Contacts of the strand formed by residues 29 - 35 (chain B) in PDB entry 5IXG


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 29 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  HIS*     4.8     1.9    -      -       -      +
    122A  SER*     5.7     1.8    -      -       -      -
    138A  VAL      4.0    14.6    -      -       -      -
    139A  ASP      5.4     0.7    -      -       -      +
    168A  THR*     3.8    21.1    -      -       -      +
    169A  ALA      4.3     0.4    -      -       -      -
    170A  GLU*     2.5    32.4    +      -       -      +
     23B  ASP*     3.9     5.9    -      -       -      +
     24B  HIS*     3.0    33.2    +      -       -      +
     27B  GLY*     3.3     2.9    -      -       -      -
     28B  LEU*     1.3    82.6    +      -       -      +
     30B  VAL*     1.3    67.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 30 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  SER*     5.7     0.7    -      -       -      +
    139A  ASP*     3.7    36.5    +      -       +      +
    168A  THR*     2.7    34.5    +      -       -      +
     21B  GLU*     3.7    25.4    -      -       +      +
     22B  ALA      3.6     8.1    -      -       -      +
     23B  ASP*     5.9     1.1    -      -       -      -
     29B  SER*     1.3    82.9    -      -       -      +
     31B  TRP*     1.3    73.9    +      -       -      +
     32B  ARG*     3.5    15.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 31 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  SER      3.4    17.7    -      -       -      -
     15A  HIS*     3.4    26.6    -      +       -      -
     17A  TYR*     3.8    19.1    -      +       -      -
     34A  LYS*     4.5     1.8    -      -       -      -
    168A  THR*     5.4     2.0    -      -       +      -
     20B  PHE*     4.3     2.2    -      +       +      -
     21B  GLU*     3.2     6.2    -      -       -      -
     22B  ALA*     2.8    40.4    +      -       +      +
     23B  ASP      4.2     9.4    -      -       -      -
     24B  HIS*     3.8    29.3    -      +       +      +
     29B  SER      4.2     0.8    +      -       -      -
     30B  VAL*     1.3    71.2    -      -       -      +
     32B  ARG*     1.3    64.5    +      -       -      +
     64B  THR*     3.2    41.7    -      -       +      -
     66B  SER*     4.2     8.7    -      -       -      -
     69B  LEU*     3.6    22.9    -      -       +      -
    201B  OTP      3.7    48.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 32 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  SER*     3.7    33.0    -      -       -      +
     34A  LYS*     2.7    31.9    +      -       -      +
    139A  ASP*     2.7    42.2    +      -       -      -
    141A  VAL*     6.1     0.8    -      -       -      +
    166A  LEU*     3.8    38.0    +      -       -      +
    168A  THR*     3.5    16.7    +      -       -      +
     20B  PHE*     3.3    15.5    -      -       -      +
     21B  GLU*     3.5    31.7    +      -       +      -
     30B  VAL*     3.5    16.7    +      -       +      +
     31B  TRP*     1.3    80.7    -      -       -      +
     33B  GLY*     1.3    57.8    +      -       -      +
     64B  THR*     3.5     6.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 33 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  LYS*     5.0     5.2    -      -       -      -
     19B  SER*     3.1     7.8    -      -       -      -
     20B  PHE*     2.8    42.3    +      -       -      -
     32B  ARG*     1.3    77.0    -      -       -      +
     34B  LYS*     1.4    62.6    +      -       -      +
     63B  HIS*     3.3    13.9    -      -       -      -
     64B  THR*     4.5     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 34 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  TRP*     4.5     1.8    -      -       -      -
     32A  ARG*     2.8    27.0    +      -       -      +
     33A  GLY*     5.0     4.3    -      -       -      -
     63A  HIS*     4.3     8.7    -      -       +      +
     64A  THR      2.7    34.7    +      -       -      +
     65A  GLY*     4.2     0.9    -      -       -      +
     17B  TYR*     3.5    36.8    -      -       +      +
     18B  PRO      3.4    13.9    -      -       -      +
     19B  SER*     3.5    15.3    -      -       -      +
     20B  PHE*     3.4     4.3    -      -       -      -
     33B  GLY*     1.4    77.3    -      -       -      +
     35B  PHE*     1.3    63.4    +      -       -      +
     36B  ASP*     3.7    18.4    -      -       -      +
     62B  ILE*     3.5     3.6    -      -       -      +
     63B  HIS*     2.7    34.8    +      -       +      +
    168B  THR*     5.7     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 35 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  TYR*     3.5    15.1    -      -       -      +
     18B  PRO*     3.1    32.0    +      -       +      +
     20B  PHE*     3.8    20.4    -      +       -      -
     34B  LYS*     1.3    76.7    -      -       -      +
     36B  ASP*     1.3    63.7    +      -       -      +
     37B  LYS      3.4     0.7    +      -       -      -
     38B  SER*     4.8     0.3    +      -       -      -
     57B  THR*     3.4    25.8    -      -       +      -
     58B  ASP      3.7    17.0    -      -       -      -
     59B  ILE*     3.8    17.7    -      -       +      -
     61B  SER*     3.6     5.2    -      -       -      +
     62B  ILE*     3.5    39.5    -      -       +      -
     79B  PHE*     3.9    13.7    -      +       -      -
    201B  OTP      3.4    41.5    -      -       +      -
----------------------------------------------------------
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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