Contacts of the strand formed by residues 245 - 250 (chain A) in PDB entry 1XI1


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 GLY 245 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244A  GLU*     1.3    75.0    -      -       -      +
    246A  MET*     1.3    59.6    +      -       -      -
    462A  LEU      3.0    14.4    -      -       -      -
    463A  THR*     4.1     0.2    -      -       -      -
    464A  GLY      3.1    11.8    +      -       -      -
    465A  THR*     4.4     1.0    -      -       -      +
    488A  THR*     3.1     8.0    -      -       -      +
    489A  PHE*     2.8    49.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 246 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245A  GLY*     1.3    73.9    -      -       -      +
    247A  VAL*     1.3    72.0    +      -       -      +
    248A  PHE*     3.4    30.7    -      -       +      -
    451A  ARG*     3.2    28.0    -      -       -      +
    460A  ILE      3.8     0.6    -      -       -      +
    461A  HIS*     3.5     0.9    -      -       -      +
    462A  LEU*     2.8    31.0    +      -       +      +
    464A  GLY      2.9    15.9    -      -       -      +
    465A  THR*     3.2    30.5    -      -       -      +
    466A  GLU      3.5     4.3    -      -       -      +
    467A  ILE*     3.5    17.0    -      -       +      +
    485A  HIS*     3.3    29.8    -      -       +      +
    487A  SER      3.4     6.1    -      -       -      -
    488A  THR*     4.7     1.1    -      -       +      +
    489A  PHE*     4.1     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 247 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  MET*     1.3    82.1    -      -       -      +
    248A  PHE*     1.3    65.1    +      -       -      +
    249A  ASP*     3.5    19.5    -      -       -      +
    459A  SER*     4.5     0.2    -      -       -      -
    460A  ILE      3.4     2.7    -      -       -      -
    461A  HIS*     3.5    39.0    -      -       +      +
    485A  HIS*     3.7     4.0    +      -       -      -
    486A  GLU*     2.8    30.9    +      -       +      +
    487A  SER*     3.0    29.0    +      -       -      +
    489A  PHE*     4.4     6.3    -      -       +      -
    502A  GLN*     4.0    20.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 248 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  MET*     3.4    41.3    -      -       +      -
    247A  VAL*     1.3    76.8    -      -       -      +
    249A  ASP*     1.3    64.7    +      -       -      +
    459A  SER*     3.0     5.2    -      -       -      -
    460A  ILE*     2.9    42.9    +      -       +      +
    462A  LEU*     3.7    29.8    -      -       +      -
    467A  ILE*     3.9    18.4    -      -       +      -
    468A  PRO*     4.1     9.0    -      -       +      -
    471A  ILE*     5.1     6.7    -      -       +      -
    475A  VAL*     4.2    21.8    -      -       +      -
    483A  TRP*     3.7    23.8    -      -       +      -
    484A  ALA      3.4     5.8    -      -       -      +
    485A  HIS*     3.7    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 249 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247A  VAL*     3.5    14.2    +      -       -      +
    248A  PHE*     1.3    75.8    -      -       -      +
    250A  VAL*     1.3    64.4    +      -       -      +
    251A  ASN*     4.1     0.2    -      -       -      +
    458A  ASP*     3.3    17.5    -      -       -      +
    459A  SER*     3.1    23.1    -      -       -      -
    483A  TRP*     4.0     2.7    -      -       -      -
    484A  ALA*     2.7    40.4    +      -       +      +
    486A  GLU*     3.1    40.3    -      -       +      +
----------------------------------------------------------
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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
----------------------------------------------------------
    249A  ASP*     1.3    75.4    -      -       -      +
    251A  ASN*     1.3    67.3    +      -       -      +
    252A  SER      3.1     8.3    +      -       -      -
    253A  LEU*     3.8    44.2    +      -       +      -
    257A  GLN*     5.1     3.4    -      -       -      +
    440A  THR*     4.4     6.7    -      -       +      -
    458A  ASP*     2.9    24.0    +      -       +      +
    481A  GLY*     3.8    22.7    -      -       -      +
    482A  TYR      3.5     4.5    -      -       -      -
    483A  TRP*     3.4    42.2    -      -       +      -
----------------------------------------------------------
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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