Contacts of the strand formed by residues 297 - 302 (chain L) 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 L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24L  VAL*     3.7    37.7    -      -       +      +
    266L  PRO      3.0    18.5    +      -       -      +
    267L  GLY*     3.8     1.6    -      -       -      -
    268L  VAL      2.8    25.0    +      -       -      -
    296L  TRP*     1.3    75.0    -      -       -      +
    298L  LEU*     1.3    63.2    +      -       -      +
    299L  THR*     3.8     7.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 298 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    254L  VAL*     4.3     5.6    -      -       +      -
    257L  LEU*     3.9    13.7    -      -       +      -
    268L  VAL*     3.6    17.7    -      -       +      -
    270L  PHE*     4.0    11.4    -      -       +      -
    284L  LEU*     3.3     4.9    -      -       -      +
    287L  ILE*     3.4    25.1    -      -       +      +
    288L  ASN*     2.8    35.8    +      -       -      +
    294L  ARG*     3.5    40.8    -      -       +      +
    296L  TRP*     3.4    33.1    +      -       +      +
    297L  ALA*     1.3    77.2    -      -       -      +
    299L  THR*     1.3    62.3    +      -       -      +
    339L  ALA      4.2     1.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 299 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24L  VAL*     4.3    20.3    -      -       +      +
     25L  ALA      5.0     0.2    -      -       -      +
     26L  PRO*     6.2     0.2    -      -       +      -
     27L  GLY      5.5     1.8    -      -       -      +
     28L  LYS      3.0    30.1    +      -       -      +
     29L  GLY*     3.5     2.1    -      -       -      -
    268L  VAL      3.2    10.0    +      -       -      -
    269L  THR*     4.2     9.1    -      -       -      +
    270L  PHE*     3.1    31.5    +      -       -      +
    284L  LEU*     3.8     8.2    -      -       -      +
    297L  ALA*     3.8     5.8    -      -       +      -
    298L  LEU*     1.3    81.4    -      -       -      +
    300L  PHE*     1.3    83.6    +      -       -      +
    339L  ALA*     3.8    22.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 300 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28L  LYS      4.1     2.0    -      -       -      -
     29L  GLY*     3.2    24.5    -      -       -      -
     30L  ILE*     2.8    53.5    +      -       -      +
     73L  CYS      3.5    13.7    -      -       -      -
     74L  ILE*     4.2     7.2    -      -       +      -
    269L  THR*     3.9     5.5    -      -       -      -
    270L  PHE      3.6     4.7    -      -       -      -
    284L  LEU*     3.7     9.0    -      -       +      -
    299L  THR*     1.3    94.6    +      -       -      +
    301L  SER*     1.3    57.7    +      -       -      +
    302L  TYR*     3.3    40.4    -      +       +      -
    306L  LEU*     3.8    17.3    -      -       +      -
    332L  ALA      4.4     5.2    -      -       -      -
    335L  ASN*     3.5    42.4    -      -       +      -
    336L  GLY*     3.9     3.6    -      -       -      -
    339L  ALA*     4.4     1.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 301 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30L  ILE*     3.4    28.4    -      -       -      +
     32L  ALA*     4.5     1.7    -      -       -      +
     78L  ILE*     3.7     5.9    -      -       -      +
    186L  ILE*     4.9     0.3    -      -       -      +
    230L  LYS*     3.3    37.7    +      -       -      +
    269L  THR*     3.2    33.6    +      -       -      -
    270L  PHE      2.7    12.9    +      -       -      +
    271L  LEU*     3.8     4.7    -      -       -      -
    272L  SER      4.3     0.2    +      -       -      -
    300L  PHE*     1.3    71.2    -      -       -      +
    302L  TYR*     1.3    61.3    +      -       -      +
    303L  GLY      4.1     0.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 302 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30L  ILE      3.3     7.1    +      -       -      +
     31L  LEU*     4.2     0.7    -      -       -      +
     32L  ALA*     2.9    26.8    +      -       -      -
    233L  MET*     3.2    16.1    -      -       +      +
    270L  PHE*     3.5    22.7    -      -       +      -
    271L  LEU      4.1     1.1    -      -       -      -
    272L  SER*     3.5    21.3    -      -       -      -
    280L  ALA*     3.1    41.8    +      -       +      -
    284L  LEU*     3.5     9.2    -      -       +      +
    300L  PHE*     3.3    28.4    -      +       +      -
    301L  SER*     1.3    75.8    -      -       -      +
    303L  GLY*     1.3    61.5    +      -       -      +
    305L  ALA*     3.4    20.0    -      -       +      -
    306L  LEU*     3.7    23.0    -      -       +      +
    335L  ASN*     3.5    31.2    -      -       -      -
----------------------------------------------------------
 Back to top of page


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