8.7    -      -       -      +
    270G  PHE*     3.1    31.5    +      -       -      +
    284G  LEU*     3.8     8.7    -      -       -      +
    297G  ALA*     3.8     6.0    -      -       +      -
    298G  LEU*     1.3    82.1    -      -       -      +
    300G  PHE*     1.3    83.9    +      -       -      -
    339G  ALA*     3.8    22.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 300 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28G  LYS      4.1     2.0    -      -       -      -
     29G  GLY*     3.2    25.3    -      -       -      -
     30G  ILE*     2.8    52.6    +      -       -      +
     73G  CYS      3.5    14.4    -      -       -      -
     74G  ILE*     4.2     7.0    -      -       +      -
    269G  THR*     3.9     5.7    -      -       -      -
    270G  PHE      3.6     4.7    -      -       -      -
    284G  LEU*     3.7    10.3    -      -       +      -
    299G  THR*     1.3    93.3    +      -       -      +
    301G  SER*     1.3    58.2    +      -       -      +
    302G  TYR*     3.3    38.8    -      +       +      -
    306G  LEU*     3.8    17.7    -      -       +      -
    332G  ALA      4.4     5.2    -      -       -      -
    335G  ASN*     3.5    42.0    -      -       +      -
    336G  GLY*     3.9     3.6    -      -       -      -
    339G  ALA*     4.4     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 301 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30G  ILE*     3.4    27.6    -      -       -      +
     32G  ALA*     4.5     1.5    -      -       -      +
     78G  ILE*     3.7     5.5    -      -       -      +
    186G  ILE*     4.9     0.2    -      -       -      +
    230G  LYS*     3.3    39.0    +      -       -      +
    269G  THR*     3.2    33.3    +      -       -      -
    270G  PHE      2.7    13.7    +      -       -      +
    271G  LEU*     3.8     4.7    -      -       -      -
    272G  SER      4.3     0.3    +      -       -      -
    300G  PHE*     1.3    70.8    -      -       -      +
    302G  TYR*     1.3    60.8    +      -       -      +
    303G  GLY      4.1     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 302 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30G  ILE      3.3     8.2    +      -       -      +
     31G  LEU*     4.2     0.7    -      -       -      +
     32G  ALA*     2.9    27.0    +      -       -      -
    233G  MET*     3.2    16.6    -      -       +      +
    270G  PHE*     3.5    22.4    -      -       +      -
    271G  LEU      4.1     0.7    -      -       -      -
    272G  SER*     3.5    22.4    -      -       -      -
    280G  ALA*     3.1    40.7    +      -       +      -
    284G  LEU*     3.5     9.6    -      -       +      +
    300G  PHE*     3.3    28.9    -      +       +      -
    301G  SER*     1.3    75.5    -      -       -      +
    303G  GLY*     1.3    62.4    +      -       -      +
    305G  ALA*     3.4    20.0    -      -       +      -
    306G  LEU*     3.7    23.2    -      -       +      +
    335G  ASN*     3.5    30.5    -      -       -      -
----------------------------------------------------------
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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