Contacts of the strand formed by residues 29 - 35 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  ASP*     3.9     5.7    -      -       -      +
     24A  HIS*     3.0    32.8    +      -       -      +
     27A  GLY*     3.3     2.8    -      -       -      -
     28A  LEU*     1.3    83.8    +      -       -      +
     30A  VAL*     1.3    67.2    +      -       -      +
     31A  TRP*     5.9     0.2    -      -       -      -
     15B  HIS*     4.7     2.8    -      -       -      +
    122B  SER*     5.8     1.3    -      -       -      -
    138B  VAL      4.1    14.4    -      -       -      -
    139B  ASP*     5.8     0.7    -      -       -      -
    168B  THR*     3.8    19.0    -      -       -      +
    169B  ALA      4.3     0.7    -      -       -      -
    170B  GLU*     2.5    35.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  GLU*     3.6    34.3    -      -       +      +
     22A  ALA      3.5     9.4    -      -       -      +
     23A  ASP*     5.9     0.7    -      -       -      -
     29A  SER*     1.3    79.3    -      -       -      +
     31A  TRP*     1.3    66.0    +      -       -      +
     32A  ARG*     3.5    15.4    +      -       -      +
    122B  SER*     5.6     1.3    -      -       -      +
    138B  VAL      5.2     0.2    +      -       -      -
    139B  ASP*     3.7    36.4    +      -       +      +
    168B  THR*     2.7    34.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  PHE*     3.8     2.7    -      -       +      +
     21A  GLU*     3.2     5.9    -      -       -      -
     22A  ALA*     2.8    46.1    +      -       +      +
     23A  ASP      4.3     3.4    -      -       -      -
     24A  HIS*     3.9    18.2    -      -       +      -
     29A  SER*     4.1     1.6    +      -       -      -
     30A  VAL*     1.3    72.1    -      -       -      +
     32A  ARG*     1.3    62.8    +      -       -      +
     64A  THR*     3.3    38.1    -      -       -      -
     66A  SER*     3.9     9.0    -      -       -      -
     69A  LEU*     3.5    24.2    -      -       +      -
    201A  OTP      2.9    64.2    +      -       +      +
     14B  SER*     3.2    20.0    -      -       -      -
     15B  HIS*     3.5    22.9    -      +       -      -
     17B  TYR*     3.7    19.1    -      +       -      -
     34B  LYS*     4.5     2.0    -      -       -      -
    168B  THR*     5.3     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  PHE*     3.3    15.0    -      -       -      +
     21A  GLU*     3.4    34.3    +      -       +      -
     30A  VAL*     3.5    12.4    +      -       +      +
     31A  TRP*     1.3    79.7    -      -       -      +
     33A  GLY*     1.3    58.6    +      -       -      +
     64A  THR*     3.5     7.6    -      -       -      +
     19B  SER*     3.7    32.8    -      -       -      +
     34B  LYS*     2.8    28.2    +      -       -      +
    139B  ASP*     2.7    42.4    +      -       -      -
    140B  ALA      5.7     0.2    +      -       -      -
    141B  VAL*     6.1     1.0    -      -       -      +
    166B  LEU*     3.7    37.7    +      -       -      +
    168B  THR*     3.4    19.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  SER*     3.2     8.1    -      -       -      -
     20A  PHE*     2.9    40.1    +      -       -      -
     32A  ARG*     1.3    77.6    -      -       -      +
     34A  LYS*     1.4    62.5    +      -       -      -
     63A  HIS*     3.2    15.0    -      -       -      -
     64A  THR*     4.4     0.4    -      -       -      -
     34B  LYS*     5.0     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  TYR*     3.5    37.0    -      -       +      +
     18A  PRO      3.3    10.5    -      -       -      +
     19A  SER*     3.5    18.2    -      -       -      +
     20A  PHE*     3.4     4.2    -      -       -      -
     33A  GLY*     1.4    75.4    -      -       -      +
     35A  PHE*     1.3    63.8    +      -       -      +
     36A  ASP*     3.7    19.3    -      -       -      +
     62A  ILE*     3.5     2.4    -      -       -      +
     63A  HIS*     2.8    35.1    +      -       +      +
    168A  THR*     5.7     1.0    +      -       -      -
     31B  TRP*     4.5     0.6    -      -       -      -
     32B  ARG*     2.7    34.9    +      -       -      +
     33B  GLY*     5.1     2.9    -      -       -      -
     63B  HIS*     4.4     9.6    -      -       +      -
     64B  THR      2.8    26.4    +      -       -      +
     65B  GLY*     4.1     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  TYR*     3.5    15.4    -      -       -      +
     18A  PRO*     3.1    33.6    +      -       +      +
     20A  PHE*     3.7    20.6    -      +       -      -
     34A  LYS*     1.3    76.9    -      -       -      +
     36A  ASP*     1.3    63.6    +      -       -      +
     37A  LYS      3.4     0.6    +      -       -      -
     38A  SER*     4.7     0.3    +      -       -      -
     57A  THR*     3.3    24.7    -      -       +      -
     58A  ASP      3.6    17.3    -      -       -      -
     59A  ILE*     3.8    18.4    -      -       +      -
     61A  SER*     3.6     5.6    -      -       -      +
     62A  ILE*     3.6    38.4    -      -       +      -
     79A  PHE*     4.0     7.6    -      +       -      -
    201A  OTP      3.4    44.6    -      -       +      -
----------------------------------------------------------
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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