Contacts of the strand formed by residues 25 - 31 (chain A) in PDB entry 4IXU


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 SER 25 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  HIS*     1.3    83.5    +      -       -      +
     26A  VAL*     1.3    63.5    +      -       -      +
     64A  HIS*     3.2    15.4    -      -       -      +
    110A  GLY      4.0    15.5    +      -       -      +
    111A  TYR*     3.4    28.5    -      -       -      -
    112A  SER*     2.9    26.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 26 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  HIS      5.1     1.1    -      -       -      +
     25A  SER*     1.3    80.6    -      -       -      +
     27A  ALA*     1.3    67.4    +      -       -      +
     28A  VAL*     4.2     9.2    -      -       +      -
     58A  LEU*     4.3     9.0    -      -       +      -
     63A  CYS*     3.8    26.2    -      -       +      -
     64A  HIS      2.7     9.1    +      -       -      -
     65A  LEU*     3.3    17.1    -      -       +      +
     66A  LYS      2.9    23.0    +      -       -      +
    111A  TYR*     3.6     3.4    -      -       -      -
    112A  SER*     3.2     6.3    -      -       -      +
    114A  VAL*     3.6    30.5    -      -       +      -
    323A  PHE*     3.7    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 27 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  VAL*     1.3    74.3    -      -       -      +
     28A  VAL*     1.3    58.1    +      -       -      +
     29A  ILE*     4.1     0.4    -      -       -      -
     66A  LYS      3.2     5.6    -      -       -      +
     68A  PHE*     3.7    28.5    -      -       +      -
    106A  ALA*     3.8    11.0    -      -       +      -
    111A  TYR*     3.7    23.4    -      -       +      +
    112A  SER      2.7    11.3    +      -       -      +
    113A  CYS*     4.5     5.6    -      -       -      -
    114A  VAL*     2.7    35.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  VAL*     4.2     6.3    -      -       +      -
     27A  ALA*     1.3    79.2    -      -       -      +
     29A  ILE*     1.3    61.1    +      -       -      +
     30A  GLY      4.2     0.2    -      -       -      -
     50A  ARG*     4.0    13.0    -      -       -      +
     54A  LEU*     4.2     8.3    -      -       +      -
     55A  MET*     3.7    35.0    -      -       +      -
     58A  LEU*     4.2    20.6    -      -       +      -
     65A  LEU*     4.6     3.4    -      -       +      -
     66A  LYS      2.8    10.7    +      -       -      +
     67A  ASP*     3.4     5.2    -      -       -      +
     68A  PHE*     2.8    32.4    +      -       -      +
    114A  VAL*     3.4    10.3    -      -       +      +
    116A  LEU*     4.0    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 29 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  VAL*     1.3    81.2    -      -       -      +
     30A  GLY*     1.3    67.8    +      -       -      +
     31A  ALA      3.7     0.3    +      -       -      -
     68A  PHE*     3.9    19.7    -      -       +      -
     69A  GLY      3.9     1.8    -      -       -      -
     71A  LEU*     3.6    34.3    -      -       +      -
     99A  LEU*     4.0     9.6    -      -       +      -
    102A  VAL*     3.6    22.7    -      -       +      +
    103A  VAL*     3.9    17.0    -      -       +      +
    106A  ALA*     5.0     0.9    -      -       +      -
    113A  CYS*     3.4    30.7    -      -       -      -
    114A  VAL      2.8    11.5    +      -       -      +
    115A  THR*     3.3     5.9    -      -       +      +
    116A  LEU*     2.8    26.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  ILE*     1.3    72.1    -      -       -      +
     31A  ALA*     1.3    57.4    +      -       -      -
     32A  PRO*     3.3     6.7    -      -       -      +
     46A  PRO*     4.1     9.0    -      -       -      -
     50A  ARG*     4.0     5.0    -      -       -      +
     69A  GLY      2.8    18.8    +      -       -      -
     70A  ASP*     3.5    15.3    -      -       -      -
     71A  LEU*     2.9    33.8    +      -       -      +
    116A  LEU*     3.9     7.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  ILE      3.7     0.4    +      -       -      -
     30A  GLY*     1.3    73.0    -      -       -      +
     32A  PRO*     1.3    55.0    -      -       -      +
     33A  PHE*     2.7    29.8    +      -       +      -
     46A  PRO*     4.0     1.0    -      -       -      +
     73A  PHE*     4.1     9.2    -      -       +      -
     99A  LEU*     4.1    13.7    -      -       +      -
    115A  THR*     3.7    25.1    -      -       +      -
    116A  LEU      2.8    15.3    +      -       -      +
    117A  GLY*     3.6     0.9    -      -       -      -
    118A  GLY*     3.4    14.4    -      -       -      -
    122A  LEU*     3.7    12.2    -      -       +      +
----------------------------------------------------------
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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