Contacts of the strand formed by residues 19 - 29 (chain X) in PDB entry 5A0Q


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 VAL 19 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13X  MET      4.0     4.5    -      -       -      +
     14X  LYS*     4.4     2.7    -      -       +      +
     17X  ASN      3.3    15.3    -      -       -      +
     18X  CYS*     1.4    68.2    -      -       -      +
     20X  ALA*     1.3    61.3    +      -       -      +
     21X  ILE*     4.6     1.0    -      -       -      +
    109X  ALA*     4.0     4.7    -      -       +      -
    110X  GLY*     3.8    25.6    -      -       -      +
    111X  LEU*     3.4    17.7    -      -       +      -
    118X  PRO*     3.4    26.2    -      -       +      -
    120X  ILE*     3.4    32.8    -      -       +      -
    187X  HIS      3.4     2.6    -      -       -      +
    188X  ILE*     4.2     0.9    -      -       -      -
    189X  ILE*     2.9    35.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 20 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12X  ALA*     3.8     0.5    -      -       -      -
     13X  MET*     2.8    40.0    +      -       +      +
     19X  VAL*     1.3    72.5    -      -       -      +
     21X  ILE*     1.4    64.0    +      -       -      +
    109X  ALA*     4.1     6.4    -      -       -      +
    162X  LEU*     3.5    27.7    -      -       +      +
    166X  ILE*     3.5    23.3    -      -       +      -
    187X  HIS      3.5     5.8    -      -       -      -
    188X  ILE*     4.2    12.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 21 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10X  VAL*     5.0     3.6    -      -       +      -
     11X  MET      3.3    16.2    -      -       -      +
     12X  ALA*     4.0     5.8    -      -       +      +
     19X  VAL      4.6     2.2    -      -       -      +
     20X  ALA*     1.4    77.8    -      -       -      +
     22X  ALA*     1.4    66.5    +      -       -      +
     41X  ILE*     4.1    24.4    -      -       +      +
     49X  TYR*     4.9     9.0    -      -       +      -
     50X  ILE*     4.3     2.9    -      -       -      +
     51X  GLY*     4.0    16.2    -      -       -      +
    107X  VAL      3.6    24.7    -      -       -      +
    109X  ALA*     3.9    24.0    -      -       +      +
    166X  ILE*     3.6     4.7    -      -       -      -
    186X  VAL*     3.5     2.8    -      -       -      +
    187X  HIS*     2.9    48.5    +      -       +      +
    189X  ILE*     5.0     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 22 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10X  VAL*     3.8     2.4    -      -       -      +
     11X  MET*     3.0    39.6    +      -       +      +
     21X  ILE*     1.4    77.1    -      -       -      +
     23X  ALA*     1.3    64.2    +      -       -      +
     41X  ILE*     3.8     5.8    -      -       -      +
    166X  ILE*     3.7    19.4    -      -       +      +
    170X  MET*     4.6    11.2    -      -       +      -
    184X  VAL*     4.9     0.2    -      -       +      -
    185X  ILE      3.0    15.7    -      -       -      +
    186X  VAL*     3.9    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 23 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9X  ALA      3.7    16.2    -      -       -      +
     10X  VAL*     4.8     3.8    -      -       +      -
     22X  ALA*     1.3    80.8    -      -       -      +
     24X  ASP*     1.4    68.1    +      -       -      +
     40X  LYS*     4.3    13.5    -      -       +      -
     41X  ILE*     3.9    21.5    -      -       +      +
     51X  GLY*     6.3     0.2    -      -       -      -
    170X  MET*     3.6    11.4    -      -       -      -
    184X  VAL*     3.6     1.9    -      -       -      -
    185X  ILE*     3.1    34.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 24 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8X  GLY*     3.6     9.5    -      -       -      -
      9X  ALA*     2.9    34.4    +      -       +      +
     23X  ALA*     1.4    73.5    -      -       -      +
     25X  ARG*     1.3    61.3    +      -       -      +
     26X  ARG*     3.5    18.8    +      -       -      +
     38X  PHE      4.3     1.0    -      -       -      +
     40X  LYS*     3.7    18.4    -      -       -      +
    170X  MET*     3.3    16.9    -      -       +      +
    179X  VAL      4.5     0.7    -      -       -      +
    180X  SER*     3.5    24.5    +      -       -      -
    181X  GLY      3.6    20.9    +      -       -      +
    183X  GLY      3.4     9.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 25 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23X  ALA      4.6     0.7    -      -       -      +
     24X  ASP*     1.3    73.7    -      -       -      +
     26X  ARG*     1.3    59.0    -      -       -      +
     36X  THR*     2.8    46.0    +      -       -      +
     37X  ASP*     4.0    25.3    +      -       -      +
     38X  PHE      3.9    26.0    -      -       -      +
     39X  GLN*     5.5     1.8    -      -       -      -
     40X  LYS      6.0     0.7    -      -       -      +
    181X  GLY      4.3     0.4    +      -       -      -
    182X  MET      3.0    14.2    -      -       -      +
    183X  GLY*     3.1    36.5    +      -       -      +
    184X  VAL      3.4    12.8    +      -       -      +
    185X  ILE*     4.1    34.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 26 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166L  ARG      4.1     3.4    +      -       -      -
    168L  ALA*     4.1    14.6    -      -       -      +
      7X  GLY      4.6     1.7    -      -       -      +
      8X  GLY*     4.9     0.2    -      -       -      -
     24X  ASP*     3.5    12.1    -      -       -      +
     25X  ARG*     1.3    78.1    -      -       -      +
     27X  PHE*     1.3    71.7    +      -       -      +
     28X  GLY*     4.6     6.1    -      -       -      -
     30X  GLN      5.7     0.2    +      -       -      -
     31X  ALA      4.0    10.7    +      -       -      -
     32X  GLN      3.9     4.4    +      -       -      -
     33X  MET*     1.4    93.9    -      -       +      +
     35X  THR      3.4    10.5    -      -       -      +
     38X  PHE*     4.4     5.7    -      -       -      +
     40X  LYS*     3.5    19.2    -      -       -      -
    178X  ALA      5.1     1.6    +      -       -      -
    179X  VAL*     4.3    22.8    +      -       -      +
    180X  SER*     5.2     1.5    -      -       -      -
    181X  GLY      3.3    20.2    -      -       -      +
    182X  MET*     3.1    31.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 27 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6X  ASN*     3.6    18.4    -      -       -      +
      7X  GLY      4.7     7.4    -      -       -      +
     26X  ARG*     1.3    84.5    -      -       -      +
     28X  GLY*     1.3    63.0    +      -       -      +
     29X  ILE*     5.9     0.2    -      -       +      -
     34X  VAL*     3.1    56.3    +      -       +      +
     35X  THR*     2.4    31.5    +      -       -      -
     38X  PHE*     3.1    51.6    -      +       +      -
     40X  LYS*     4.8     0.2    -      -       -      +
     56X  ALA*     5.2     6.1    -      -       +      -
    179X  VAL      5.7     2.9    -      -       -      -
    117Y  TYR*     4.7     7.6    -      +       -      -
    119Y  ASP*     6.0     1.3    -      -       -      -
    123Y  ALA*     4.7    13.9    -      -       +      -
    125Y  ALA*     3.5    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 28 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6X  ASN*     3.0    33.0    +      -       -      +
     26X  ARG*     4.6     5.8    -      -       -      +
     27X  PHE*     1.3    79.1    -      -       -      +
     29X  ILE*     1.3    62.7    +      -       -      -
     30X  GLN      3.4    12.0    +      -       -      +
     32X  GLN      3.3    15.3    -      -       -      -
     33X  MET*     4.3     1.1    -      -       -      -
     34X  VAL*     4.0     1.6    -      -       -      -
    179X  VAL      5.6     1.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 29 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27X  PHE*     5.9     0.4    -      -       +      -
     28X  GLY*     1.3    67.4    -      -       -      -
     30X  GLN*     1.3    73.7    +      -       +      +
     32X  GLN*     3.0    36.7    +      -       +      +
     34X  VAL*     3.3    22.6    -      -       +      +
    117Y  TYR*     3.6    18.6    -      -       +      +
    119Y  ASP*     3.1    37.9    -      -       -      +
    120Y  TYR*     4.7    12.3    -      -       +      +
    121Y  LEU*     5.9     1.3    -      -       +      -
    137Y  PHE*     5.3     6.8    -      -       +      -
----------------------------------------------------------
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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